ProgramBook workFinalScientificProgram RC111 2019 12 21 12 ... · "Translational Genomics of Forage Legumes to Advance Molecular Breeding of Seed Traits in Cover Crop Legumes" 9:40am

P L A N T & A N I M A L G E N O M E X X V I I I

� PLANT CO-ORGANIZERSAntonio Costa De Oliveira, Federal

University of Pelotas, BrazilCarolyn J. Lawrence Dill, Iowa State

University, USA Catherine Feuillet, Inari Agriculture, USA

Perry Gustafson, University of Missouri, USAand University of Nottingham, UK

Fangpu Han, Chinese Academy of Sciences, China

Jerome P. Miksche, Emeritus Director, USDA, Plant Genome Program, USA

Rod A. Wing, University of Arizona, USA

� ANIMAL CO-ORGANIZERS Greger Larson, University of Oxford, UK Brenda Murdoch, University of Idaho, USA Chris Tuggle, Iowa State University, USA Alison L. Van Eenennaam, University of

California Davis, USA

� ABSTRACTS COORDINATORS David Grant, Iowa State University, USA Gerard Lazo, USDA/ARS/WRRC, USA Victoria Carollo Blake, Montana State University, USA

� DIGITAL TOOLS AND RESOURCES COORDINATORS Monica Munoz-Torres, Oregon State University, USA Brian Smith-White, NIH/NLM/NCBI, USA

� TRAVEL GRANTS COORDINATORS Tom Blake, Montana State University

(Retired), USA Max Rothschild, Iowa State University, USA

� VISA LETTERS COORDINATOR Hans Cheng, USDA/ARS, USA

F I N A L P R O G R A M & E X H I B I T G U I D E

CONFERENCE MANAGEMENT

184 S. Livingston Avenue

Suite 9, #184

Livingston, New Jersey 07039

USA

Phone: (201) 653-5141

Email: [email protected]

Website: www.intlpag.org

January 11-15, 2020

Town & Country Hotel

San Diego, CA

Organizing CommitteeChairman: Stephen R. Heller, NIH (USA)

Sponsors and Supporters� USDA, Agricultural Research Service

� USDA, National Agricultural Library

� USDA, National Institute of Food and Agriculture

� John Innes Centre

Cover artwork provided by Applied Biosystems. Originally developed for the company’s “Genetic Harvest” Agriculture Seminars, this image represents the importance of molecular genetic approaches in plant and animal research.

T H E I N T E R N AT I O N A L CO N F E R E N C E

O N T H E S TAT U S O F P L A N T & A N I M A L

G E N O M E R E S E A R C H

Table of Contents

Registration and Meeting Schedule 2

Scientific Program: Friday – Jan 10 3-4

Saturday – Jan 11 5-41 Sunday – Jan 12 42-69 Monday – Jan 13 70-88 Tuesday – Jan 14 89-111 Wednesday – Jan 15 112-120

Corporate Sponsors 121

Exhibit Hall Floorplan 122

Lower Level Poster Floorplan 123

Hotel Property Map 124

Mark Your Calendar For:

PAG Asia 2020 – June 17-19, 2020 – Shenzhen, China

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Plant & Animal Genome XXVIII Registration & Meeting Schedule

Registration - ATLAS FOYER Friday January 10 12:00pm - 9:00pm Saturday January 11 7:00am - 8:00pm Sunday-Monday January 12-13 7:00am - 5:00pm Tuesday January 14 7:00am - 3:00pm Wednesday January 15 7:00am - 12:00pm

Plenary Sessions - ATLAS BALLROOM Sunday January 12 6:15pm - 7:00pm Monday January 13 8:00am - 10:00am Tuesday-Wednesday January 14-15 8:00am - 9:30am

Poster Access Hours - GRAND EXHIBIT HALL & LOWER LEVEL Saturday January 11 7:00am - 9:00pm Sunday January 12 7:00am - 9:00pm Monday January 13 7:00am - 9:00pm Tuesday January 14 7:00am - 3:00pm Wednesday January 15 7:00am - 12:00pm ALL POSTERS MUST BE REMOVED BY 12:00PM WEDNESDAY, JANUARY 15. Speaker Ready Room - TERRACE SALON 2 Friday January 10 12:00pm - 7:00pm Saturday - Tuesday January 11-14 7:00am - 7:00pm Wednesday January 15 7:00am - 12:00pm

Poster Sessions - GRAND EXHIBIT HALL & LOWER LEVEL Monday (Even Numbers) January 13 10:00am - 11:30am Monday (Odd Numbers) January 13 3:00pm - 4:30pm Exhibit Hours - GRAND EXHIBIT HALL Sunday January 12 (Reception: 7:15-8:45) 3:00pm - 8:45pm Monday January 13 9:30am - 5:00pm Tuesday January 14 9:30am - 3:00pm

Computer Room - CALIFORNIA Friday January 10 12:00pm - 10:00pm Saturday - Tuesday January 11-14 6:00am - 10:00pm Wednesday January 15 6:00am - 3:00pm Digital Tools & Resources: Computer system demonstrations will be conducted Sunday - Wednesday in the "computer room", located in the California Room.

Welcome Reception - GRAND EXHIBIT HALL & LOWER LEVEL Sunday January 12 7:15pm - 8:45pm

Closing Banquet Dinner - GRAND EXHIBIT HALL Wednesday January 15 7:00pm - 12:00am

Friday - January 10, 2020

8:00am - 8:00pm Show Management Office - WEST 1

12:00pm - 6:00pm Speaker Ready Room - CALIFORNIA - HANDLERY HOTEL

12:00pm - 7:00pm Speaker Ready Room - TERRACE SALON 2

12:00pm - 9:00pm Registration - ATLAS FOYER

1:00pm - 6:40pm Functional Annotations of Animal Genomes (FAANG) – PACIFIC SALON 3 Organizer: Huaijun Zhou, Department of Animal Science, University of California

1:00pm Welcoming Remarks

1:05pm Bing Ren, University of California, San Diego "Decrypting the Noncoding Genome"

1:35pm Lakshmi Matukumalli, NIFA-USDA "Perspective from NIFA on FAANG Effort"

1:45pm Pablo J. Ross, Department of Animal Science, University of California "Functional Annotation of the Bovine Genome"

2:00pm R. David Hawkins, University of Washington "Epigenomic Annotation of Candidate Cis-regulatory Elements in the Chicken Genome"

2:15pm Christopher K. Tuggle, Animal Science, Iowa State University "Functional Annotation of the Porcine Genome- 2019 Update"

2:30pm Colin Kern, Department of Animal Science, University of California "Genome-Wide Identification and Annotation of Functional Regulatory Regions in the Chicken, Cattle, and Pig Genomes"

2:45pm Brenda M. Murdoch, University of Idaho "Ovine Faang Update"

2:55pm Carrie Finno, University of California Davis "Equine Faang: Off to the Races"

3:05pm Mohamed (Moh) Salem, University of Maryland, College Park "Functional Annotation of the Rainbow Trout Genome"

3:15pm Devising efficient annotation strategies across several domesticated species (Round Table discussion)

3:45pm Break

4:15pm Perspective from Europe Commission on FAANG effort

4:25pm Elisabetta Giuffra, INRA, UMR de Génétique Animale et Biologie Intégrative "The EU-H2020 Project GENE-Switch (The regulatory GENomE of SWine and CHicken: functional annotation during development)"

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Friday - January 10, 2020

4:35pm Christa Kuehn, Leibniz Institute for Farm Animal Biology (FBN)

"Bovreg (Cattle) Update" 4:45pm Ross D. Houston, The Roslin Institute

"AQUA-Faang (Fish species) Update" 4:55pm Peter W Harrison, European Bioinformatics Institute (EMBL-EBI)

"The FAANG Data Coordination Centre: New European Perspectives for Our Continued Global Effort"

5:15pm Peter W Harrison, European Bioinformatics Institute (EMBL-EBI) "A Vision for Bioinformatics within the Global Faang Project"

5:25pm Ruidong Xiang, University of Melbourne "Annotation of Sequence Variants in the Bovine Genome with the Functional-and-Evolutionary Trait Heritability (FAETH) Score"

5:55pm Implementing the next phase of FAANG (Round Table Discussion)

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Saturday - January 11, 2020

7:00am - 8:00am Continental Breakfast - GOLDEN BALLROOM

7:00am - 6:00pm Speaker Ready Room - CALIFORNIA - HANDLERY HOTEL

7:00am - 7:00pm Speaker Ready Room - TERRACE SALON 2

7:00am - 8:00pm Registration - ATLAS FOYER


7:00am - 9:00pm Poster Access - GRAND EXHIBIT HALL

8:00am - 10:10am The Analysis and Role of the Microbiome - TERRACE ROOM - HANDLERY HOTEL Organizer: Alessandra Stella, National Research Council of ItalyCo-Organizer: Mick Watson, The Roslin Institute and R(D)SVS, University of Edinburgh

8:00am Leluo Guan, University of Alberta, Edmonton, AB, Canada "Impact of Host Genetics on the Rumen Microbiome"

8:20am Trevor C. Charles, University of Waterloo "Microbiome Enrichment in Controlled Environment Vegetable Production"

8:40am Olga Francino, Autonomous University of Barcelona "Long Reads for Non-Model Metagenomes: From Structural Variation to Pangenomes in Colonization and Infection"

9:00am Andrew S Hess, AgResearch Limited, Invermay Agricultural Centre "Metagenomic Profiling of Thousands of Samples to Aid Selection of Environmentally Friendly Ruminants"

9:20am Piergiorgio Stevanato, DAFNAE, Università degli Studi di Padova "Metagenomic Sequencing of Seven Hypervariable Regions with Ion Genestudio S5 in Sea Beet"

9:40am Marion Borey, GABI, INRA, AgroParisTech, Université Paris-Saclay "Searching for Links between Gut Microbiota Collected before Vaccination and Variabilities of Vaccine Response in Pigs"

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8:00am - 10:10am Forage, Feedstocks & Turf - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: German C. Spangenberg, Agriculture Victoria

8:00am E. Charles Brummer, University of California, Davis "An Empirical Test of Genomic Selection to Improve Alfalfa Forage Yield"

8:20am Iain Donnison, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University

"Greenhouse Gas Removal and Climate Resilient Grassland Crops" 8:40am Roland Kölliker, Molecular Plant Breeding, Institute of Agricultural

Sciences, ETH Zurich "Harnessing Genetic Diversity to Improve Key Traits in Red Clover"

9:00am Zengyu Wang, College of Grassland Science "The Roles of Spl Genes in Flowering Regulation and Axillary Bud Information in Switchgrass"

9:20am Maria J. Monteros, Noble Research Institute "Translational Genomics of Forage Legumes to Advance Molecular Breeding of Seed Traits in Cover Crop Legumes"

9:40am Torben Asp, Department of Molecular Biology and Genetics, Aarhus University "Multi-Omics Prediction of Deep Root Development in Perennial Ryegrass"

8:00am - 10:10am Arthropod Genomics and Genome Engineering - EAST 2 Organizers: Lindsey Perkin, USDA-ARS ICCDRU and Marce Lorenzen, North Carolina State University

8:00am Lindsey Perkin, Agricultural Research Service, USDA "Overview of Genomic Tools to Support Boll Weevil Eradication Programs"

8:30am Erik B. Dopman, Tufts University, Department of Biology "Genomic Insights into the Seasonal Biology of the European Corn Borer Moth"

8:55am Katrina Schlum, University of Tennessee, Department of Genome, Science & Technology

"Population Structure and Impact on Resistance to Transgenic Crops in Fall Armyworm (Spodoptera frugiperda) from Diverse Locations"

9:20am Zach Adelman, Texas A&M University "Disruption of Genes Important for Flight, Feeding and Femaleness in the Disease Vector Mosquito, Aedes Aegypti"

9:45am Jeff Fabrick, USDA-ARS "CRISPR/Cas9 Gene Editing Confirms the Function of a Bacillus thuringiensis Resistance Receptor Gene"

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8:00am - 10:10am International Wheat Genome Sequencing Consortium (IWGSC) - TOWN AND COUNTRY Organizers: Kellye Eversole, IWGSC and Etienne Paux, INRA GDEC

8:00am Kellye Eversole, IWGSC "IWGSC Workshop Welcome"

8:10am Tingting Zhu, Department of Plant Sciences, University of California, Davis "Improved Reference Genome Sequence of 'Chinese Spring' Wheat Provides Insights into Structural Changes of the Wheat Genome"

8:30am Fei He, Department of Plant Pathology, Kansas State University "Adaptive Introgression from Wild Emmer into Bread Wheat Revealed By Sequencing 1000 Wheat Exomes"

8:50am Philomin Juliana, International Maize and Wheat Improvement Center (CIMMYT)

"Extending the Frontiers of Genomics-Assisted Breeding for Grain Yield, Stress-Resilience and Quality of Bread Wheat Using the Reference Sequence"

9:10am James D. Higgins, University of Leicester "Releasing Natural Variation in Bread Wheat by Modulating Meiotic Crossovers"

9:30am Harriet Rose Benbow, University College Dublin "Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum"

9:50am Nicholas Santantonio, Cornell University "Homeologous Epistasis in Wheat: The Search for an Immortal Hybrid"

8:00am - 10:10am Plant Phenotypes - PACIFIC SALON 2 Organizers: Trevor Garnett, Grains Research and Development Corporation and Darwin Campbell, Iowa State University Co-Organizer: Colleen Yanarella, Iowa State University

8:00am Robert P. Davey, Earlham Institute "Laying the Foundations: Why Are Semantics Difficult in Agriculture?"

8:18am Amy Tabb, USDA-ARS "Communication across Multidisciplinary Lines for Plant Phenotyping Research: An Engineer’s Perspective"

8:36am Ian Stavness, University of Saskatchewan "UAV Imaging and Analysis for Field Phenotyping"

8:54am François Tardieu, INRA "Combining Phenomics, Modeling and Genomic Prediction for Identifying Ideotypes Adapted to a Changing Climate"

9:12am Nadia Shakoor, Donald Danforth Plant Science Center "Integrated Phenomics for Connecting Plant Phenotypes to Genotypes with Real-Time Crop Management"

9:30am Suma Sreekanta, University of Minnesota "Developing New Methods to Measure Traits Impacting Soybean Shoot Architecture"

7


8:00am - 10:10am CSSA: Translational Genomics - SAN DIEGO Organizers: Monica Schmidt, University of Arizona and Fredy Altpeter, Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute University of Florida - IFAS

8:00am Avjinder Kaler, University of Arkansas "Marker Set Optimization for Genomic Selection"

8:20am Erik W. Vollbrecht, Iowa State University "Maize Yabby Genes Drooping leaf1 and Drooping leaf2 Regulate Plant Architecture"

8:40am Yiping Qi, University of Maryland "CRISPR-Cas12 Genome Engineering Systems in Plants"

9:00am Lotte Westerhof, Hudson River Biotechnology "Unbiased Genome-Wide Screening of Regulatory Elements Provides Targets for CRISPR-Mediated Optimization of Gene Expression Levels in Plants"

9:20am Sally A Mackenzie, Pennsylvania State University "Incorporating Epigenetic Variation into Directed Breeding for Enhanced Crop Performance"

9:40am Steven Burgess, University of Illinois at Urbana Champaign "Mapping Transcription Factor Binding Sites in C4 Grasses for Predictable Crop Engineering"

8:00am - 10:10am Advanced Computational Methods – Machine Learning, Containers, and Clouds - CALIFORNIA Organizers: Jason Williams, Cold Spring Harbor Laboratory, Dave Micklos, DNA Learning Center, Cold Spring Harbor Laboratory and Nirav Merchant, CyVerse

8:00am Introductory Remarks

8:15am Ian Braun, Iowa State University "Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction"

8:30am Fernanda Foertter, NVIDIA "With the Power of AI Comes Great Responsibility"

8:45am Philipp E. Bayer, University of Western Australia "Predicting Gene Loss in Plants - Lessons Learned from Laptop-Scale Data"

9:00am Felix Shaw, Earlham Institute "Plenty of Fish - Identifying Tilapia Species from Images"

8


8:00am - 10:10am Evolution of Genome Size - GOLDEN WEST Organizer: William S. Sanders, The Jackson Laboratory

8:00am Welcoming Remarks

8:05am Elvis Tembang Katche, Department of Plant Breeding, Justus-Liebig University Giessen

"Hybrid Speciation in Brassica" 8:35am Ning Jiang, Michigan State University

"The Interaction between LTR Retrotransposons and DNA Transposons in Plants"

9:05am Rick Masonbrink, Iowa State University "Gene Expansion in the Tylenchomorpha: Detecting Genes Involved in Plant Host Rewiring"

9:35am John Bowers, University of Georgia "Chromosome Number and Success of Polyploid Lineages"

8:00am - 10:10am Legumes - ROYAL PALM SALON 5-6 Organizers: Aaron J. Lorenz, University of Minnesota and Sandra Bensmihen, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Université de Toulouse


8:05am Sandra Bensmihen, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Université de Toulouse

"Symbiotic Stimulation of Root Development in Medicago truncatula through the Eyes of GWAS"

8:25am Nadim Tayeh, INRAE, UMR1347 Agroécologie "Beyond the Sequencing of the Pea Genome: Opportunities for Genomics-Based Breeding and Translational Approaches"

8:45am Ali Soltani, Michigan State University "A Single Major Effect Locus Controls Seed Imbibition and Flooding Tolerance in Common Bean (Phaseolus vulgaris L.)"

9:05am Timothy J. Close, University of California, Riverside "Cowpea Genome Information Resources"

9:25am Feng Zhang, University of Minnesota "Towards Precision and Scalable Genome Editing in Crops"

9:45am Matthew E. Hudson, University of Illinois "Structural Variation Underlies Multiple Agronomically Important Soybean Traits"

10:05am Concluding Remarks

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8:00am - 12:40pm Cattle/Swine - PACIFIC SALON 1 Organizer: Benjamin D. Rosen, Animal Genomics and Improvement Laboratory, USDA-ARSCo-Organizer: Daniel Ciobanu, University of Nebraska - Lincoln


8:05am Elizabeth Ross, Queensland Alliance For Agriculture and Food Innovation - University of Queensland

"Beyond the Genome: What Having a Platinum Quality Brahman (Bos indicus) Genome Can Teach Us about What Makes a Useful Reference Genome"

8:35am John B. Cole, Animal Genomics and Improvement Laboratory, USDA-ARS "Identification, Validation, and Management of Mendelian Traits in Livestock Breeding Programs"

9:05am Martien A.M. Groenen, Wageningen University & Research, Animal Breeding and Genomics

"Pig Genome Evolution: De Novo Assembly and Annotation of the Genome of the Visayan Warty Pig (Sus cebifrons)"

9:35am Joe Pickrell, Gencove "Development of a Low-Pass Sequencing Platform to Support Genomic Selection in Livestock"

10:05am Break

10:35am Yana Safonova, University of California San Diego "Analyzing Population Signatures of Cattle Antibody Repertoires"

11:00am Paula R. Chen, University of Missouri "Anthrax Toxin Receptor 1 Knockout Pigs are Protected from Senecavirus A Infection"

11:25am Ruidong Xiang, University of Melbourne "Analysis of Multi-Trait and Multi-Omics Data Supports Cattle as a Model Species for Large Scale Genome-Wide Studies"

11:50am Brittney N. Keel, USDA, ARS, U.S. Meat Animal Research Center "Using SNP Weights Derived from Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs"

12:15pm Jared E. Decker, Division of Animal Sciences, University of Missouri "Matching Cow’s Genetics to the Environment using Genomics"

10


8:00am - 12:40pm Functional Genomics of Complex Traits in Diverse Organisms: the Next Leading EDGE (Enabling Discovery through GEnomic Tools) - ROYAL PALM SALON 1-2 Organizer: Diane Jofuku Okamuro, National Science Foundation/BIO/Division of Integrative Organismal Systems Chair: Daniel Bolnick, University of Connecticut Co-organizers: Donal T. Manahan, National Science Foundation and Edda (Floh) Thiels, National Science Foundation/BIO/Division of Integrative Organismal Systems

8:00am Welcome and Introductory Remarks

8:20am Edward S. Buckler, Institute for Genomic Diversity, Cornell University

8:40am Christina Grozinger, Penn State University/College of Agricultural Sciences/Huck Institutes of the Life Sciences

"Unraveling the Complex Pathways Underpinning Honey Bee Social Behavior and Health Using Genomics"

9:00am Giovanna Capovilla, MIT "Juggling Genes in Prochlorococcus: Discoveries, Challenges, and Opportunities"

9:20am Michael Lynch, Biodesign Center for Mechanisms of Evolution/School of Life Sciences/ASU

"Expanding Functional Genomics to the Daphnia pulex Model System"

9:40am Break

10:40am Panel Discussion


8:00am - 12:40pm Fruit/Nuts - PACIFIC SALON 3 Organizer: Hamid Ashrafi, North Carolina State University


8:01am Ray Ming, University of Illinois at Urbana-Champaign "The Bracteatus Pineapple Genome and Domestication of Clonally Propagated Crops"

8:21am Zhongchi Liu, University of Maryland "Genome Assembly and Early Stage Fruit Transcriptome Analysis of Red Raspberry Rubus idaeus"

8:41am Cecilia H. Deng, The New Zealand Institute for Plant & Food Research Limited

"Deciphering the Blue Colour in Blueberry" 9:01am Raquel Sánchez-Pérez, CEBAS-CSIC

"Mutation of a bHLH Transcription Factor Allowed Almond Domestication"

9:21am Kenta Shirasawa, Kazusa DNA Research Institute "Sequence Analysis of the Sakura Genome Toward Cherry Blossom Forecast"

11


9:41am Luis Felipe V. Ferrão, University of Florida "On the Road to Molecular Breeding for Flavor: Linking Metabolomics and Genomics for Blueberry Improvement"

10:01am Break

10:21am Veronique Decroocq, UMR BFP 1332 - INRA-Universite de Bordeaux "High-Throughput Genomics in Armeniaca Species Reveal a Genome-Wide Impact of Domestication on the Apricot Chromosomal Organization and Gene Architecture"

10:41am Jiali Yu, University of Tennessee, Knoxville "Distinctive Gene Expression Patterns Define Endodormancy to Ecodormancy Transition in Apricot and Peach"

11:01am Loren A Honaas, USDA-ARS Tree Fruit Research Lab "Functional Genomics of Postharvest Physiology in Pome Fruits"

11:21am Alexander Trouern-Trend, University of Connecticut "Comparative Genomics of Six Juglans Species Reveals Disease-Associated Gene Family Contractions"

11:41am Anthony Bernard, INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie and Ctifl, centre opérationnel de Lanxade

"Association and Linkage Mapping of Walnut (Juglans regia L.) Phenological Traits"

12:01pm Jennifer J. Randall, New Mexico State University "Flowering Networks in Hardy Pecan (Carya illinoinensis)"

12:21pm William J. Palmer, Genome Center, University of California, Davis "Loci Determining Trunk Caliper of Interspecific Pistachio Rootstock Identified using Phased, Chromosome-Scale Genome Assemblies"

12:41pm Concluding Remarks

8:00am - 6:10pm Poultry 1 - EAST 1 Organizers: Kent M. Reed, University of Minnesota and Gale Strasburg, Michigan State University


8:20am Marcia M. Miller, Beckman Research Institute, City of Hope "Major Advances in Defining Variability and Function of Chicken MHC-Y Region Genes"

8:40am Huaijun Zhou, Department of Animal Science, University of California "Role of Humoral Immunity in Clearance of Lentogenic Newcastle Disease Virus in Chickens"

9:00am Marcia M. Miller, Beckman Research Institute, City of Hope "Major Advances in Defining Variability and Function in Genes of the Chicken MHC-Y Region"

9:20am Giridhar Athrey, Texas A&M University "New Insights into Genome Structural and Somatic Variation in Chicken"

12


9:40am Kent M. Reed, University of Minnesota "Non-Coding Circular RNA Expression in Turkey Skeletal Muscle"

10:00am Androniki Psifidi, Royal Veterinary College, University of London "Integrating Genetics and "Omics" Data to Dissect Chicken Resistance to Infectious Disease in Low and Middle Income Countries (LMICs)."

10:20am Break

10:40am Yvonne Drechsler, College of Veterinary Medicine, Western University of Health Sciences

"Infectious Bronchitis Virus Infection Affects Chromatin Accessibility and RNA Differential Expression in a Tissue-Specific Manner"

11:00am Hans Cheng, USDA, ARS, Avian Disease and Oncology Laboratory "Role of the Chicken T Cell Receptor-Beta Repertoire in Genetic Resistance to Marek's Disease"

11:20am Susan J. Lamont, Department of Animal Science, Iowa State University "Differential, Allele Specific, and Co-Expression in the Chicken Spleen Transcriptome Under Avian Pathogenic Escherichia coli Infection"

11:40am Adnan Alrubaye, University of Arkansas/Fayetteville "Prophylactic Reduction of Bacterial Chondronecrosis with Osteomyelitis in Broilers"

12:00pm Samuel E. Aggrey, University of Georgia "Host Response to Eimeria Spp Infection in Meat-Type Chickens"

12:20pm Lunch

1:40pm Wayne Kuenzel, University of Arkansas "Hypothalamic Structures Containing Corticotropin Releasing Hormone and Vasotocin Neurons and Receptors Involved in Sustaining the Stress Response in Poultry"

2:00pm Tom E. Porter, University of Maryland "Gene Networks Expressed in the Endocrine System Controlling Egg Production Rates in Turkey Hens"

2:20pm Eric A. Wong, Virginia Tech "Delayed Access to Feed Affects Goblet Cell Distribution in Chickens"

2:40pm Roger A Sunde, University of Wisconsin "Impact of High Dietary Selenium on the Transcriptome and Selenometabolites in Turkeys"

3:00pm Douglas D. Rhoads, University of Arkansas, Cell and Molecular Biology Program

"Genetics of Ascites Revealed by Whole Genome Resequencing in Two Distinct Broiler Lines"

3:20pm Break

13


3:40pm Brynn Voy, University of Tennessee Science "Probing the Capacity for Synthesis of Long Chain Omega-3 Polyunsaturated Fatty Acids in the Developing Broiler Chick"

4:00pm Katy Tarrant, California State University, Fresno "Mitochondria Presence in Breast Muscle from Broilers with Woody Breast"

4:20pm Byungwhi C. Kong, University of Arkansas "Blood Plasma Biomarkers Representing Woody Breast in Broiler"

4:40pm Behnam Abasht, University of Delaware "Genetic Basis of Wooden Breast and White Striping in Commercial Broiler"

5:00pm Christopher M. Ashwell, North Carolina State University "Prediction of Wooden Breast in the Liver and Pectorals Major using Machine Learning"

5:20pm Mary E. Delany, Animal Science, University of California "The Chicken Wingless-2 Mutation Takes Flight"

8:00am - 6:10pm Aquaculture - ROYAL PALM SALON 3-4 Organizer: Louis Plough, Univ. Maryland Center for Environmental Science

8:00am Welcome Remarks

8:20am Guangtu Gao, USDA-ARS-NCCCWA "A Long Reads-Based De-Novo Assembly of the Rainbow Trout Arlee-Line Genome"

8:40am Dina A. Proestou, USDA ARS National Cold Water Marine Aquaculture Center

"Differences in Global Gene Expression Response to Dermo Disease Among Eastern Oyster Families Reveal Mechanisms of Resistance" (PO0443)

9:00am Anne Beemelmanns, Memorial University of Newfoundland and Department of Ocean Sciences

"DNA Methylation Dynamics in Atlantic Salmon (Salmo salar) after Being Challenged with High Temperature and Moderate Hypoxia”"

9:20am Ross D. Houston, The Roslin Institute and R(D)SVS "Applications of Genomics to Expedite Genetic Improvement in Aquaculture Species"

10:00am Break 1

10:20am Samuel FM Hart, University of Washington "Genome of the Soft-Shell Clam and Its Transmissible Cancer"

10:40am Sixin LIU, USDA-ARS-NCCCWA "Identification of Additional Single Nucleotide Polymorphisms Associated with Resistance to Bacterial Cold Water Disease in Rainbow Trout Using Whole Genome Resequencing"

14


11:00am Nuala A. O'Leary, NCBI/NLM/NIH "National Center for Biotechnology Information’s (NCBI) Genome Annotation Resources for Aquaculture Species"

11:20am Kahlil Lawless, Illumina "Genomics Technologies in Genomic Selection, and Case Studies"

11:40am Shawn Narum, Columbia River Inter-Tribal Fish Commission "Evidence for Locally Adapted Phenotypes of Steelhead in the Columbia River"

12:00pm Alexandra J McCarty, University of Maryland Center for Environmental Science

"QTL and Joint-Association Mapping Reveal Loci Associated with Acute Low Salinity Tolerance in the Eastern Oyster (Crassostrea virginica)"

12:20pm Lunch

1:30pm Herman Raadsma, University of Sydney "Genomic Selection in Aquaculture: From Wild Stock to Advanced Breeding Schemes in Penaeus Monodon"

2:10pm Sarah Berry, James Cook University "Stress Regulation and Tolerance in Shrimp: The Transcriptomic Response to Ammonia Exposure in the Black Tiger Shrimp, Penaeus Monodon."

2:30pm Jacob W Bledsoe, University of Idaho "Impacts of Functional Feed Ingredients on Mucosal Immunity and Microbiota of Atlantic Salmon and Potential Implications for Sea Lice Resistance"

2:50pm Daniela Lourenco, University of Georgia "Genomic Selection: From SNP Chips to Whole-Genome Sequence Data"

3:30pm Break 2

3:50pm Christine G. Elsik, University of Missouri "Genomic Data Mining Tools for Domesticated Animal Species"

4:10pm James W. Kijas, CSIRO Animal, Health and Food Science "DNA Methylation and Transcriptomic Changes Involved in Atlantic Salmon Sexual Maturation"

4:30pm Shelly A. Trigg, University of Washington "Influence of Ocean Acidification on DNA Methylation Patterns in Geoduck"

4:50pm NRSP8 Bioinformatics update - James Reecy

5:10pm Closing Remarks

5:20pm Business Meeting

6:00pm Aquaculture Banquet Reception

9:30am - 10:30am Coffee Break - ATLAS FOYER

15


10:30am - 12:40pm Ecological Genomics - ROYAL PALM SALON 5-6 Organizer: Karolina Heyduk, Yale University

10:30am Justin O. Borevitz, The Australian National University "Precision Agroforesty for carbon, ecosystem and climate resilience"

10:50am Trevor Krabbenhoft, University at Buffalo "Fifty Years after Ohno: Catostomid Fishes As a Model for Understanding the Role of Whole Genome Duplication in Ecological Diversification"

11:10am Christina Richards, University of South Florida "Using Genomics Approaches to Understand Mechanisms of Response to Complex Environmental Conditions in Non-Model Plants"

11:30am Scott Hotaling, Washington State University "Genome Evolution in Polar Fishes"

11:50am Mariano Alvarez, Duke University "Within- and Trans-Generational Plasticity in Response to Climate Cues"

12:10pm Lani Gleason, California State University, Sacramento "Transcriptome-Wide Gene and Protein Expression Differences in the Intertidal Mussel Mytilus californianus Exposed to Field and Lab Treatments"

10:30am - 12:40pm A Global Vision for Crop Improvement and Food Security: Connecting the Dots - GOLDEN BALLROOM Organizers: Nora Lapitan, U.S. Agency for International Development, Angela Records, USAID Bureau for Food Security, Gary Atlin, Bill & Melinda Gates Foundation and Jeffrey Ehlers, Bill and Melinda Gates Foundation

10:30am Nora Lapitan, USAID Bureau for Food Security "A Strategic Approach to Modernization of the Breeding Pipeline and Delivery of Genetic Gains"

10:45am Stephen Kresovich, Clemson and Cornell Universities "Vision for the Feed the Future Innovation Lab for Crop Improvement"

11:00am Biswanath Das, CIMMYT "The CGIAR Excellence in Breeding Platform and Crops to End Hunger Initiative"

11:15am Teyoure Benoit Joseph Batieno, Institut de l'Environnement et de Recherches Agricoles and INERA

"Cowpea Research in Burkina Faso: Progress, Challenges to Crop Improvement, and the Place of the Crop Improvement Innovation Lab Initiative."

11:30am Joshua N. Cobb, International Rice Research Institute "The Evolution of a Revolution: Re-Designing Green Revolution Breeding Programs in Asia and Africa to Increase Rates of Genetic Gain"

11:45am Gary Atlin, Bill & Melinda Gates Foundation "Delivering Genetic Gains to Smallholder Farmers in the Face of Climate Change"

16


10:30am - 12:40pm Interoperability and Federation Across Bioinformatic Platforms and Resources - CALIFORNIA Organizer: Eric Lyons, University of Arizona; BIO5 Institute; CyVerseCo-Organizer: James C Schnable, Department of Agronomy and Horticulture, University of Nebraska-Lincoln

10:30am Tyson Swetnam, CyVerse "Calliope: Ecological Drone Data"

10:48am Margaret Woodhouse, USDA/ARS/MaizeGDB "MaizeGDB Interoperability for Multiple Genomes"

11:06am Pete Selby, Cornell University "BrAPI: RESTful Specifications to Enable Interoperability among Plant Breeding Databases Focused on Plant Phenotype/Genotype Databases"

11:24am Brian D. Gregory, University of Pennsylvania "TBD"

11:42am Amy Tabb, USDA-ARS-AFRS "A Calibration Method for Accurate and Reproducible Two-Dimensional Plant Measurements from Consumer Cameras."

12:00pm Bryan Runck, University of Minnesota "A Status Update and Preliminary Valuation of the GEMS Platform"

12:18pm Felix Shaw, Earlham Institute "COPO: A Metadata Platform for Brokering FAIR Data in the Life Sciences"

10:30am - 12:40pm Genomics of Genebanks - PACIFIC SALON 2 Organizers: Clarice J Coyne, USDA-ARS Western Regional Plant Introduction Station and Christopher M. Richards, USDA ARS National Laboratory for Genetic Resources Preservation

10:30am Hai Ying Yuan, University of Saskatchewan "Genomic Approaches for Exploring and Utilizing Germplasm Diversity in Lentil"

10:55am Nahla Bassil, USDA-ARS National Clonal Germplasm Repository "Diversity and Structure of the USDA Fragaria x Ananassa Collection"

11:20am Anne V. Brown, USDA-ARS-CICGRU "Characterizing and Comparing International Soybean Germplasm Collections"

11:45am Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research "Genebank Genomics - a Barley Case Study"

12:10pm Loren H. Rieseberg, University of British Columbia "Diversity Lost and Diversity Regained: The Promise and Perils of Tapping Crop Wild Relatives for Improvement"

17


10:30am - 12:40pm Connecting Crop Phenotype and Genotype Data - GOLDEN WEST Organizers: Clay Birkett, USDA-ARS and Star Yanxin Gao, Cornell University

10:30am Star Yanxin Gao, Cornell University "Transforming Breeding through Enterprise Breeding System and Analytics"

10:50am Jenna M. Hershberger, Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University

"Development and Validation of a Low-Cost, Rapid NIRS-Based Phenotyping Approach for Improving Cassava Root Quality Traits"

11:10am Guillaume Ramstein, Institute for Genomic Diversity, Cornell University "Prioritization of Genetic Variants by Biological and Evolutionary Annotation: Functional Assessments in Diverse Maize Populations"

11:30am Parthiban Prakash, International Rice Research Institute "Empowering Global Rice Breeding Programs using Genomic Selection"

11:50am José Crossa, International Maize and Wheat Improvement Center (CIMMYT) "Utilizing Phenomics, Genomics, and Deep Learning Methods to Accelerate the Development of Climate Resilient Crop Varieties"

12:10pm Mary J. Guttieri, USDA Agricultural Research Service "Integrating Genotype and Phenotype in Real-Time Trait-Targeted Wheat Breeding"

10:30am - 12:40pm Brassicas - SAN DIEGO Organizers: Ian Bancroft, University of York and J. Chris Pires, Division of Biological Sciences, University of Missouri

10:30am Varanya Kittipol, University of York "Genetic Architecture of Glucosinolate Variation in Brassica napus"

10:50am Elizabeth Ihien, Department of plant breeding Justus Liebig University "Can Resynthesized Rapeseed be Genomically Stable?"

11:10am Patrick Edger, Department of Horticulture, Michigan State University "Replaying the Evolutionary Tape to Investigate Subgenome Dominance in Neoallopolyploid Brassica napus"

11:30am Gail Taylor, University of California "New Genomic Resource in Watercress (Nasturtium officinale, R.) Enabling Molecular Breeding for Improved Anti-Cancer Properties, Flavour and Nutrient Density"

11:50am Sarah Turner, Center for Population Biology, University of California-Davis "Influence of Selection on Leaf Morphology in a Diverse Panel of Brassica oleracea"

12:10pm Won Yim, University of Nevada - Reno "Genome Sequencing of the Ethiopian Mustard (Brassica carinata): Investigation of the Genetic Evolution and Diversity for Agronomic Traits"

18


10:30am - 12:40pm Engineering NUE - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: David A. Lightfoot, Southern Illinois University and Ashok Shrawat, Bayer

10:30am Ju-Kon Kim, Seoul National University "Identification of a Key Player on Nitrogen Use Efficiency of Rice"

10:50am Bo Shen, R & D Trait Discovery; Corteva Agriscience "Ms44 Male Sterile Hybrid Improves NUE in Maize"

11:10am Guo-Qing Song, Michigan State University "Manipulation of Flowering Pathway Genes for High Fruit Productivity"

11:30am Gabriel Krouk, CNRS "Nitrogen Phosphate Signaling Interactions in Plants from Arabidopsis to Crops"

11:50am Jos van Boxtel, Arcadia Biosciences "Nitrogen Use Efficient Rice Heading into Regulatory Field Trials in Africa"

10:30am - 12:40pm Functional Genomics of C4 and CAM photosynthesis - EAST 2 Organizer: John C. Cushman, University of Nevada - RenoCo-Organizer: Rowan F. Sage, Ecology & Evolutionary Biology, University of Toronto

10:30am Rowan F. Sage, Ecology & Evolutionary Biology, University of Toronto "Comparative Evolutionary Genomics of C4 Evolution: A Wealth of Possibilities"

10:50am Eva Maleckova, Heinrich Heine University "Unraveling Crassulacean Acid Metabolism (CAM) Induction in Facultative CAM Species Talinum Triangulare: A Transcriptome Analysis"

11:10am Anthony J. Studer, University of Illinois at Urbana-Champaign "Genomics, Physiology, and Breeding Implications of Leaf Stable Carbon Isotope Composition in Maize"

11:30am James Hartwell, University of Liverpool "Functional Genomics of CAM in Kalanchoe"

11:50am Ian S. Gilman, Yale University "Genome Sequencing of Portulaca amilis, a C4+CAM Plant"

12:10pm Degao Liu, Center for Precision Plant Genomics, and Center for Genome Engineering, University of Minnesota

"CRISPR/Cas9-Mediated Genome Editing for Photosynthesis Research"

19


10:30am - 12:40pm Grasslands (Lolium Genome Initiative) - TERRACE ROOM - HANDLERY HOTEL Organizer: Iain Donnison, Aberystwyth University

10:30am Claudio Cropano, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich

"Mapping of Self-Compatibility for Hybrid Breeding in Perennial Ryegrass (Lolium perenne L.)"

10:50am Noel O.I. Cogan, Agriculture Victoria, AgriBio, Centre for AgriBioscience and School of Applied Systems Biology, La Trobe University

"Advanced Phenomics Integrated into Rapid Genomic Sub-Selection in Perennial Ryegrass"

11:10am Andrew G. Griffiths, AgResearch Grasslands Research Centre "Genomic Selection for Better Clover-Rhizobium Symbiosis"

11:30am Stephen Byrne, Teagasc, Crop Science Department "Genomic Selection for Forage Yield in Tetraploid Perennial Ryegrass"

11:50am Leif Skot, IBERS, Aberystwyth University "Step-up to Gain: Prediction of Genomic Breeding Values and Variance in Perennial Ryegrass (Lolium perenne L.) Crosses."

10:30am - 12:40pm Triticeae Genetics and Genomics, Session 1: Progress in structural and functional genomics - TOWN AND COUNTRY Organizers: Hana Simkova, Institute of Experimental Botany and Matthew J. Moscou, The Sainsbury Laboratory

10:30am Yi-Jing Zhang, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

"The Bread Wheat Epigenomic Map Reveals Distinct Chromatin Architectural and Evolutionary Features of Functional Genetic Elements"

10:50am Thomas Wicker, University of Zurich "What Transposable Element Populations Tell Us about Triticeae Evolution"

11:10am Jizeng Jia, Chinese Academy of Agricultural Sciences "Progress Report of International Triticeae genome Initiative (ITGC) 2019"

11:30am Murukarthick Jayakodi, IPK Gatersleben "Exploring Barley Genetic Diversity with Chromosome-Scale Assemblies for 20 Diverse Genotypes "

11:50am Alessandro Tondelli, CREA - Research Centre for Genomics and Bioinformatics

"Detecting Gene Duplications and Copy Number Variants in Barley from Exome Sequencing Data"

12:10pm Kirby T. Nilsen, Brandon Research and Development Centre, Agriculture and Agri-Food Canada

"Multiple Reference Genome Assemblies Identify Two Independent Sources of Stem-Solidness in Wheat"

20


10:30am - 12:40pm Genomic features and chromosome functionality - GARDEN 1 - HANDLERY HOTEL Organizer: Xiyin Wang, North China University of Science and Technology

10:30am Hongbin Zhang, Department of Soil and Crop Sciences, Texas A&M University

"The DNA “Jigsaw Puzzle” Structure Model As the Molecular Basis of Biology: Variation and Interaction of Genome Constituting Elements"

10:55am Xiaoming Song, North China University of Science and Technology "Preferential Retention of Cold Tolerance Genes Increases Robustness of Cold Resistance Regulatory Network in Paleo-Polyploid Plants"

11:20am Ian R Henderson, University of Cambridge "Interactions between Meiotic Recombination and Sequence Diversity in Arabidopsis"

11:45am Xiyin Wang, North China University of Science and Technology and North China University of Science and Technology

"Karyotype Evolution and Tetraploid Formation of Peanuts"

12:10pm Jiang Hu, GrandOmics Biosciences Co.,Ltd. "Fast and Accurate Genome Assembly and Polish Tools for Third Generation Sequencing (TGS) Reads"

12:30pm - 1:30pm Lunch - ROYAL PALM COURT & TIKI PAVILION COURT

1:30pm - 3:40pm Sugar Beet Workshop - EAST 2 Organizer: Piergiorgio Stevanato,

1:30pm Mitch McGrath, USDA-ARS Sugarbeet & Bean Research Unit "Getting to the Root of Sugar Beet: Generalizable Gene Discovery via Agron-Omics"

1:47pm Subhashini Srinivasan, Institute of Bioinformatics and Applied Biotechnology

"Potential of Novel Sequencing Technologies in Advancing Sugar Beet Genomics"

2:04pm Chiara Broccanello, University of Padova "Cercospora Leaf Spot (CLS) affects Leaf Microbiome of Sea Beets"

2:21pm Christopher M. Richards, USDA ARS National Laboratory for Genetic Resources Preservation

"Building a Genomic Resource in Beta Maritima" 2:38pm Rebecca E Spanner, North Dakota State University

"A Genome-Wide Association Study of the Sugar Beet Pathogen Cercospora beticola Identifies Novel Fungicide Resistance Mutations"

2:55pm Elena Orsini, Strube Research GmbH Co. KG "BeetRES-MaBS: Mapping by Sequencing for Economically Relevant Traits in Sugar Beet"

21


1:30pm - 3:40pm Crop Evolution Genomics & Future Agricultural Productivity - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Shahal Abbo, The Hebrew University of Jerusalem and Yong-Bi Fu, Plant Gene Resources of CanadaCo-Organizer: Yehoshua Saranga, R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem

1:30pm Martin Mascher, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

"Discovery of Chromosomal Inversions in Domesticated Barley"

1:50pm Peter L. Morrell, University of Minnesota "Long-Read Sequence Evidence of Structural Variants in Wild Barley"

2:10pm Sariel Hubner, Galilee Research Institute "Separating the Barley from the Chaff: Studying Adaptation in Structured Wild Barley Populations"

2:30pm Wenqian Kong, University of Georgia "Evolution of Sorghum halepense and its Potential for Perennial Agriculture"

2:50pm Xianran Li, Iowa State University "Co-Evolution of Crops, Birds, and Farmers in African Agroecosystem Linked by Secondary Metabolites"

3:10pm Paul Gepts, University of California "Can Wild Beans be a Source of Higher Yield and Drought Tolerance for Domesticated Beans?"

1:30pm - 3:40pm Allele Mining - PACIFIC SALON 2 Organizer: Jeremy D. Edwards, USDA-ARS Dale Bumpers National Rice Research Center

1:30pm Georgia C Eizenga, USDA-ARS Dale Bumpers National Rice Research Center

"SNP Markers for Panicle Architecture and Grain Traits Developed from Gwa-QTL and Available for japonica Rice Improvement"

1:51pm Haidong Yan, School of Plant and Environmental Sciences, Virginia Tech, USA "TE-Marker, a Transposon-Based Marker System for Identifying Alleles Associated to Agronomic Traits"

2:12pm Tingting Guo, Iowa State University "Dynamic Effects of Interacting Genes underlying Rice Flowering-Time Phenotypic Plasticity and Global Adaptation"

2:33pm Gary J. Muehlbauer, University of Minnesota "Allele Discovery in a Six-Row Barley Multiparent Population"

22


1:30pm - 3:40pm Digital Tools and Resources Session 1 - CALIFORNIA Organizers: Brian Smith-White, and Monica C. Munoz-Torres, Translational and Integrative Sciences Lab, Oregon State University

1:30pm Nathan A Dunn, Lawrence Berkeley National Laboratory "Quick and Easy Genome Annotation Editing with Apollo"

1:50pm Runxuan Zhang, The James Hutton Institute "3D RNA-Seq - a Powerful and Flexible Tool for Rapid and Accurate Differential Expression and Alternative Splicing Analysis of RNA-Seq Data for Biologists"

2:10pm Dzianis Prakapenka, University of Minnesota "Computing Pipeline for Genomic Prediction and Estimation ssing Haplotypes and SNP Markers"

2:30pm Emily Grau, Department of Plant Sciences "TreeGenes and CartograTree: Tools for Forest Tree Genomics"

2:50pm Laurel Cooper, Oregon State University "Planteome: Ontologies and Resources for Integrative Plant Genomics"

1:30pm - 3:40pm Plant Interactions with Pests and Pathogens - GARDEN 1 - HANDLERY HOTEL Organizer: Shubha Subramanyam, USDA-ARS/Purdue University

1:30pm Aardra Kachroo, University of Kentucky "Chemical Signaling in Plant Defense and Nodulation"

1:50pm Steven S. Xu, USDA-ARS "Molecular Characterization of Hessian Fly Resistance Genes in Aegilops tauschii"

2:10pm Raka Mitra, Carleton College "The Molecular Battle between the Bacterial Wilt Pathogen and its Plant Hosts"

2:30pm Andrew Michel, Dept. of Entomology, OARDC - The Ohio State University "Molecular Interactions between Soybean Aphids and Aphid-Resistant Soybean"

2:50pm Fangming Xiao, University of Idaho "Signal Transduction in Resistance to Bacterial Speck Disease in Tomato"

3:10pm Scott Diehn, Corteva Agriscience "Insect Control using Proteins from Non-Bt Sources and Expression through Novel Regulatory Elements"

23


1:30pm - 3:40pm Maize - PACIFIC SALON 3 Organizer: Patrick S. Schnable, Iowa State University

1:30pm Sanzhen Liu, Kansas State University "Long-Read A188 Maize Genome Assembly and Short-Mer Guided Error Estimation"

1:50pm Jianbing Yan, Huazhong Agricultural University 2:10pm R. Kelly Dawe, University of Georgia

"Pangenome of the Maize NAM Founder Inbreds"

1:30pm - 3:40pm Cool Season Legumes - PACIFIC SALON 1 Organizer: Kirstin Bett, Dept of Plant Sciences/University of Saskatchewan

1:30pm Sukhjiwan Kaur, Agriculture Victoria, AgriBio, Centre for AgriBioscience

"Genomic Selection in Cool Season Legumes" 1:50pm Teketel A. Haile, University of Saskatchewan

"Comparison of Alternative Methods of GWAS for Mapping Phenology Traits in Lentil"

2:10pm Silke Jacques, Centre for Crop and Disease Management, Curtin University "Putting the Pulse Back into Chickpeas – How Exploiting Wild Germplasm to Expand the Genetic Diversity could Revamp the Adaptive Potential of Domesticated Chickpea"

2:30pm Leandro Escobar-Herrera, Aarhus University "The Faba Bean Pan-Transcriptome"

2:50pm Himabindu Kudapa, ICRISAT "Integrated Omics Approach Reveals Drought Tolerance Mechanism in Chickpea (Cicer arietinum L)"

3:10pm Jonathan Kreplak, INRAE, UMR1347 Agroécologie "The Pea Genome, Now and after ..."

3:30pm Carolyn T. Caron, University of Saskatchewan "Long Read Assemblies Reveal the Complexity of Lens Genomes"

24


1:30pm - 3:40pm Genome to Phenome: Next Generation Sensors for Sensing Plants and Environment - PACIFIC SALON 6-7 (2ND FLOOR) Organizers: Kusum Naithani, University of Arkansas, Pankaj Jaiswal, Oregon State University and D. Keith Roper, Utah State University


1:35pm Chet Udell, Oregon State University "Egreenhouse in-a-Box and Other Gadgets from the Openly Published Environmental Sensing Lab"

2:05pm Scott Jones, Utah State University "Multifunctional Sensing of the Plant Root Zone: Water Status, Gas Exchange, Nutrient Level and Beyond"

2:35pm D. Keith Roper, Utah State University "Integrating High-Resolution Sensors in Convergent Systems to Manage Risks to Crop Productivity"

3:05pm Grégoire Hummel, Phenospex "Sensors and Robots–the Future of Plant Phenotyping?"


1:30pm - 3:40pm Triticeae Genetics and Genomics, Session 2: Trait genetics and gene identification - TOWN AND COUNTRY Organizers: Hana Simkova, Institute of Experimental Botany and Matthew J. Moscou, The Sainsbury Laboratory

1:30pm Ryan Joynson, Earlham Institute "Optimising Source:Sink Balance: Association Mapping of Photosynthetic/Photoprotective Pigment Composition in Spring Wheat"

1:50pm Jorge Dubcovsky, University of California "Regulation of Spikelet Number per Spike in Wheat Development"

2:10pm Zengcui Zhang, USDA-ARS "A Novel Class of Homoeologous Genes Targeted By a Fungal Necrotrophic Effector Triggers Disease Susceptibility in Wheat"

2:30pm Helen J. Brabham, The Sainsbury Laboratory "Multiple Pathogen Recognition at the Mla Locus in Barley"

2:50pm Javier Sanchez-Martin, University of Zurich "Mutchromseq Identifies a Plant Immune Receptor with a Non-Canonical Domain Architecture That Confers Race-Specific Resistance to Wheat Powdery Mildew"

3:10pm Ravi Koppolu, IPK "Characterization of the Barley Spike Transcriptome during Development using Laser Micro Dissected Meristems"

25


1:30pm - 3:40pm Plant Molecular Breeding - GOLDEN WEST Organizers: Jinguo Hu, USDA ARS and Zhi-Kang Li, Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural SciencesCo-organizers: Jianbing Yan, Huazhong Agricultural University, Heqiang Huo, University of Florida and Jauhar Ali, PBGB, International Rice Research Institute

1:30pm John Z. Yu, USDA-ARS, Southern Plains Agricultural Research Center "Exploiting Genetic Variation of Gossypium Gene Pools for Cotton Improvement"

1:50pm Paul Vollrath, Justus Liebig University "Phenotypic Implications of Structural Genome Variation in Elite Winter Canola (Brassica napus)"

2:10pm Lin Li, Huazhong Agricultural University "Qtg-Seq Accelerates QTL Fine-Mapping in the Era of “Big Data”"

2:30pm Allen Van Deynze, University of California "Understanding and Addressing the Complexity of Integrating Disease Resistance from Unadapted Germplasm in Pepper"

2:50pm Gota Morota, Virginia Polytechnic Institute and State University "Variance Heterogeneity Genome-Wide Mapping for Cadmium in Bread Wheat Reveals Novel Genomic Loci and Epistatic Interactions"

3:10pm Michael A Hardigan, University of California, Davis "Accelerating Molecular Breeding of Octoploid Strawberry through Development of Allo-Polyploid Reference Genomes and Subgenome-Specific Marker Platforms"

1:30pm - 3:40pm Citrus Genome - TERRACE ROOM - HANDLERY HOTEL Organizer: Fred G. Gmitter, University of Florida, IFAS-CREC


1:31pm Concetta Licciardello, CREA Research Centre for Olive, Citrus and Tree Fruit "Genetic Improvement of Citrus Fruits Rich in Anthocyanins and Lycopene through Modern Biotechnology Approaches"

1:49pm Marco Aurélio Takita, Citrus Center, IAC, Sao Paulo State Secretary of Agriculture and Supply

"Differences in the Genomes of Phyllosticta citricarpa and Phyllosticta capitalensis"

2:07pm Yoko Eck, University of California "Diversity Study in Citrus with High-Density SNP Array Data"

2:25pm Dorrie Main, Department of Horticulture, Washington State University "Citrus Genome Database Resources for Citrus Genomics, Genetics, and Breeding Research"

26


2:43pm Goutam Gupta, Biolab New Mexico Consortium "Suppression of Citrus Innate Immune Defense By Two Effectors from Clas That Causes HLB"

3:01pm Surya Saha, Boyce Thompson Institute "Citrusgreening.Org: An Open Access and Integrated Systems Biology Portal for the Huanglongbing (HLB) Disease Complex"

3:19pm Ed W. Stover, U. S. Horticultural Research Laboratory, USDA-ARS "Developing Huanglongbing Resistant Transgenic Citrus using Tissue-Specific Promoters from Citrus Small Cyclic Amphipathic Peptides (SCAmpPs) Genes"


1:30pm - 3:40pm Analysis of Complex Genomes - GOLDEN BALLROOM Organizers: David M. Stelly, Department of Soil & Crop Sciences, Texas A&M University, Texas A&M Agrilife Research and Hong-Bin Zhang, Department of Soil and Crop Sciences, Texas A&M University

1:30pm Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research "Insights into Rye Biology and Triticeae Relationships based on a Chromosome-Scale Genome Assembly"

1:50pm Mark Borodovsky, Georgia Institute of Technology "Improving Methods of Automatic Annotation of Plant Genomes"

2:10pm Andrew G. Sharpe, Global Institute for Food Security (U of S) "Long Read Sequence Technology Resolves Hidden Features Among Brassica Genomes"

2:30pm Zhou Zhou, Southern Illinois University at Carbondale "Tilling By Target Capture Sequencing (TbyTCS) to Improve Soybean Seed Composition Traits"

2:50pm Kevin R Bredemeyer, Texas A&M University "Using Contiguous Long-Read Assemblies to Investigate Interspecific Macrosatellite Evolution and Speciation"

3:10pm Jian Zhao, Anhui Agricultural University "Comparative Transcriptomics and Metabolite Profiling to Unravel Defense and Defensive Secondary Metabolite Formation in Tea Trichomes"

27


1:30pm - 6:10pm Cattle/Sheep/Goat 1 - SAN DIEGO Organizer: Benjamin D. Rosen, Animal Genomics and Improvement Laboratory, USDA-ARSCo-organizers: Erdogan Memili, Mississippi State University and Darren Hagen, Oklahoma State University

1:30pm George E. Liu, Animal Genomics and Improvement Laboratory, USDA-ARS "Comparative Epigenomics and Genotype-Phenotype Association Analyses Revealed Conserved Genetic Architecture underlying Complex Traits between Cattle and Human"

1:50pm Elizabeth Ross, Queensland Alliance For Agriculture and Food Innovation - University of Queensland

"Using Long Read Sequencing to Derive an Epigenetic Aging Clock for Cattle"

2:05pm Emily Stassen, University of Vermont "Identification of 5-Hydroxymethylcytosine Markers in the Cattle Brain"

2:17pm Emily L. Clark, The Roslin Institute and R(D)SVS, University of Edinburgh

"The Ovine FAANG Project: A High-Resolution Atlas of Transcription Start Sites in the New Rambouillet Ovine Reference Genome"

2:37pm Raluca Mateescu, Department of Animal Sciences, University of Florida "Integrated -Omics Approaches for Meat Quality Improvement"

2:52pm Farai C. Muchadeyi, ARC-Biotechnology Platform "Exploring the Genetic Resistance to Haemonchus Contortus Infection in Dohne Merino Sheep Using RNA-Seq"

3:07pm Break

3:35pm Céline Bourdon, INRA UMR1313 Animal Genetics and Integrative Biology

"Identification and Characterization of microRNA Genetic Variants in Dairy Cattle, from their Detection to the Analysis of their Biological Impacts"

3:50pm Joseph R Owen, UC Davis "Harnessing Endogenous Repair Mechanisms for Targeted Gene Knock-in during Pre-Implantation Development of Bovine Embryos"

4:05pm Christian J Posbergh, Cornell University "Estimating Partial Lactation Yield Heritabilities and Genetic Correlations in a Dairy Goat Herd using a Restriction Enzyme-Reduced Representational Sequencing Derived Relationship Matrix"

4:20pm Katy Kesler, Michigan State University and CentralStar Cooperative "Profiling Host Transcriptome during Bovine Leukemia Viral Pathogenesis"

28


4:32pm Keabetswe Tebogo Ncube, Agricultural Research Council

"Differential Gene Expression and Identification of Growth-Related Genes in the Pituitary Gland of South African Goats"

4:44pm Kaysie J. Jennings, Colorado State University "Genes Regulating Calcium Availability and Utilization in Angus Steers may be useful in Identifying Cattle with Reduced Susceptibility to Pulmonary Hypertension in High Altitude Beef Production Systems"

4:56pm Kaitlyn M Sarlo Davila, University of Florida "Genome-Wide Association Study for Hair Length in Brangus Heifers"

5:08pm Lakshmi Matukumalli, NIFA-USDA "NIFA Update"

5:18pm James E. Koltes, Iowa State University "NRSP8 Bioinformatics Report"

5:28pm NRSP8 Station Report

5:53pm NRSP8 Business Meeting

1:30pm - 6:10pm Swine - ROYAL PALM SALON 1-2 Organizer: Daniel Ciobanu, University of Nebraska - Lincoln

1:30pm Dan Nonneman, USDA, ARS, USMARC "The Porcine Muscle Thanatotranscriptome"

1:50pm Martijn F.L. Derks, Wageningen University & Research, Animal Breeding and Genomics

"From GWAS Peak to Causal Mutation; Utilizing p(ig)CADD Scores to Prioritize Sequence Variation"

2:10pm Juan P. Steibel, Department of Animal Science, Michigan State University "Phenomics of Pig Behavior and Estimation of Social Effects in Pigs"

2:30pm Claire Rogel-Gaillard, GABI, INRA, AgroParisTech, Université Paris-Saclay "Updating the Annotation of the SLA Complex from the Genome Assembly Sscrofa 11.1"

2:45pm Wen Huang, Michigan State University "High Throughput Phenotyping and Integrative Analysis of Feeding Behavior and Feed Efficiency Traits in Pigs"

3:00pm Marta Godia, Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB

"An Integrative GWAS and RNA-Seq Study to Identify SNPs and Transcripts Related to Sperm Quality Traits in Pigs"

3:10pm Kyu-Sang Lim, Iowa State University "Quantitative Genetic Analysis of the Blood Transcriptome of Young Healthy Pigs to Improve Disease Resilience"

29


3:20pm Juber L. Herrera-Uribe, Iowa State University "Combined Analysis Reveal Association of Changes in Gene Expression and H3K27ac Chromatin Modification at Regulatory Regions in Porcine Alveolar Macrophage in Response to LPS and Poly(I:C)"

3:30pm Paula R. Chen, Division of Animal Sciences, University of Missouri "Jorgensen Award: Anthrax Toxin Receptor 1-Knockout Pigs are Protected from Senecavirus a Infection"

3:40pm Yulu Chen, Iowa State University "Jorgensen Award: Protein Levels in Blood of Young Healthy Pigs as Indicators of Disease Resilience"

3:50pm Break

4:05pm NIFA Administration Report

4:10pm NRSP8 Bioinformatics Coordinator Update

4:15pm NRSP8 Swine Genome Coordinator Update

4:20pm Swine Industry Comments

4:25pm Swine Subcommittee Panel Discussion on Multi-Station Collaborations

4:40pm Christopher K. Tuggle, Animal Science, Iowa State University "Iowa State University Swine Workshop Station Report"

4:50pm Ryan J. Corbett, Genetics & Genome Sciences Graduate Program, Michigan State University

"Whole-Genome DNA Methylation Analyses in Pig Fetal and Immune Tissues"

5:00pm Christian Maltecca, NC State University "NCSU Station Report"

5:10pm Gary A. Rohrer, USDA, ARS, U.S. Meat Animal Research Center "Genomic Analysis of Weaning to Estrus Interval from Crossbred Sows Spanning 4 Parities"

5:20pm Joan Lunney, Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA

"Distinguishing Fetal and Placental Immune Responses to Congenital Infection with Porcine Respiratory and Reproductive Syndrome Virus with Nanostring Arrays"

5:30pm Daniel C. Ciobanu, University of Nebraska - Lincoln "University of Nebraska - Lincoln Station Report"

5:40pm NRSP8 Business Meeting and Election

30


1:30pm - 6:10pm Equine 1 - ROYAL PALM SALON 5-6 Organizer: Annette M McCoy, University of Illinois Co-Organizer: Michael J. Mienaltowski, University of California, Davis

1:30pm Introductory Remarks

1:35pm Marcio Costa, University of Montreal "Current Knowledge of the Equine Microbiome"

2:30pm Bioinformatics Update

2:40pm USDA Update

2:50pm Ludovic Orlando, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark

"Equine Hybrids and their Genetic Foundation in History" 3:10pm Caitlin Castaneda, Texas A&M University

"Equine Y Chromosome Variability" 3:25pm Break

3:40pm Discussion

4:25pm Break

4:40pm Jocelyn L. Tanaka, University of California - Davis "An 8.7kb Deletion in MITF Explains a Novel Splashed White Phenotype in the American Paint Horse"

4:55pm Elaine M Norton, University of Minnesota "Genome-Wide Association Analyses of Equine Metabolic Syndrome Phenotypes in Welsh Ponies and Morgan Horses"

5:10pm Victor Rivas, University of California-Davis "Inherited Hypocalcemia in Thoroughbred Foals is associated with a Nonsense Mutation in RAPGEF5"

5:25pm Yael Leah Hack, University of California- Davis "Whole Genome Sequencing Identifies Missense Mutation in GRM6 as the Putative Cause of Congenital Stationary Night Blindness in a Tennessee Walking Horse"

5:40pm Erin A. Hisey, University of California, Davis School of Veterinary Medicine "A 16 Kilobase Deletion on ECA13 Is Strongly Associated with Distichiasis in Friesian Horses"

5:55pm Sian Ann Durward-Akhurst, University of Minnesota "The Frequency of Loss of Function Alleles in the Equine Population"

3:00pm - 4:00pm Coffee Break - ATLAS FOYER

31


4:00pm - 6:10pm Non-Seed Plants - EAST 2 Organizers: Stefan A. Rensing, University of Marburg and Stuart McDaniel, University of Florida

4:00pm James Umen, Donald Danforth Plant Science Center "Sex Determination in Volvocine Algae"

4:20pm Sarah Carey, University of Florida "Remarkable Genome Stability in Autosomes Contrasts with Dynamic Sex Chromosomes in Mosses"

4:40pm Kirsten Fisher, California State University, Los Angeles "The Genome of the Desiccation Tolerant Moss Syntrichia caninervis and its Response to Abiotic Stress"

5:00pm Adam Healey, HudsonAlpha Institute For Biotechnology "The Sphagnome Project: Sphagnum As a Model Organism for Carbon Sequestration and Niche Ecosystem Evolution"

5:20pm Peter Szovenyi, University of Zurich "The First High-Quality Reference Genome for Hornworts (Anthoceros) "

5:40pm Andrea Braeutigam, Bielefeld University "Evolutionary Analyses of Machine-Learned Gene Regulatory Networks in Plants"

4:00pm - 6:10pm Challenges and Opportunities in Plant Science Data Management - an International Workshop - TERRACE ROOM - HANDLERY HOTEL Organizers: Robert P. Davey, Earlham Institute and Darwin Campbell, Iowa State UniversityCo-Organizer: Ian Braun, Iowa State University

4:00pm Eva Huala, Phoenix Bioinformatics "Relieving the Curation Bottleneck: A Multi-Pronged Approach"

4:15pm Ricardo Humberto Ramirez Gonzalez, John Innes Centre "Larger Datasets, Faster Query Times. Improving the Performance of ExpVIP, an Expression Browser."

4:30pm Hugh Williamson, University of Exeter "Tracking Data Linkage for Intelligent and Responsible Reuse"

4:45pm Guillaume J. Bauchet, Boyce Thompson Institute "Breedbase: A Digital Ecosystem for Plant Breeding of Root and Tuber Crops and Beyond "

5:00pm Yo Yehudi, Department of Genetics, University of Cambridge "Integrated Data and Cross-Organism Queries with Intermine"

5:15pm David LeBauer, University of Arizona " Software to Streamline Sharing of Agricultural Algorithms and Data"

32


4:00pm - 6:10pm Teaching Genetics, Genomics, Biotechnology, and Bioinformatics - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Abdelmajid Kassem, Department of Biological and Forensic Sciences, Fayetteville State University

4:00pm Saurabh Babanrao Whadgar, Institute of Bioinformatics and Applied Biotechnology

"Delivering Bioinformatics Lectures and Hands-on Training Using State-of-the-Art Solutions."

4:20pm Mohammad Heydarian, Galaxy Project - Johns Hopkins University "Galaxy as an Educational Tool and Community Resource for Undergraduate Training"

4:40pm Scott Woody, UW-Madison "Enhancement of Experiments in Artificial Selection: QTL Analysis of Loci That Condition Expression of Variable Traits in Rapid-Cycling Brassica Rapa"

5:00pm Khalid Meksem, Southern Illinois University at Carbondale "Integration of Research and Teaching in Plant Genetics and Genomics: Two Decades Experience"

4:00pm - 6:10pm Population and Conservation Genomics 1 - PACIFIC SALON 3 Organizer: Om P. Rajora, University of New BrunswickChair: Om P. Rajora, University of New Brunswick

4:00pm Om P. Rajora, University of New Brunswick "Population and Conservation Genomics: Challenges and Opportunities"

4:10pm Rebekah L. Horn, Columbia River Inter-Tribal Fish Commission "Detecting Genomic Variation Underlying Phenotypic Characteristics of Reintroduced Coho Salmon (Oncorhynchus kisutch)"

4:30pm Marco Todesco, University of British Columbia, "Massive Haplotypes Underlie Ecotypic Differentiation in Sunflowers"

4:50pm Rachel Meyer, University of California Santa Cruz, "Population Genomics and Improved Reference Genomes of African Rice (Oryza glaberrima) and Its Wild Ancestor Allow Comparisons of 44 Characterized Domestication Genes to Demystify Longstanding Assumptions of Parallel Evolution"

5:10pm Vanessa Carina Bieker, NTNU University Museum, Norwegian University of Science and Technology (NTNU)

"Inferring Plant Genome Evolution of an Invasive Species (Ambrosia artemisiifolia L.) using Historic Herbarium Specimens"

5:30pm Hari Chhetri, West Virginia University "Local Adaptation in Populus trichocarpa Torr. & Gray"

5:50pm Philip Lavretsky, University of Texas at El Paso "Population Genetics and Hybridization of Mallards and Mallard-like Ducks in North America"

33


4:00pm - 6:10pm Bioenergy Grass Biology: Genomes, microbiomes, traits and applications - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Kerrie Farrar, IBERS, Aberystwyth University and Kankshita Swaminathan, University of Illinois Urbana-Champaign

4:00pm Kerrie Farrar, IBERS, Aberystwyth University "Exploiting the Plant Microbiome to Boost Plant Growth and Resilience"

4:25pm Emily Heaton, Iowa State University "Trials with Clonal Miscanthus Reveal Background Environmental x Management Variability in Perennial Energy Grasses"

4:45pm Joel Oliver, Texas A&M University "Sorghum Dw2 (AGCVIII kinase) Regulates Lipid Signaling, Endomembrane Function, and Stem Growth"

5:05pm Matthew E. Hudson, University of Illinois "Cropsr, a CRISPR Design Solution for Biofuel Crops"

5:25pm Mao Li, Donald Danforth Plant Science Center "Comprehensive Above and below Ground 3D Phenomics for Grasses"

5:45pm Flavia Pilar Forte, Aarhus University "Transcriptome Analysis of a Mutualistic Association between Perennial Ryegrass (Lolium perenne) and Its Fungal Endophyte Epichloë Festucae"

4:00pm - 6:10pm Climate Change and ICRCGC 1 - GOLDEN BALLROOM Chair: Chittaranjan Kole, ICAR-National Institute for Plant Biotechnology Co-Organizer: Jeffrey Ehlers, Bill and Melinda Gates Foundation

4:00pm Chittaranjan Kole, ICAR-National Institute for Plant Biotechnology "Harnessing Plant Genomics for Climate Resilience"

4:15pm Robert J. Henry, University of Queensland/QAAFI "Genomics of Trait Discovery for Climate Adaptation"

4:30pm Jauhar Ali, Rice Breeding Platform, International Rice Research Institute "Strengthening Food Security through Climate-Smart Rice Hybrids"

4:45pm Kiyosumi Hori, National Agriculture and Food Research Organization "Deciphering Genetic Basis of Responses to Climate Temperature Fluctuations in Rice"

5:00pm Marco Maccaferri, University of Bologna, Bologna "Efficient Characterization of Tetraploid Wheat Plant Genetic Resources for Wheat Resilience Improvement "

5:15pm Philomin Juliana, International Maize and Wheat Improvement Center (CIMMYT)

"Perspectives from Integrating Genomic and High-Throughput Phenotyping Tools in Breeding for Climate-Resilience in Bread Wheat"

5:30pm John C. Cushman, University of Nevada - Reno "Strategies for Improving Plant Drought Tolerance for a Hotter, Drier World" Mallard-like Ducks in North America"

34


4:00pm - 6:10pm Next Generation Genome Annotation and Analysis - GARDEN 1 - HANDLERY HOTEL Organizer: Carson Holt, Department of Human Genetics, University of Utah

4:00pm Cristina F. Marco, DNA Learning Center, Cold Spring Harbor Laboratory

"Making Sense of a New Assembled Genome: Finding and Fixing Genome Annotation Errors through Community Curation Approaches"

4:25pm Sofia Robb, Stowers Institute for Medical Research "Using Open-Source Software at SIMRbase to Share Genomic Data with the Sea Lamprey Community"

4:50pm Jill L. Wegrzyn, University of Connecticut "Approaches and Tools to Improve the Identification of Protein-Coding Regions in Large and Complex Genomes"

5:15pm Ralf Christian Mueller, Max Planck Institute of Animal Behavior. University of Konstanz, Konstanz

"High-Quality Annotation of the Tufted Duck genome" 5:40pm Carson Holt, Department of Human Genetics, University of Utah

"Fastqforward: Whole Genome Sequencing Analysis in Under 10 Minutes"

4:00pm - 6:10pm Genomic Selection and Genome-Wide Association Studies - GOLDEN WEST Organizers: Jianming Yu, Iowa State University and Dorian J. Garrick, Iowa State University


4:05pm Andrew Cromie, ICBF "GS/GWAS ICBF"

4:30pm Eduard Akhunov, Kansas State University "Integrating Gene Expression Mapping, Epigenetics and GWAS to Understand the Genetic Control of Agronomic Traits in Hexaploid Wheat"

4:55pm Timothy D. W. Luke, Agriculture Victoria Research and La Trobe University "A Multi-Omics Approach to Improving the Metabolic Health of Dairy Cows"

5:15pm Aaron Lorenz, University of Minnesota "Genomic Prediction for Plant Breeding: Beyond Gebvs and Cross Validation"

5:40pm Gertje Petersen, AbacusBio "The Fascinating Genetic Architecture of Honeybees"


35


4:00pm - 6:10pm Small RNA - PACIFIC SALON 2 Organizers: Blake Meyers, Donald Danforth Plant Science Center and Julie A. Law, Salk Institute for Biological Studies

4:00pm Eric Van Nostrand, University of California, San Diego "Unambiguous Deep Profiling of microRNA Targets with Chimeric-Eclip "

4:20pm Sascha Duttke, University of California, San Diego "Dynamic Quantification and Annotation of Regulatory Elements and Gene Bodies using Total RNA"

4:40pm Jianxin Ma, Purdue University "Rhizobial tRNA-Derived Small RNAs are Signal Molecules Regulating Plant Nodulation"

5:00pm Kun Huang, University of Delaware "Quantitative, Super-Resolution Imaging of Small RNAs with sRNA-PAINT"

5:20pm Kelly Dew-Budd, University of Arizona "Elucidating the Influence of Rddm during Reproduction through Comparative Small Rnaseq in Two Capsella Species"

4:00pm - 6:10pm Oats, Wild and Cultivated - PACIFIC SALON 1 Organizers: Nicholas Tinker, Agriculture and Agri-Food Canada and Rick N. Jellen, Brigham Young UniversityCo-Organizer: Wubishet Bekele, Agriculture and Agri-Food Canada

4:00pm Tim Langdon, IBERS, Aberystwyth University "Oat Genomes: Their Sequences, Diversity, and Domestication"

4:20pm Martin Mascher, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

"Panoat: Prospects of Pan-Genomics in Oat" 4:40pm Eric N. Jellen, Brigham Young University

"Toward the World’s Most Interesting Pan Genome" 5:00pm Wubishet Bekele, Agriculture and Agri-Food Canada

"Prospects for Improved Genomic Selection through Pan Genomics"

5:15pm Annis Fatmawati, MacDonald Campus, McGill University "Towards an Understanding of Beta-Glucan Regulation in Oat"

5:30pm Kathy L. Esvelt Klos, USDA-ARS "Harvesting Oat CORE QTLs: Milling Quality, Seedling Growth, and Phenotypic Stability"

36


4:00pm - 6:10pm CyVerse - Software, Tools, and Services for Data-Driven Discovery and Learning - CALIFORNIA

Organizer: Jason Williams, Cold Spring Harbor Laboratory

4:00pm Eric Lyons, The University of Arizona "Cyverse 2020"

4:15pm Fiona McCarthy, University of Arizona "i5k and CyVerse: Tools for Predicting Genome-Wide Function"

4:35pm Siavash Mirarab, University of California, San Diego "Phylogenomic Analyses of the Thousand Plant Transcriptomes."

4:55pm Brian Lee, Univ. Calif. Santa Cruz "Hosting Data at CyVerse to Visualize and Analyze on the UCSC Genome Browser"

5:15pm Judy A. Brusslan, California State University, Long Beach "CyVerse/DNA Subway: Incorporating Both Fundamental Coding Skills and Modern RNA-Seq Tools into the Undergraduate Curriculum"

5:35pm Peter W Rose, UC San Diego "Deploying Scalable, Interactive Bioinformatics Analyses Via Vice"

5:55pm Sateesh Peri, Genetics Graduate Interdisciplinary Group, University of Arizona "Phytooracle: A Scalable, Modular Framework for Phenomics Data Processing and Trait Extraction"

6:20pm - 8:30pm What Early Career Scientists Need to Know: Developing and Executing Successful Broader Impact Programs for Current and Future Grants - PACIFIC SALON 1 Organizer: Michael D. Gonzales, University of Georgia/MG ConsultingChair: Diane Jofuku Okamuro, National Science Foundation/BIO/Division of Integrative Organismal Systems

6:20pm Welcome and Introductory Remarks

6:25pm Jamie A. O'Rourke, USDA-ARS-MWA-CICGRU "Mentoring for Science, Mentor for Life"

6:45pm Alejandro Cortez, UC-Riverside "The Dynamic Genome Program: An Experiential Learning Experience."

7:05pm Lucas Busta, University of Nebraska Lincoln "Using Citizen Science to Communicate and Catalyze Plant Chemical and Genomic Research"

7:25pm Funding Opportunities Panel Discussion with Program Directors

7:45pm Discussion and Networking

37


6:20pm - 8:30pm Bioactive, Nutraceutical and Therapeutic Molecules in Plants - ROYAL PALM SALON 3-4 Organizer: Jiazheng (John) Yuan, Department of Biological and Forensic Sciences, Fayetteville State University

6:20pm Benito de Lumen, Nutritional Sciences & Toxicology/University of California, Berkeley

"Lunasin: An Anti-Cancer Soybean Peptide" 6:35pm Abdelmajid Kassem, Fayetteville State University

"Genetic Mapping of Seed Isoflavone Content in Soybean" 6:50pm David Lightfoot, Southern Illinois University

"The Tuareg Pharmacopeia: Basil; Aloe and Willow Teas; Work on Drug Resistant Cancers"

7:05pm Benoit Bizimungu, Agriculture and Agri-Food Canada "Improvement of Bioactive Ingredients in Potato: Starch and Antioxidant Compounds as Breeding Targets"

7:20pm Yong-Qiang Charles An, USDA-ARS Plant Genetics Research Unit, Donald Danforth Plant Science Center

"Explore Genetic Diversity of Soybean Fatty Acid Biosynthetic Pathway by Seed Transcriptome Sequencing"

7:35pm Naoufal Lakhssassi, Southern Illinois University at Carbondale "TILLING by Target Exome Capture Sequencing as New and Effective Platform for Gene Functional Analysis"

6:20pm - 8:30pm IWGSC Business Meeting - PACIFIC SALON 4-5 (2ND FLOOR)

6:20pm - 8:30pm Flavor, Nutrition, and Post-Harvest Genomics - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Vincent Colantonio, University of Florida

6:20pm Vincent Colantonio, University of Florida "Welcoming Remarks"

6:25pm Christine Diepenbrock, University of California Davis "Genetics of Carotenoids, Kernel Color, and Vitamin E in Maize Grain"

6:45pm Marcio F. R. Resende, University of Florida "Metabolomic Selection for Enhanced Fruit Flavor"

7:05pm Macarena Farcuh, University of Maryland, College Park "Sugar Metabolism Reprogramming during Ripening of a Climacteric Fruit and Its Non-Climacteric Mutant"

7:25pm Mitchell J. Feldmann, University of California, Davis "Pedigree-Informed Genome-to-Phenome Mapping of Morphometric Traits in Strawberry"

7:45pm Tie Liu, University of Florida "Use of Genomics Tools to Study Postharvest Senescence in Brassica vegetables"

38


6:20pm - 8:30pm Systems Biology and Machine Learning - ROYAL PALM SALON 5-6 Organizer: Shahid Mukhtar, University of Alabama at Birmingham


6:30pm Katherine Denby, University of York "Elucidating and Re-Designing Regulatory Networks Underlying Plant-Pathogen Interaction"

6:50pm Jiyoung Lee, Virginia Tech "Comparing Time Series Transcriptome Data between Plants using a Network Module Finding Algorithm"

7:00pm Cranos Williams, North Carolina State University "Multiscale Modeling of Lignin Biosynthesis in P. trichocarpa"

7:20pm Shin-Han Shiu, Michigan State University "Transcriptome-Based Prediction of Complex Traits in Maize"

7:40pm Steven Briggs, University of California San Diego "Resolution of Alternative Maize Genome Annotations by Machine Learning"

8:00pm Daniel Jacobson, Oak Ridge National Laboratory "Exascale Biology: From Genome to Climate with a Few Stops Along the Way"

8:20pm Haidong Yan, School of Plant and Environmental Sciences, Virginia Tech "DeepTE: A Computational Method for de novo Classification of Transposons with Convolutional Neural Network"

6:20pm - 8:30pm Machine Learning and Artificial Intelligence in Genomics and Phenomics - EAST 1 Organizers: Stephen P. Ficklin, Dept of Horticulture, Washington State University, Sindhuja Sankaran, Washington State University and F. Alex Feltus, Clemson University

6:20pm Ian Stavness, University of Saskatchewan "Deep Learning for Image-Based Plant Phenotyping"

6:40pm Jill L. Wegrzyn, University of Connecticut "EASEL: An Integrated and Accessible Framework for the Annotation of Eukaryotic Reference Genomes"

7:00pm Koushik Nagasubramanian, Iowa State University "An Empirical Analysis of Deep Active Learning Methods for Image-Based Plant Phenotyping"

7:20pm Yueyao Gao, Clemson University "A Differential Expression Computational Workflow for Time-Series Transcriptomic Studies"

7:40pm Therin Young, Iowa State University "Determining Effective Dimensionality Reduction Tools for Genetic Data used in Deep Learning Models"

8:00pm Tyler Biggs, Dept of Horticulture, Washington State University "Gsforge: A Package for Condition-Specific Gene Set Selection, Comparison, Quality Assessment and Visualization for Traditional and Machine Learning Approaches"

39


6:20pm - 8:30pm Extremophile Genomes - PACIFIC SALON 2 Organizer: Bjoern Pietzenuk, Ruhr-University Bochum

6:20pm Guannan Wang, Louisiana State University "Learning from Nature: Multi-Ion Salt Stress Adaptation Explored using Extremophyte Genomics Exemplified by Boron Toxicity"

6:40pm Nadja Mobjerg, University of Copenhagen "New Insights into Cryptobiotic Survival of Tardigrades"

7:00pm Zhang Heng, Shanghai Center for Plant Stress Biology, CAS "The Genome of Broomcorn Millet, a Cereal with Extremely High Water Use Efficiency"

6:20pm - 8:30pm Application of New Genomic Tools and Techniques in Arthropods - ROYAL PALM SALON 1-2 Organizers: Marcé D. Lorenzen, North Carolina State University and Lindsey Perkin, Agricultural Research Service, USDA

6:20pm Marce Lorenzen, North Carolina State University "Application of New Genomic Tools and Techniques in Arthropods"

6:45pm Wayne Hunter, USDA-ARS "BAPC-Assisted CRISPR/Cas9 System: Targeted Delivery into Adult Ovaries for Heritable Germline Gene Editing (Hemiptera)"

7:10pm Valentino M. Gantz, University of California, San Diego " Novel Trans-Complementing Split-Gene Drive System Provides Flexible Application for Safe Laboratory Investigation"

7:35pm Fu-Chyun Chu, All Things Bugs LLC "The ABCs of using CRISPR in Non-Model Organisms"

8:00pm Allah Bakhsh, Nigde Omer Halisdemir University "Knock Down of Imidacloprid Resistant Genes in Colorado Potato Beetle, Leptinotarsa decemlineata (Chrysomelidae: Coleoptera)"

6:20pm - 8:30pm Apiaceae - EAST 2 Organizers: Philipp W. Simon, USDA, ARS and University of Wisconsin, Madison and Shelby L. Ellison, University of Wisconsin-Madison

6:20pm Philipp W. Simon, USDA, ARS and University of Wisconsin, Madison "Trait Identification and Genomic Database Development for Carrot (Daucus carota) Improvement"

6:40pm Massimo Iorizzo, Plants for Human Health Institute, North Carolina State University

"Improved Hybrid de novo Genome Assembly, Gene Prediction and Annotation of Carrot (Daucus carota)"

7:00pm Shelby L. Ellison, University of Wisconsin-Madison "Genome-Wide Association Analysis of Carotenoids in Carrot"

7:20pm Allen Van Deynze, University of California "Characterization of the Tendency for Bolting among Carrot Germplasm Accessions"

7:40pm Dariusz Grzebelus, University of Agriculture in Krakow "Abundance and Insertional Polymorphism of Carrot Mites and Demography of Daucus carota"

40


6:20pm - 8:30pm Genomic Advances in Fruit and Vegetable Breeding - PACIFIC SALON 3 Organizer: Seonghee Lee, University of FloridaCo-Organizer: Upinder Gill, University of Florida

6:20pm Chris Barbey, University of Florida "Multi-Omics Identification of Flavor and Aroma Genes in Strawberry"

6:40pm Upinder Gill, North Dakota State University "Genetics Characterization of New and Existing Sources of Tomato Yellow Leaf Curl Virus Resistance in Tomato"

7:00pm Jinhee Kim, National Institute of Horticultural and Herbal Science "Genome Assembly of Homozygous Octoploid Strawberry Inbred Line Provides Insights into Crop Improvement"

7:20pm Nahla Bassil, USDA-ARS National Clonal Germplasm Repository "Using Synteny and Candidate Genes to Identify Loci Controlling Fruit Sweetness in Blackberry"

7:40pm Ying Hu, University of Florida "The Sweet Corn Genome Assembly and Comparative Analysis with Other Field Corn Genomes"

8:00pm Seanna Hewitt, Washington State University "Genomic Characterization of Novel Fruit Ripening Pathways"

41

Sunday - January 12, 2020







8:00am - 10:10am Equine 2 - ROYAL PALM SALON 5-6 Organizer: Annette M McCoy, University of IllinoisCo-Organizer: Michael J. Mienaltowski, University of California Davis

8:00am Sichong Peng, University of California, Davis "Mapping CTCF Binding Regions in the Equine Genome"

8:15am Nicole B. Kingsley, University of California, Davis "Functionally Annotating Regulatory Elements in the Equine Genome using Histone Mark ChIP-Seq"

8:30am Deborah Velez-Irizarry, Michigan State University "Integrating Transcriptomics, Proteomics, and cis-Regulatory Networks to Understand Muscle Physiology and Pathophysiology"

8:50am Lucia Younger, Cornell University "Single Nucleotide Polymorphism Characterization of Major Histocompatability Complex Haplotype Diversity in Standardbred Horses"

9:10am Station Reports

9:45am Havemeyer Update and Other New Business


42


8:00am - 10:10am Sorghum/Millet - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Yinghua Huang, USDA ARS

8:00am Yinghua Huang, USDA ARS "Introduction of Sorghum and Millet Workshop"

8:03am Elizabeth Cooper, University of North Carolina at Charlotte "Structural Genomic Variation and the Evolution of Sugar Accumulation in Sweet Sorghum"

8:28am Qi Mu, Iowa State University "A Step Forward in Predicting Phenotypic Performance in Diverse Field Environments"

8:53am Xuemin Wang, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland

"Large Scale Genome-Wide Association Study Reveals that Drought Induced Lodging in Grain Sorghum is associated with Plant Height and Traits Linked to Carbon Remobilisation"

9:18am Andrea L. Eveland, Donald Danforth Plant Science Center "Genomics-Enabled Dissection of Enhanced Water and Nitrogen Use Efficiency in Sorghum"

9:43am Hongxu Dong, Plant Genome Mapping Laboratory, University of Georgia "Genetic Dissection of Drought Tolerance in a Sorghum Backcross Nested Association Mapping Population"

8:00am - 10:10am New Approaches for Developing Disease Resistance in Cereals - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Jesse Poland, and Burkhard Steuernagel,

8:00am Sreya Ghosh, John Innes Centre "Exploring Leaf Rust Resistance in Aegilops tauschii Using Association Genetics Coupled with Resistance Gene Capture"

8:25am Pilar Corredor-Moreno, John Innes Centre "Field Transcriptomics Identifies a Novel Wheat Susceptibility Factor which Modulates Resistance to Rust"

8:50am Markus C. Kolodziej, University of Zurich "Use of a High-Quality Wheat Genome Assembly Allows Cloning of a Novel Non-NLR Leaf Rust Resistance Gene"

9:15am Katherine E Dibley, CSIRO Agriculture & Food "Lr67 Resistance Beyond Wheat: A Broad-Spectrum Disease Resistance Gene Functions in Multiple Crop Species"

43


8:00am - 10:10am Gene Introgression - PACIFIC SALON 2 Organizers: Theresa A. Musket, University of Missouri and Julie King, University of Nottingham

8:00am Kathy Dibley, CSIRO Agriculture and Food "MAGIC and Pre-Breeding Advances"

8:20am Moises Cortes Cruz, Instituto Nacional do Investigaciones Forestales, Agricolas Pecuaries

"Detection Activities of LMO Introgressions on Maize Landraces at the National Genetic Resources Center in Mexico"

8:40am Handong Su, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

"New Alien Translocation Lines from Thinopyrum intermedium"

9:00am Glenn Bryan, The James Hutton Institute "Tracking Alien Introgression in Cultivated Potato: An Example using Cyst Nematode Resistance from the Wild Potato Species Solanum spegazzinii"

9:20am Manel Othmeni, University of nottingham "Increasing Durum Wheat Genetic Diversity By Wild Relative and D-Genome Introgressions"

9:40am David Bonnett, BASF Corporation "Hybrid Wheat - Building on Diversity"

8:00am - 10:10am Buffalo Genomics - PACIFIC SALON 3 Organizer: John Williams, Davies Research Centre, University of Adelaide

8:00am John Williams, Davies Research Centre, University of Adelaide "Workshop Introduction"

8:05am Ananthasayanam Sudhakar, National Dairy Development Board "De novo Haplotype Phased Genome Assembly and Genomic Selection of Buffaloes in India"

8:30am Josue Chinchilla Vargas, Iowa State University "Marker Discovery and Associations with Beta-Carotene Content in Indian Buffalo and Dairy Cattle Breeds"

8:55am Andre Vieira do Nascimento, São Paulo State University "Updating the Buffalo Array Map and Prediction of QTL Positions in the New Water Buffalo Genome"

9:20am Tingzhu Ye, Huazhong Agricultural University "Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) using Transcriptome Data"

9:45am Christelle Robert, The Roslin Institute "The African Buffalo and its Genomic Diversity"

44


8:00am - 10:10am Feline and Canine Genomics Workshop - PACIFIC SALON 1 Organizers: Elinor K. Karlsson, UMass Med School & Broad Institute and Ellie Armstrong, Stanford University

8:00am Alexandra N. Myers, Texas A&M University "Genetics of Severe Ringworm in Persian Cats"

8:12am William J. Murphy, Texas A&M University "Ultracontiguous Genome Assemblies from Felid F1 Interspecies Hybrids"

8:24am Reuben M. Buckley, University of Missouri-Columbia "Human Gene Constraint Guided Disease Variant Identification in Cats"

8:36am Laurent Frantz, Queen Mary University of London "Dire Wolves Were the Last of an Ancient New World Canid Lineage"

8:48am Adam R. Boyko, Cornell University "Breed Trends, Health Risk Variant Frequency, and Outcomes in over 100,000 Companion Dogs Genotyped on a Direct-to-Consumer High-Density SNP Microarray."

9:00am Adam R. Boyko, Department of Biomedical Sciences Cornell University "Breed Trends, Health Risk Variant Frequency, and Outcomes in over 100,000 Companion Dogs Genotyped on a Direct-to-Consumer High-Density SNP Microarray."

9:12am Frédéric Delsuc, Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier

"High Quality Reference Genomes from Roadkill Enable Species Delimitation in Aardwolf and Bat-Eared Fox"

9:24am Molly R Cassatt-Johnstone, University of California, Santa Cruz "Genomic Analysis of the Extinct American Cheetah Reveals a New Evolutionary History of Carnivores in Pleistocene Beringia"

9:36am Safia Janjua, Wright State University "DNA Capture: Challenges and Utility for Non-Invasive Samples"

8:00am - 10:10am Comparative Genomics - TOWN & COUNTRY BALLROOM Organizers: Yong Q. Gu, and Nathan M. Springer

8:00am Julia Bailey-Serres, UC RIverside "Conservation and Variation in Stress-Responsive Gene Regulatory Circuitry across Angiosperms"

8:20am Kathleen Greenham, University of Minnesota "Temporal Expansion and Diversification of the Polyploid B. Rapa Transcriptome"

8:40am Rebecca A. Mosher, University of Arizona "Using Orthologous Mutations to Understand the Role of RNA-Directed DNA Methylation during Seed Development"

9:00am Li-zhi Gao, South China Agricultural University "Comparative Chloroplast, Mitochondrial and Nuclear Genomics of the Genus Oryza"

9:20am Ksenia Krasileva, Department of Plant and Microbial Biology UC Berkeley "Structural and Allelic Variation in Plant NLR Immune Receptors"

9:40am Ning Jiang, Michigan State University "Pack-Mule Transposable Elements in Rice and Its Wild Relatives"

45


8:00am - 10:10am Resources and Programs for Undergraduate Education in Genomics - TERRACE ROOM - HANDLERY HOTEL Organizer: Scott Woody, UW-Madison

8:00am Scott Woody, UW-Madison "Introductory Remarks"

8:10am Vincent Buonaccorsi, Juniata College "The Genomics Education Alliance (GEA)"

8:30am Wilson Leung, Washington University in St. Louis "Using Genome Browsers Constructed by G-OnRamp to Provide Students with a Course-Based Undergraduate Research Experience in Genome Annotation"

8:50am Jason Williams, Cold Spring Harbor Laboratory "Tools and Approaches for Making Bioinformatics Work in the Classroom"

9:10am Ray Enke, James Madison University "Undergraduates Contain Multitudes: Course-Based Metagenomics Analysis using the DNA Subway Purple Line"

9:30am Ed Himelblau, California Polytechnic State University, San Luis Obispo "Engaging Students in Gene Mapping Using Gametemaker"

9:50am Matthew Collin, University of California Riverside "Using NGS Technology to Sequence Amplicons En Masse to Solve Two Problems: Cost and Heterozygosity"

8:00am - 10:10am Development and Application of Genome Engineering and Transgenic Technology to the Agriculture - GOLDEN WEST Organizer: Ashok Shrawat, Bayer

8:00am James Dale, Centre for Tropical Crops and Biocommodities "The Long Road to the Golden Banana"

8:20am Bing Yang, University of Missouri "Genome Editing in Grass Plants"

8:40am Markita P. Landry, University of California Berkeley "Nanomaterials Enable Delivery of Genetic Material without Transgene Integration in Mature Plants"

9:00am Wanlong Li, South Dakota State University "Genome Editing of Wheat Grain-Regulatory Genes"

9:20am Roger Thilmony, USDA-Agriculture Research Service "GAANTRY, a Novel Agrobacterium-Based Transgene Stacking System for Improved Crop Biotechnology"

9:40am Diego Orzaez, IBMCP-CSIC "Expanding Multiplex Genome Editing Tools for Accelerated Breeding in Industrial Crops"

46


8:00am - 10:10am Systems Biology and Ontologies - ROYAL PALM SALON 3-4 Organizers: Pankaj Jaiswal, Dept. of Botany and Plant Pathology, Oregon State University, Laurel Cooper, Dept. of Botany and Plant Pathology, Oregon State University and Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University


8:05am Daniil Prigozhin, Lawrence Berkeley National Laboratory "Computational Identification of Target-Binding Sites in Plant Immune Genes"

8:25am Anne Thessen, Oregon State University "Predicting Phenotype from Multi-Scale Genomic and Environment Data using Neural Networks and Knowledge Graphs: An Introduction to the NSF GenoPhenoEnvo Project"

8:45am James C Schnable, University of Nebraska-Lincoln "Genes and Gene-like Sequences in Maize, Sorghum, and Arabidopsis."

9:05am Amit Dhingra, Molecular Plant Sciences, Washington State University "Are All Plastids Created Equal?"

9:25am Laura-Jayne Gardiner, IBM Research "Can We Use Machine Learning to Predict Circadian Genes in Wheat Using DNA Sequence?"

9:40am Cedar Warman, Oregon State University "Novel Maize Ear Phenotyping Methods Enable Large-Scale Functional Validation of Transcriptome Data"

9:55am Daemon Dikeman, Oregon State University "Gene Structure and Expression of the Rice S-Domain Kinase (SD-RLK) Gene Family"

8:00am - 12:40pm Poultry 2 - EAST 1 Organizers: Kent M. Reed, University of Minnesota and Gale Strasburg, Michigan State University

8:00am James M. Reecy, Department of Animal Science, Iowa State University "NRSP-8 Update"

8:20am Muhammed Walugembe, Iowa State University "Genetic Analyses of African Local Chicken Ecotypes Challenged with Newcastle Disease Virus to Improve their Disease Resilience"

8:40am Rosemary Walzem, Texas A&M University "Poultry Genetic Resources: Catalyst for Common Use"

9:00am Jingyi Li, Texas A&M "A Genetic Duplication Is Associated with Ectopic Expressions of HOX Genes and Alters Body Region Identity in Crested Chickens"

9:20am Jing Li, Life Sciences Institute, Zhejiang University "Chromosome-Level Genome and Comparative Analyses of Duck Uncover Genome and Chromatin Architecture Evolution of Birds"

9:40am Break 10:00am Neal A. Jorgenson Genome Travel Award - Nnamdi Ekesi 10:15am Lightning Talks 10:40am NC1170 Business Meeting

47


8:00am - 12:40pm Cattle/Sheep/Goat 2 - SAN DIEGO

Organizer: Benjamin D. Rosen, Animal Genomics and Improvement Laboratory, USDA-ARSCo-organizers: Erdogan Memili, Mississippi State University and Darren Hagen, Oklahoma State University


8:05am Amanda Warr, The Roslin Institute, The University of Edinburgh "The Cattle Rumen Microbiome and Its Effect on Methane Emissions and Feed Efficiency"

8:25am Connor E. Owens, Virginia Polytechnic Institute and State University "Identification of Potential Biomarkers for Disease in the Microbiome of the Peripartum Reproductive Tract and Colostrum of Multiparous Holstein Cows"

8:35am Andrew S Hess, AgResearch Limited, Invermay Agricultural Centre "Considerations for Designing Imputation Studies Using Whole Genome Sequence Data: A Study in a Diverse New Zealand Sheep Population"

8:55am Jan Henkel, Institute of Genetics, Vetsuisse Faculty, University of Bern "Identification of Selection Signatures in 20 Diverse Goat Breeds"

9:10am Zaira Magdalena Estrada-Reyes, Fort Valley State University "Signatures of Selection for Resistance to Haemonchus contortus in Sheep and Goats"

9:25am Wilson Nandolo, University of Natural Resources and Life Sciences "Detection of Copy Number Variations in African Goats Using Whole Genome Sequence Data"

9:40am Haile Berihulay Gebereselas, Mekele University "Selection Signatures associated with important Traits in Ethiopian Indigenous Goat Populations"

9:55am Benjamin D. Rosen, Animal Genomics and Improvement Laboratory, USDA-ARS

"Indian Cattle SNP Discovery" 10:10am Virginie Clément, Institut de l'Elevage

"Genomic Selection in French Dairy Goats" 10:25am Break

10:55am Timothy P.L. Smith, USDA, ARS, USMARC "Individual Breed Genome Assembly to Create the Cattle Pangenome"

11:20am John Williams, Davies Research Centre, University of Adelaide "Haplotype-Resolved Cattle Genomes"

11:40am C. Titus Brown, School of Veterinary Medicine, University of California, Davis "Tools and Resources for Cattle Pangenomics"

12:05pm Danang Crysnanto, ETH Zurich "Mapping Sequencing Reads to Bovine Breed-Specific Genome Graphs"

12:25pm Terence D. Murphy, NCBI/NLM/NIH "Genomic Resources for Agricultural Animals at NCBI"

48


8:00am - 12:40pm Sugar Cane (ICSB) - ROYAL PALM SALON 1-2 Organizer: Nathalie Piperidis, SUGAR RESEARCH AUSTRALIA


8:05am Adam Healey, HudsonAlpha Institute For Biotechnology "Leveraging Multiple Sequencing Technologies to Generate a Haplotype Specific Assembly of Sugarcane R570"

8:35am Adhini Sudhindra Kumar Pazhany, Queensland Alliance for Agriculture and Food Innovation,The University of Queensland

"Sequencing the Transcriptome of R570 to Explore the Complexity of the Sugarcane Genome"

9:05am Virginie Perlo, University of Queensland "Characterisation of Metabolic Regulation of Carbon Partitioning in the Sugarcane Culm through different Stages of Development using Transcriptome and Metabolome Data"

9:35am Patrick J Mason, University of Queensland/QAAFI "Investigation of UDP-Glucose Metabolism in Sugarcane"

10:05am Intermission 10:35am Renesh Bedre, Texas A&M AgriLife Research

"Genome-Wide Alternative Splicing Landscapes Modulated by Biotrophic Sugarcane Smut Pathogen"

11:05am Katrina J.M. Hodgson-Kratky, Queensland Alliance for Agriculture and Food Innovation, University of Queensland

"Variation in Biomass Composition and Enzymatic Hydrolysis Efficiency in Sugarcane"

11:35am Nathalie Piperidis, SUGAR RESEARCH AUSTRALIA "Exploiting Erianthus Diversity to Enhance Sugarcane Cultivars"


8:00am - 12:40pm Genome annotation resources at the EBI - CALIFORNIA Organizer: Sandra Orchard, EMBL-EBI

8:00am Astrid Gall, EMBL-EBI "Accessing Plant and Animal Genomic Data with Ensembl"

9:00am Jane Loveland, EMBL-EBI "Manual Genome Annotation in Ensembl"

9:30am Baron Koylass, EMBL-EBI "The European Variation Archive: Genetic Variation Archiving and Accessioning for All Species"

10:00am Nancy George, European Bioinformatics Institute (EMBL-EBI) "Submission, Archival and Visualisation of Single-Cell Sequencing Data"

10:30am Damien Lieberherr, SIB Swiss Institute of Bioinformatics "Expert Manual Curation of Plant Protein Sequences and Plant Metabolic Pathways in Uniprotkb/Swiss-Prot"

11:00am Sandra Orchard, EMBL-EBI "Open-Access Tools for Genome Annotation"

11:30am Charles E Cook, Global Biodata Coalition "The Global Biodata Coalition: Sustaining Life Science Data Resources"

49


8:00am - 12:40pm Forest Tree - EAST 2 Organizers: Amanda de la Torre, Nothern Arizona University, Richard Cronn, USDA Forest Service and Gancho Slavov, Scion

8:00am Abdul Azeez, School of Forest Resources and Environmental Science, MTU

"The Early Bud-Break Regulon in Poplar" 8:20am Hari Chhetri, West Virginia University

"Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa Torr. & Gray"

8:40am Danielle Roodt, University of Pretoria "Evo-Devo of Secondary Growth Traits in the Seed Plant Lineage"

9:00am Andrew T. Groover, US Forest Service "Genome-Wide Scans Reveal How Gene Dosage Affects Quantitative Trait Variation in Populus"

9:20am Colin Jackson, North Carolina State University "Development of a High-Throughput Genome-Wide Genotyping Array for Tropical and Subtropical Pine Species"

9:40am Xiaohan Yang, Biosciences Division, Oak Ridge National Laboratory "Can Poplar Plants Use Mobile Protein Signals to Influence Mycorrhizal Fungi?"

10:00am Matthew Weiss, Northern Arizona University "Genomics of Quantitative Resistance to White Pine Blister Rust in Sugar Pine"

10:20am Alexander A. Myburg, University of Pretoria "Landscape Genomics, Ancestry Mapping and Nested Association Analysis in Eucalyptus grandis and its Interspecific Hybrids"

10:40am Susan McEvoyUniversity of Connecticut "Sweet Genomes: Sequencing, Assembling, and Annotating Three Maples"

11:00am Brandon Lind, University of British Columbia "Convergence of Polygenic Climate Adaptation in Conifers"

11:20am Nathaniel W. Ellis, University of Florida "The Open Chromatin Regulation of Complex Traits"

11:40am Matthew Huff, University of Tennessee "The Hardwood Genomics Project: An Online Database for Tree Genetic and Genomic Data"

12:00pm Michael Gordon, Oregon State University "RNAi-Mediated Disease Resistance against Septoria (Sphaerulina musiva) in Populus"

12:20pm Anthony Piot, Université Laval "Genetic Diversity in Populus trichocarpa for Rare Variant Genetic Associations Querying 1,000+ Genomes"

12:28pm Benjamin Wilhite, Northern Arizona University "Genome-Wide Association of Cold-Related Traits in Coastal Douglas-fir"

50


9:30am - 10:30am Coffee Break - Sponsored by: Bayer CropScience - ATLAS FOYER

10:30am - 12:40pm Abiotic Stress - GOLDEN BALLROOM Organizer: Henry T. Nguyen, University of Missouri

10:30am Wolfgang Busch, Salk Institute for Biological Studies "Harnessing Natural Variation to Identify Gene Variants and Their Molecular Mechanisms That Confer Stress Resilience"

10:50am Sean Cutler, University of California-Riverside "New Tools for Dynamically Maximizing Crop Productivity"

11:10am Benildo G. de los Reyes, Texas Tech University "Genomic and Epigenomic Bases of Transgressive Segregation: Using an Old Science to Create Novel Adaptive Phenotypes in Rice"

11:30am Jeffrey Habben, Corteva Agriscience "Overexpression of a Maize Transcription Factor in Maize Increases Grain Yield in the Field"

11:50am Roberto Tuberosa, University of Bologna, Bologna, Italy "Dissecting the Qtlome for Osmotic Adjustment and Chlorophyll Fluorescence in Field Grown Durum Wheat"

12:10pm Annapurna Chitikineni, ICRISAT ""Next Generation Sequencing Technologies for Trait Dissection and Molecular Breeding Legumes""

10:30am - 12:40pm Quinoa and close relatives - GARDEN 1 - HANDLERY HOTEL Organizers: David E Jarvis, Brigham Young University and Mark A. Tester, King Abdullah University of Science and Technology (KAUST)

10:30am Zhang Heng, Shanghai Center for Plant Stress Biology, CAS "An Improved Genome Assembly for the Highland Ecotype of Quinoa"

10:50am Brian Cox, Brigham Young University "Developing an EMS Quinoa Population"

11:10am Oscar Estrada, The University of Adelaide "Ancient Chloroplast and Nuclear Genomes Provide Insights into the Evolutionary History of Quinoa (Chenopodium quinoa Willd.)"

11:30am Joel Sharbrough, Colorado State University "Cytonuclear Evolution in Allopolyploid Quinoa"

11:50am Thomas Jordan Kerby, Brigham Young University "C. berlandieri Genome"

12:10pm Subhashini Srinivasan, Institute of Bioinformatics and Applied Biotechnology

"deciphering/Comparing Genomes of a Few Landraces of Grain Amaranths from India"

51


10:30am - 12:40pm Cacao Genomics Workshop - ROYAL PALM SALON 3-4 Organizers: Siela Maximova, The Pennsylvania State University and Mark J. Guiltinan, The Pennsylvania State University

10:30am Eric K. Wafula, The Pennsylvania State University "Prospects for Pan-Genomics in Theobroma Cacao: A High-Resolution Diversity Panel Including Tolerant and Susceptible Genotypes"

10:55am Tuomas T. Hamala, University of Minnesota "Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao"

11:20am Leidy Paola Delgadillo Duran, Colombian Corporation Agriculture Research (AGROSAVIA)

"Gene Expression Analysis of the Response of Theobroma cacao to the Infection of Phytophthora palmivora"

11:45am Jim M Dunwell, The University of Reading, UK "Molecular Genetic Approaches to Reducing Cadmium Accumulation in Cocoa"

12:10pm Osman Ariel Gutierrez, Subtropical Horticultural Research Station, USDA-Agricultural Research Service

"Establishment of Cacao Reference Genotypes from Different Genetic Groups using SNP Markers"

10:30am - 12:40pm Climate Change and ICRCGC 2 - PACIFIC SALON 2 Chair: Chittaranjan Kole, ICAR-National Institute for Plant BiotechnologyCo-Organizer: Jeffrey Ehlers, Bill and Melinda Gates Foundation

10:30am Rajeev K Varshney, ICRISAT "Translational Genomics for Developing Climate Resilient and High Yielding Chickpeas"

10:50am Graham J. King, Southern Cross Plant Science, Southern Cross University "Selecting Optimal Allelic Portfolios in Domesticated Genepools for Seasonal and Climatic Adjustment"

11:10am David Lightfoot, Southern Illinois University "Climate Change in the Midwest: What Soybeans and Corn Are Telling Us about Food Security"

11:30am Roberto Papa, Marche Polytechnic University (UNIVPM) " Food-Legume Genetic Resources for Sustainable Agriculture, Food Security and Human Health"

11:50am Kirstin Bett, University of Saskatchewan "Adapting Lentil to Changing Environments"

12:10pm Nagendra K. Singh, ICAR-National Institute for Plant Biotechnology "Genomics-Assisted Utilisation of Landraces and Wild Species for Development of Flooding and Salt-Tolerant High-Yielding Rice Cultivars"

52


10:30am - 12:40pm Non-coding RNA - PACIFIC SALON 3 Organizer: Keith Adams, University of British Columbia

10:30am Kyle R Palos, University of Arizona "Identification of Conserved and Novel Characteristics of Salt-Responsive Long Non-Coding RNAs in Brassicaceae"

10:50am Runxuan Zhang, The James Hutton Institute "Accurate Characterization of Expression and Alternative Splicing in Arabidopsis for Protein Coding and Long Non-Coding RNAs"

11:10am Naoki Hirose, RIKEN Center for Integrative Medical Sciences "Functional Annotation of Non-Coding Genomic Regions of Non-Human Primates"

11:30am Petr Fajkus, Institute of Biophysics, CAS, v.v.i. "Plant Telomerase RNA Genes: Conserved Motifs, Pol-III Transcription, and Scenario of Telomere Divergence"

11:50am Keith Adams, University of British Columbia "Origins of Long Intergenic Non-Coding RNAs in Angiosperms"

10:30am - 12:40pm Degraded DNA and Paleogenomics - GOLDEN WEST Organizer: Greger Larson, University of Oxford

10:30am Caitlin Curry, Texas A&M University "Spatiotemporal Genetic Diversity of Lions"

10:44am Bridgett vonHoldt, Princeton University "Ghost Genomics: The Persistence of Red Wolf Ancestry in Southeastern Canids"

10:58am Roselyn Ware, University of Warwick "The Identification of the First Storegga Slide Tsunami Deposits in the Southern North Sea using a Multi-Proxy Approach"

11:12am Eleni L. Petrou, School of Aquatic and Fishery Sciences, University of Washington

"Hybridization Capture of Ancient DNA Reveals Harvest of Winter-Spawning Herring Populations By Coast Salish Fisheries over 900 Years"

11:26am Ludovic Orlando, Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark

"Tracking Early Horse Domestication Stages in the 3rd and 4th Millennium BCE"

11:40am Anders Gotherstrom, Stockholm University "The Ever Changing Genepool of Scandinavia"

11:54am Melinda Yang, University of Richmond "Genetic History of Northern and Southern East Asians from 9,500-3,900 Years Ago"

12:08pm Shu-Jin Luo, Peking University "An Ancient Genomic Perspective of the Tiger Evolution"

53


10:30am - 12:40pm Solanaceae - ROYAL PALM SALON 5-6 Organizers: Shelley Jansky, USDA-ARS and Mathilde Causse, INRA

10:30am Francesco Sunseri, University Mediterranea of Reggio Calabria "Contrasting N-Use Efficient Eggplants and Differential Expressed Genes in the N-Metabolism Pathway"

10:45am Ilan Paran, Agricultrual Research Organization "Development of Introgression Lines Containing Segments from a Wild Pepper and their use for QTL Mapping"

11:00am Mathilde Causse, INRA "Meta-Analysis of GWAS Provides New Insights into Genetic Control of Tomato Flavor"

11:15am Hiroshi Ezura, Faculty of Life and Environmental Sciences, University of Tsukuba and Tsukuba Plant Innovation Research Center, University of Tsukuba

"Toward the First Commercialization of Gene Edited Tomato with Improved Nutrition"

11:30am Sally A Mackenzie, Pennsylvania State University "Accessing Epigenetic Variation within Tomato Germplasm Toward Improved Heterosis"

11:50am Dennis Halterman, USDA-ARS "Diseases of Potato: Breaking Down Resistance"

12:10pm Ek Han Tan, University of Maine "Uncovering the Mysteries of Haploid Induction in Potato"

10:30am - 12:40pm Plant Chromosome Biology - PACIFIC SALON 1 Organizer: Fangpu Han, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

10:30am Gernot Presting, University of Hawaii "A centromere’s perspective on genetic recombination"

10:50am Luca Comai, Plant Biology and Genome Center, UC Davis "Homologous and Non-Homologous Somatic Recombination Leads to Genome Remodeling during Clonal Growth of Potato"

11:10am Jonathan I Gent, University of Georgia "Motor Proteins and Tandem Repeats in Maize Meiotic Drive"

11:30am Jing Yuan, State Key Laboratory of Plant Cell and Chromosome Engineering, Institution of Genetics and Developmental Biology - Chinese Academy of Sciences

"Effects of CENH3 Modifications on its Deposition in Maize"

11:50am Yang Liu, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

"The Kinetochore Protein Knl1 Affects Spindle Assembly Checkpoint Architecture in Maize"

12:10pm Takayoshi Ishii, Arid Land Research Center, Tottori university "Functional Characterization of Cowpea Centromeres"

54


10:30am - 12:40pm Organellar Genetics - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Pal Maliga, Rutgers University

10:30am Shin-ichi Arimura, The University of Tokyo "Talen-Based Mitochondrial Genome Editing in Plants"

10:50am Meng Chen, University of California Riverside "Nucleus-to-Plastid Phytochrome Signaling in Controlling Plastid Transcription"

11:10am Martin Jonikas, Princeton University "Structure, Biogenesis and Engineering of the Eukaryotic CO2-Concentrating Organelle, the Pyrenoid"

11:30am Douglas Orr, Lancaster University "Engineering a Cyanobacterial Carbon-Concentrating Mechanism into Plants"

11:50am Maureen R. Hanson, Cornell University "Carbonic Anhydrase Mutants for Engineering of Carbon-Concentrating Mechanisms into Chloroplasts"

12:10pm Pal Maliga, Rutgers University "Target Excision by Direct Export of a Site-Specific Recombinase from Agrobacterium to Tobacco Chloroplasts"

10:30am - 12:40pm Graft Genetics and Genomics - TERRACE ROOM - HANDLERY HOTEL Organizers: Gan-Yuan Zhong, USDA-ARS and Guo-Qing Song, Michigan State University

10:30am Guo-Qing Song, Michigan State University "Scion-to-Rootstock Transfer of Endogenous Small RNAs in Sweet Cherry"

10:50am Dustin G. Wilkerson, Horticulture Section, School of Integrative Plant Science, Cornell University

"Rootstock by Scion Interaction in Polyploid Shrub Willow (Salix)"

11:10am Wei Qiang Yang, Oregon State University "Rootstocks As an Exciting Research Frontier in Blueberry Science"

11:30am Nathalie Ollat, EGFV, Bordeaux Sciences Agro - INRA - University of Bordeaux, ISVV

"Understanding Scion/Rootstock Interactions in Grapevine" 11:50am Muhammad Umair Ahsan, Cornell University

"The Long-Distance Signaling and Tree Maturity - microRNA Perspective"

12:10pm Zheng Wang, University of California Cooperative Extension "Effects of in-Row Spacing on Grafted Watermelon Productivity and Fruit Quality"

55


10:30am - 12:40pm Computational Gene Discovery - TOWN AND COUNTRY Organizer: Mark Borodovsky, Wallace H Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, GA

10:30am Terence D. Murphy, NCBI/NLM/NIH "Stand-Alone PGAP: The NCBI Open-Source Pipeline for the Annotation of Prokaryotic Genomes"

10:50am Vyacheslav Yurchenko, University of Ostrava and Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University

"Blastocrithidia, a “Non-Stop” Trypanosome" 11:10am Katharina J. Hoff, Institute for Mathematics and Computer Science,

University of Greifswald and Center for Functional Genomics of Microbes, University of Greifswald

"Fully Automated and Accurate Annotation of Eukaryotic Genomes with BRAKER2"

11:30am Evgeny M. Zdobnov, University of Geneva Medical School & Swiss Institute of Bioinformatics

"BUSCO v4 and OrthoDB v10 Perspective on Genes and Genomes"

11:50am Pavel Pevzner, Computer Science Dept., UCSD "Toward Complete Genome Assemblies"

12:10pm Pavel Pevzner, Computer Science Dept., UCSD "Toward Complete Genome Assemblies 2"

12:30pm - 1:30pm Lunch - ROYAL PALM COURT & TIKI PAVILION COURT

1:30pm - 3:40pm Palm Genetics and Genomics - EAST 2 Organizers: Norbert Billotte, CIRAD and Frederique Aberlenc-Bertossi, IRD

1:30pm Hayde C. Flandez-Galvez, University of the Philippines Los Baños "Coconut Genetics and Genomics: Updates and Opportunities Towards a Vibrant Coconut Industry"

2:00pm David Cros, CIRAD, UMR AGAP "Inbreeding Management and Optimization of Genetic Gain with Phenotypic and Genomic Selection in Oil Palm (Elaeis guineensis)"

2:30pm Hernán Mauricio Romero, Universidad Nacional de Colombia / Cenipalma "Defense Strategies of Oil Palm Against Phytophthora palmivora Causal Agent of Bud Rot"

3:00pm Hayde Flandez-Galvez, University of the Philippines Los Banos "Coconut Genetics and Genomics: Updates and Opportunities Towards a Vibrant Coconut Industry"

3:30pm Joel Malek, Weill Cornell Medicine-Qatar "A Genetic Map Linked, Long-Read Reference Genome for Date Palm and Its Application in Genotype:Phenotype Mapping"

56


1:30pm - 3:40pm Functional Genomics - PACIFIC SALON 1 Organizer: David Lightfoot, Southern Illinois University

1:30pm Naoufal Lakhssassi, Southern Illinois University at Carbondale "Molecular Cross Talk between Resistant and Defense Genes Promote Resistance to Heterodera Glycines."

1:42pm Anjana Raina Vatsan, NCBI/NLM/NIH "NCBI Refseq Resources for Plant Genomics"

1:54pm Oussama Badad, University Mohamed the Fifth, Rabat, Morocco "olive Epigenomics "

1:30pm - 3:40pm Climate Change and ICRCGC 3 - PACIFIC SALON 2 Chair: Chittaranjan Kole, ICAR-National Institute for Plant BiotechnologyCo-Organizer: Jeffrey Ehlers, Bill and Melinda Gates Foundation

1:30pm Etienne Paux, INRA GDEC "Tapping Wheat Diversity to Cope with Climate Change"

1:50pm Michael Abberton, International Institute of Tropical Agriculture (IITA) "Studies on Genetic Diversity and Key Traits in Underutilised Legumes to Address Climate Change in West Africa"

2:10pm Toshihiko Yamada, Field Science Center for Northern Biosphere, Hokkaido University and Graduate School of Global Food resources, Hokkaido University

"Saccharum × Miscanthus Intergeneric Hybrids (Miscanes) Show Low Temperature Stress Tolerance"

2:30pm Niranjan Baisakh, School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center

"Development of Water Use Efficient Rice Varieties Suitable for Alternative Irrigation Systems"

2:50pm Antonio Costa De Oliveira, Universidade Federal de Pelotas "Climate-Ready Rice for South America: The Search for Stress Response Genes"

3:10pm Cory D. Hirsch, University of Minnesota "Detecting and Classifying Abiotic and Biotic Stress Response Using Phenomic Tools"

57


1:30pm - 3:40pm Plant Cytogenetics - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: James Higgins, University of Leicester

1:30pm Kim Osman, University of Birmingham "SPO11-1 Mutants Provide Insights into Recombination Progression and Crossover Formation in Hexaploid Bread Wheat"

1:50pm Daisy Ogle, University of Leicester "Investigating the Role of the Meiotic Chromosome Axes in Mediating Crossover Designation in Wheat"

2:10pm Pierre Sourdille, INRA UMR 1095 GDEC "Controlling Homoeologous Pairing in Bread Wheat: A Step Towards Identification of Ph2"

2:30pm Adel Sepsi, Centre for Agricultural Research, Agricultural Institute and Budapest University of Technology and Economics, Faculty of Chemical Technology and Biotechnology

"Centromere Behaviour during Synaptonemal Complex Formation in the Female and Male Meiosis of Wheat"

2:50pm Bikram S. Gill, Kansas State University "Fishing eccDNA Elements that Defy Chromosome Control of Mitosis and Meiosis and Drive Rapid Adaptive Evolution"

3:10pm James A. Birchler, University of Missouri "Oligopaints for the Maize Chromosome Set and Some Applications"

1:30pm - 3:40pm Grape Genome Initiative - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Grant R. Cramer, University of Nevada, Reno

1:30pm Dario Cantu, University of California Davis "The Wild Side of Grape Genomics"

1:50pm Michael J Considine, University of Western Australia "Role of microRNAs in Mediating the Effect of Leafroll Virus on Fruit Ripening in Table Grapes"

2:10pm Yongfeng Zhou, University of California Irvine "Population Genomics of Structural Variants in Grapevine Domestication"

2:30pm Cheng Zou, Cornell University "Molecular Characterization of the Sex Loci in Wild and Domesticated Grapes"

2:50pm Claudio Meneses, Universidad Andrés Bello, Centro de Biotecnología Vegetal, Santiago

"Elucidating the Clonal Diversity of Vitis vinifera cv. Cabernet Sauvignon"

3:10pm Laurent G. Deluc, Dept. of Horticulture, Oregon State University "Influence of Seed Development of the Transcriptional Program of Grape Berries during the Ripening Phase"

58


1:30pm - 3:40pm Plant Reproductive Genomics - PACIFIC SALON 3 Organizer: Alex Harkess, Donald Danforth Plant Science Center

1:50pm Rebecca Povilus, Whitehead Institute "Evolution of Parental Genome Dosage Sensitivity during Seed Development – a New Perspective from Water Lilies"

2:10pm Haoran Xue, University of Toronto "The Genetic Architecture of Tristyly"

2:30pm Chong Teng, Donald Danforth Plant Science Center "Dicer-like 5 Deficiency Confers Temperature-Sensitive Male Sterility in Maize"

2:50pm Daniel Jones, University of North Carolina "CLE-Family Peptide Signaling Regulates Diverse Floral Morphologies across Plant Taxa"

3:10pm Stuart McDaniel, University of Florida "Genomic Evidence for Sexual Selection in a Moss"

1:30pm - 3:40pm JBrowse, JBrowse 2 and Apollo - CALIFORNIA Organizer: Scott Cain, Ontario Institute for Cancer Research Co-Organizer: Robert Buels, Bioengineering

1:30pm Colin Diesh, University of California Berkeley, Bioengineering "Comparing Genomes and Visualizing Synteny with JBrowse 2"

1:55pm Nathan A Dunn, Lawrence Berkeley National Laboratory "Apollo Provides Collaborative Genome Annotation Editing with the Power of JBrowse"

2:15pm Scott Cain, Ontario Institute for Cancer Research "JBrowse: A Hands on Tutorial"

1:30pm - 3:40pm Transposable Elements - GOLDEN BALLROOM Organizers: Clémentine Vitte, GQE - Le Moulon and Meixia Zhao, Miami University

1:30pm Wei Guo, Purdue University "Rapid, Heat-Induced Transgenerational Reactivation of a Silenced Transposable Element in Maize"

1:50pm Cristina Vieira, UMR 5558, LBBE, Université Lyon 1, University Lyon "Transposable Element Dynamics in Sitophilus oryzae"

2:10pm Carles Borredá, Centro de Genomica, Instituto Valenciano de Investigaciones, IVIA "Reprogramming of Citrus Retrotransposons during their Early Speciation"

2:30pm Sarah N. Anderson, Iowa State University "Transposable Element Contributions to Dynamic Maize Genomes and Transcriptomes"

2:50pm Shujun Ou, Iowa State University "Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline"

3:10pm R. Keith Slotkin, Donald Danforth Plant Science Center "Long-Read Transcriptome Annotation Enables High Resolution Transposable Element Bioinformatics"

59


1:30pm - 3:40pm Statistical Genomics - GOLDEN WEST Organizers: Zhenyu Jia, University of California and Shizhong Xu, Dept. of Botany & Plant Sciences, University of California

1:30pm Peter L. Morrell, Department of Agronomy and Plant Genetics, University of Minnesota

"The Limits of Recombination in Cultivated Barley" 1:50pm Hairong Wei, Michigan Technological University

"A Statistics, Machine Learning and Optimization Combined Approach Toward Identifying Hub Genes from Multi-Source Gene Expression Data"

2:10pm Patrick X. Zhao, Noble Research Institute "Plant Genotype-Phenotype (G2P) Association Discovery via Integrative Genome-Scale Biological Network & Genome-Wide Association Analysis"

2:30pm Meiyue Wang, University of California, Riverside "Deshrinking Ridge Regression for Linkage Analyses and Association Studies"

2:50pm Shizhong Xu, Dept. of Botany & Plant Sciences, University of California "A Tutorial on the Beavis Effect for QTL Mapping and Genome-Wide Association Studies"

1:30pm - 3:40pm Polyploidy - ROYAL PALM SALON 1-2 Organizer: Julie Ferreira-De-Carvalho, INRA IGEPPCo-Organizer: Alison Dawn Scott, Department of Plant Sciences, University of California, Davis

1:30pm Tom Ruttink, ILVO Plant Sciences "Novel Approaches in Phylogenomics Reveal Extensive Interspecific Hybridization and Polyploidization in the Genus Phytophthora"

1:50pm Julie Ferreira-De-Carvalho, INRA IGEPP "Genome Stabilization after Allopolyploidization in Nascent Brassica napus"

2:10pm Yuannian Jiao, Institute of Botany, The Chinese Academy of Sciences "Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms"

2:30pm Christina L. Richards, University of South Florida "Ecological Epigenetics in Polyploid Spartina"

2:50pm Patrick Edger, Department of Horticulture, Michigan State University "Origin and Evolution of the Octoploid Strawberry Genome"

3:10pm Sarah Carey, University of Florida "Implications of Whole-Genome Duplications on Dioecy and Sex Chromosomes in Mosses"

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1:30pm - 3:40pm The National Plant Genome Initiative: Catalyzing Transdisciplinary Frontiers in Genomics for Breakthroughs, Innovation, and Community Development - SAN DIEGO Organizers: Catherine Ronning, U.S. Dept. of Energy, Diane Jofuku Okamuro, National Science Foundation/BIO/Division of Integrative Organismal Systems and Jack K. Okamuro, USDA ARS

1:30pm Welcome and Introductory Remarks

1:40pm Sharlene Weatherwax, Office of Biological and Environmental Research / Department of Energy

"20 Years of Interagency Coordination and Cooperation on Plant Genomics"

1:50pm Donal T. Manahan, National Science Foundation "Frontiers in Genomics"

2:00pm Daniel Jacobson, Oak Ridge National Laboratory 2:10pm Patrick S. Schnable, Department of Agronomy, Iowa State University

"New Technologies for Predictive Plant Phenomics" 2:20pm Wayne A. Parrott, University of Georgia

"Challenges and Opportunities in Genomics and Precision Breeding"

2:30pm Julia Bailey-Serres, UC RIverside 2:40pm Christopher Dardick, USDA-ARS Appalachian Fruit Research Station

"Redesigning Fruit Crops for the Future: Understanding Genome to Phenome Plasticity."

2:50pm Robert Bertram, US Agency for International Development 3:00pm Questions and Discussion


1:30pm - 3:40pm Genomics of Non-Classical Model Animals - ROYAL PALM SALON 3-4 Organizer: Aaron Avivi, Institute of Evolution , University of Haifa,

1:30pm Michael Hiller, Max Planck Institute of Molecular Cell Biology and Genetics "The Importance of cis-Regulatory Divergence for Eye Degeneration in Subterranean Mammals"

2:00pm Richard E. Green, Dovetail Genomics "Detection and Interpretation of Archaic Ancestry in Extant Humans"

2:30pm Claudio V. Mello, Oregon Health and Science University "What Comparative Studies of Parrot Genomes Can Teach Us about Longevity, Large Brains and Cognition"

3:00pm Bridgett vonHoldt, Princeton University "Everyone Is Your Friend! the Molecular Architecture of Hypersocial Canines"

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1:30pm - 3:40pm Camelids - EAST 1 Organizers: Kylie Munyard, Curtin University, School of Pharmacy & Biomedical Sciences, CHIRI Bioscience and Felipe F Avila, UC Davis


1:35pm Benjamin T. Gillard, University of Bristol "The Camelome: Combining and Comparing the Transcriptome, Proteome, and Phosphoproteome in the Dehydrated Camel Kidney"

1:50pm Panjiao Lin, University of Bristol "Transcriptome of Supraoptic Nucleus in Dehydrated Dromedary Camel"

2:00pm Sara Lado, Veterinary Medicine University, Vienna "Applying Shotgun Sequencing to Detect Early Dromedary-Bactrian Camel Hybrids"

2:15pm Gustavo A. Gutierrez Reynoso, Universidad Nacional Agraria La Molina "Development of a SNP Microarray for Alpacas"

2:30pm Brian W. Davis, Texas A&M "Molecular Studies of the Minute Chromosome Syndrome in Alpacas"

2:45pm Matthew Jevit, Texas A&M University "A 2.1 Mb Assembly of the Alpaca Y Chromosome"

3:00pm Panel Discussion


1:30pm - 6:20pm US National Animal Genome Research Program (NRSP8) - ROYAL PALM SALON 5-6 Organizer: Alison Van Eenennaam, University of California Co-Organizer: Brenda Murdoch, University of Idaho


1:35pm Finn Grey, The Roslin Institute "High Throughput Phenotypic Screening in Livestock Species"

2:15pm Elinor K. Karlsson, UMass Med School & Broad Institute "The 200 Mammals Project: Evolutionary Conservation at Single Base Resolution"

2:55pm Harly J. Durbin, Division of Animal Sciences, University of Missouri "Leveraging Genotype-by-Environment Interactions across Discrete Climate Regions to Select More Sustainable Beef Cattle"

3:07pm Alexandra J McCarty, University of Maryland Center for Environmental Science

"QTL and Joint-Association Mapping Reveal Loci Associated with Acute Low Salinity Tolerance in the Eastern Oyster (Crassostrea virginica)"

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3:19pm Sian Ann Durward-Akhurst, University of Minnesota "The Frequency of Loss of Function Alleles in the Equine Population"

3:31pm Christian J Posbergh, Cornell University "Chasing Colors: Identifying the Genetic Variants Responsible to Coat Color Variation in Sheep"

3:43pm Break

4:00pm Paula R. Chen, University of Missouri "Anthrax Toxin Receptor 1 Knockout Pigs are protected from Senecavirus A Infection"

4:12pm Yulu Chen, Iowa State University "Protein Levels in Blood of Young Healthy Pigs as Indicators of Disease Resilience"

4:24pm Nnamdi Simon Ekesi, University of Arkansas, Cell and Molecular Biology program

"Genomic, and Virulence Comparisons of Different Bacterial Isolates from BCO Lesions in Broilers"

4:36pm Beth M Lett, University of Wisconsin Madison "Analysis of Copy Number Variation in Jersey Dairy Cattle using Whole Genome Sequencing"

4:48pm Discussion about future plans for NRSP8 activities

5:25pm USDA NIFA update, Dr. Parag Chitnis

5:45pm NRSP-8 Business Meeting


3:00pm - 4:00pm Coffee Break - Sponsored by: Bayer CropScience - GRAND EXHIBIT HALL

3:00pm - 8:45pm Exhibits Open - GRAND EXHIBIT HALL

4:00pm - 6:10pm Annotation Jamboree - TERRACE ROOM - HANDLERY HOTEL Organizer: Monica C. Munoz-Torres,

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4:00pm - 6:10pm Sequencing Complex Genomes - PACIFIC SALON 1 Organizer: Robert Henry, University of Queensland QAAFI

4:00pm Olivier Panaud, University of Perpignan "The Oryza australensis Genome: A Complex Rice Genome"

4:20pm Harmeet Singh Chawla, Justus Liebig University "Widespread Gene-Scale Structural Variants Revealed by Long-Range Sequencing"

4:40pm Victor A. Albert, University at Buffalo "Sequencing and Assembling Highly Heterozygous and/or Repeat-Rich Plant Genomes Using Oxford Nanopore Technology"

5:00pm Adhini Sudhindra Kumar Pazhany, Queensland Alliance for Agriculture and Food Innovation,The University of Queensland

"The Importance of Sequencing Depth for a Complex Transcriptome"

5:20pm Sudharsan Padmarasu, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK)

"The Landscape of Large Chromosomal Inversions in Barley"

5:40pm Valentine Murigneux, Institute for Molecular Biosciences - The University of Queensland

"Comparison of Long Read Methods for Sequencing and Assembly of a Plant Genome"

4:00pm - 6:10pm Fungal Genomics - ROYAL PALM SALON 3-4 Organizer: Stephen B. Goodwin, USDA ARS

4:00pm Roger P Wise, Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service

"Next-Generation Screening for Pathogen-Effector, Host-Target Interactions"

4:20pm Richard D Hayes, US Department of Energy Joint Genome Institute "Enabling High-Throughput Pan-Genome Analysis on Mycocosm"

4:40pm Jonathan K. Richards, Louisiana State University "Evidence of Local Adaptation and Regional Effector Repertoires in Parastagonospora nodorum"

5:00pm Michael F. Seidl, Utrecht University "Linking Genome Organization to Function and Evolution - the Impact of Transposons on a Plant Pathogenic Fungus"

5:20pm Kathryn Bushley, University of Minnesota "Chromosomal Rearrangements Drive the Evolution of Secondary Metabolic Gene Clusters within the Entomopathogenic Fungus Tolypocladium Inflatum"

5:40pm Emile Gluck-Thaler, University of Pittsburgh "Evolutionary Pan-Genomics of the Charcoal Rot Fungus, Macrophomina Phaseolina"

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4:00pm - 6:10pm Tripal Database Network and Initiatives - CALIFORNIA Organizer: Jill L. Wegrzyn, University of ConnecticutCo-organizers: Lacey-Anne Sanderson, Dept of Plant Sciences/University of Saskatchewan and Christopher Childers, USDA/Agricultural Resarch Service/National Agricultural Library

4:00pm Introductory Remarks 4:03pm Stephen P. Ficklin, Dept of Horticulture, Washington State University

"Tripal, an Open-Source Toolkit for Construction of Online, Searchable, Extendable and FAIR Biological Databases."

4:20pm Sook Jung, Washington State University "Tripal MegaSearch: An Interactive and Customizable Tool for Query and Download of Big Data from Tripal Databases"

4:37pm Sean Buehler, University of Connecticut "Tripal Eutils and Tripal HQ – New Modules to Enable FAIR Metadata"

4:54pm Carolyn T. Caron, University of Saskatchewan "Knowpulse: Building a Tripal Ecosystem for Pulse Crop Research and How It Can Help You"

5:11pm Margaret Elizabeth Staton, University of Tennessee Institute of Agriculture "rnaseq Data in Tripal - Two Steps Forward, One Step Back"

5:28pm Nic Herndon, East Carolina University "Tapping into the Tripal Galaxy: Association Mapping Studies on Forest Trees with CartograTree"

5:45pm Blake T. Inderski, Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS

"The United States Swine Pathogen Database: Integrating Diagnostic Sequence Data of Emerging Pathogens of Swine"


4:00pm - 6:10pm Cucurbit Genomics - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Amnon Levi, USDA, ARS, U.S. Vegetable Laboratory and Yaakov (Kobi) Tadmor, Newe Yaar Research Center, AROChair: Jordi Garcia-Mas, IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBCo-Organizer: Patrick Wechter, USDA-ARS

4:00pm Jordi Garcia-Mas, Center for Research in Agricultural Genomics "Resequencing of 1,175 Melon Accessions Reveals Multiple Domestication Events and Loci Influencing Agronomic Traits"

4:18pm Antonio J. Monforte, IBMCP. CSIC-UPV "Cloning of a Melon Fruit Shape QTL Contributes to Identify a Common Mechanism that underlies Organ Morphological Diversity in Plants"

4:36pm Yiqun Weng, USDA ARS/ Universtiy of Wisconsin "Fruit Size and Shape in Cucurbits: A Comparative Perspective"

4:54pm Rebecca Grumet, Department of Horticulture, Michigan State University "QTL and Transcrptomic Analyses Implicate Cuticule Transcription Factor Shine as a Source of Natural Variation for Epidermal Traits in Cucumber"

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5:12pm Shan Wu, Boyce Thompson Institute, Cornell University

"De novo Genome Assembly of Sweet Watermelon Relatives and a Pan-Genome of Citrullus Species"

5:30pm Sandra E. Branham, Clemson University "Genomics-Assisted Breeding of Fusarium Wilt Resistance in Watermelon"

4:00pm - 6:10pm Ornamentals - PACIFIC SALON 3 Organizer: Mohammed Bendahmane, Ecole Normale Supérieure

4:00pm Andrew P. Sherwood, University of Minnesota "Genetic Structure in Hydrangea quercifolia Bart. throughout its Natural Range"

4:20pm Neil O. Anderson, University of Minnesota, Department of Horticultural Science "DArTseq LD Differentiates Species and Populations of Historic and Extant Wild Chrysanthemum arcticum, C.a. subsp. arcticum, and C.a. subsp. polaré"

4:40pm Ryan M. Warner, Michigan State University "Dissecting Genetic Diversity and Genomic Background of Petunia Cultivars with Contrasting Growth Habits using Transcriptome-Derived SNPs"

5:00pm Steven H. Strauss, Oregon State University "Sterile Eucalyptus for Ornamental and Forestry Uses through CRISPR Disruption of Leafy Function"

4:00pm - 6:10pm International Cotton Genome Initiative (ICGI) - EAST 1 Organizer: B. Todd Campbell, USDA-ARS

4:00pm Welcoming Remarks 4:02pm Z. Jeffrey Chen, The University of Texas at Austin

"Upland Cotton Genome Sequence" 4:22pm Xueying Guan, Zhejiang University

"Neofunctionalization of lncRNAs Originated in Cotton Interspecific Hybridization and Polyploidization"

4:42pm Avinash Sreedasyam, HudsonAlpha Institute for Biotechnology "Genome-Wide Variations Provide Insight into the Genetic Architecture of Cotton Elite Lines"

5:02pm Jeevan Adhikari, The University of Georgia "Development and Characterization of a Reciprocal Set of Interspecific Near Isogenic Lines in Cotton"

5:22pm Gregory Thyssen, Cotton Fiber Bioscience & Cotton Chemistry and Utilization Units "MAGIC Population from 11 Upland Cotton Varieties Reveals Genetic Loci Affecting Agronomic and Fiber Phenotypes Including Flame Retardancy of Textiles"

5:42pm Shuangxia Jin, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University

"New Variants of CRISPR RNA-Guided Genome Editing System in Cotton"

6:02pm Presentation of ICGI 2020 Conference Israel

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4:00pm - 6:10pm Genomics of Plant Development - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Khalid Meksem, Southern Illinois University at Carbondale

4:25pm Mary Wildermuth, Dept of Plant and Microbial Biology "Whole Genome Duplication by Demand: Biotroph-Induced Localized Host Endoreduplication"

4:50pm Z. Jeffrey Chen, The University of Texas at Austin "Rice Circadian Clock Regulates Tillering and Panicle Development through Sugar Response and Strigoractone Signaling"

5:15pm Paul Vollrath, Justus Liebig University "Structural Genome Variations Associate with Juvenile Development and Flowering Time Modulation in Elite Winter Canola (Brassica napus)"

5:40pm Martha Ibore, Department of Agronomy "Transcriptomic Response of Sorghum Bicolor to a Brassinosteroid Inhibitor: Gene Targets for Developing a “Smart Canopy”"

4:00pm - 6:10pm Domestication Genomics - PACIFIC SALON 2 Organizers: Emily Warschefsky, Florida International University and Emily Josephs, Michigan State University

4:00pm Esther van der Knaap, Department of Horticulture, Institute of Plant Breeding, Genetics and Genomics, University of Georgia

"Exploitation of Semi-Domesticated Tomato Accessions for Crop Improvement Traits"

4:20pm Jacob B Landis, University of California Riverside and Cornell University "Genomic Diversity of Saamaka Rice Varieties in Suriname"

4:40pm Paul D Blischak, University of Arizona "Assessing the Impact of Inbreeding on Demographic Estimates of Domestication"

5:00pm Elaine A. Ostrander, National Human Genome Research Institute, National Institutes of Health

"Genetics of Breed Formation and Associated Traits in the Domestic Dog"

5:20pm Daniel Koenig, University of California-Riverside "The Genetic Architecture of Adaptation in the Long Term Barley Composite Cross Experiments"

5:40pm Paul Gepts, University of California "Counter-Domestication: Maintenance of Atavisms Under Domestication"

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4:00pm - 6:10pm Plant Epigenetics and Epigenomics - GOLDEN BALLROOM Organizer: Rob Martienssen, HHMI-Cold Spring Harbor Laboratory

4:00pm Craig Pikaard, Howard Hughes Medical Institute, Indiana University "Biogenesis of Short-Interfering RNAs Guiding RNA-Directed DNA Methylation: Rules of Substrate Recognition by DICER-LIKE3"

4:30pm Thomas Gingeras, Cold Spring Harbor Laboratory "Maize and Maizecode"

5:00pm Ian R Henderson, University of Cambridge "The Centromeres of Arabidopsis - Genetic and Epigenetic Features"

5:30pm Xuemei Chen, University of California "The RNA NAD+ Cap"

4:00pm - 6:10pm Big Data: Manage your data before your data kills you - ROYAL PALM SALON 1-2 Organizers: Rex Nelson, USDA-ARS-CICGRU and Jamie A. O'Rourke, USDA-ARS-MWA-CICGRU

4:00pm Megan O'Donnell, Iowa State University "Librarians are here to Help but We Can't Read Minds"

4:20pm Jill Wait, BioMarin Pharmaceutical Inc. "Managing Multi‐Site Academic Studies: The Trials and Tribulations and the Techniques to Enable Studies and Investigators to be Successful"

4:40pm Bridget McFarland, University of Wisconsin-Madison "Data Resources and Implementation for the Genomes to Fields (G2F) Initiative"

5:00pm Katy Martin Rainey, Purdue University "Managing UAS Imagery for Developmentally-Driven Decision Making"

5:20pm Susan Vanderplas, University of Nebraska Lincoln "Big Data, Big Experiments, and Big Problems: Strategies for Experimental Design, Execution, and Analysis"

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4:00pm - 6:10pm Sex Chromosomes and sex determination - EAST 2 Organizer: Ray Ming, University of Illinois at Urbana-Champaign

4:00pm Diego Cortez, Center for Genome Sciences, UNAM "Convergent Origination of Dosage Compensation Mechanism"

4:20pm Michael F Scott, UCL "Haploid Selection Drives Transitions between Sex Determination Systems"

4:40pm Wen-Juan Ma, Amherst College "Differential Gene Expression between Fungal Mating Types is associated with Sequence Degeneration"

5:00pm Li'ang Yu, University of Illinois at Urbana Champaign "Identification of Sex Determination Region of the Y Chromosome in Spinach"

5:20pm Niels A. Müller, Thünen Institute of Forest Genetics "An Ancient Master Regulator Determines Sex in Poplars"

5:40pm Brennan Hyden, Cornell University "Elucidating Genetic Pathways of Sex Determination and Dimorphism in Salix purpurea"

4:00pm - 6:10pm New breeding technologies: Prospects and regulatory hurdles - GARDEN 1 - HANDLERY HOTEL Organizer: Thorben Sprink, Julius Kühn InstitutChair: Frank Hartung, Julius Kühn-InstitutCo-Organizer: Janina Metje, Julius Kuehn-Institut

4:00pm Janina Metje, Julius Kuehn-Institut "Introduction to the Topic"

4:25pm Thorben Sprink, Julius Kühn Institut "Genome Editing; A Global Perspective"

4:50pm Werner Schenkel, Federal Office of Consumer Protection and Food Safety Germany

"Novel Developments in Gene Drive Technologie and Regulation"

5:15pm Makiko Matsuo, the University of Tokyo "New Biotechnology and Governance Issues - Regulatory Clarification of Gene-Edited Products in Japan"

5:40pm Trine Hvoslef-Eide, Norwegian University of Life Sciences "Genome Editing -Current Situation in Norway-"

6:15pm - 7:00pm Plenary Lecture: Jack Bobo - TOWN & COUNTRY BALLROOM Chair: Max F. Rothschild, Iowa State University

6:15pm Jack Bobo, Futurity Food "Can Agriculture Save the Planet Before It Destroys It"

7:15pm - 8:45pm Opening Reception - GRAND EXHIBIT HALL

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Monday - January 13, 2020







8:00am - 8:45am Plenary Session: Sarah Davidson Evanega - TOWN & COUNTRY BALLROOM Chair: Alison Van Eenennaam, University of California

8:00am Sarah Davidson Evanega, Cornell University "Embracing Effective Science Advocacy"

8:45am - 9:30am Plenary Lecture: Eske Willerslev - TOWN & COUNTRY BALLROOM Chair: Alison Van Eenennaam, University of California

8:45am Eske Willerslev, University of Copenhagen "What We Can Learn from Ancient Genomics"

9:30am - 11:30am Coffee Break - GRAND EXHIBIT HALL

9:30am - 5:00pm Exhibits Open - GRAND EXHIBIT HALL

12:00pm - 12:50pm Lunch - EXHIBIT HALL, LION COURT & ROYAL PALM COURT

12:50pm - 3:00pm LGC Group - Innovative approaches to advance agrigenomics. Panel discussion to follow speaker presentations - PACIFIC SALON 2 Organizer: Jill Walerius, LGC, Biosearch Technologies

12:50pm Jason Hein, LGC, Biosearch Technologies "Introduction"

12:55pm Marine Herlin, Aquicultura Balear, S.A.U. "Development and Application of Tailor-Made Genomic Tools in a Commercial Atlantic Salmon Breeding Program"

1:25pm Andrew Brueggeman, Bayer - Crop Science "Coprimer Assays for Multiplex PCR"

1:55pm Marcus Wills, LGC, Biosearch Technologies "Breeding Tools from NGS to PCR – a Look at the Trade-Offs"

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12:50pm - 3:00pm PacBio - Accessing All Parts of Plant and Animal Ecosystems – One SMRT Cell at a Time - GOLDEN WEST Organizers: Jonas Korlach, Pacific Biosciences and Donal Murphy, PacBio

12:50pm Mark Blaxter, Wellcome Sanger Institute "Endless Forms: Genomes from the Darwin Tree of Life Project"

1:10pm Jana U'Ren, University of Arizona "Phylogenetic Insights into the Endophyte Symbiosis Using Pacbio Ribosomal DNA Sequencing"

1:30pm Bart Nijland, Genetwister Technologies B.V. "The Impact of Highly Accurate Pacbio Sequence Data on the Assembly of a Tetraploid Rose"

1:50pm Zev Kronenberg, PacBio "Characterizing Genetic Differences between Great Apes Using Iso-Seq Data"

2:10pm Michelle Vierra, PacBio "Pacbio Update on Products and Hifi Applications"

12:50pm - 3:00pm Genomics of Tissue Regeneration in Plants and Animals - EAST 2 Organizer: Moshe Reuveni, ARO, Volcani Center

12:50pm Mark Sussman, SDSU Heart Institute, "Myocardial Regeneration: Uncommon Sense for Common Problems"

1:20pm Nathan M. Springer, University of Minnesota "Documenting the Changes in DNA Methylation following Tissue Culture in Maize"

1:50pm Ricardo M. Zayas, San Diego State University "Flat Worms Big on Regeneration"

2:20pm Moshe Reuveni, ARO, Volcani Center "Signaling for Regeneration"

12:50pm - 3:00pm Kyazma®: JoinMap® and MapQTL® Demonstration - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Johan Van Ooijen, Kyazma B.V.


12:55pm JoinMap ® 5 – General Demonstration

1:45pm Break

1:50pm MapQTL ® 6 – General Demonstration

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12:50pm - 3:00pm Thermo Fisher Scientific – “Innovating and Sustaining Global Agriculture with Genomics and Breeding” - PACIFIC SALON 3 Organizer: Delaney Wermuth, Thermo Fisher Scientific

12:50pm Ravi Ramadhar, Thermo Fisher "Driving Agrigenomics Forward"

1:20pm Patrick Cumbie, PhD, Manager, Pine Development ArborGen, Inc. "Applying genomic tools to loblolly pine: Adding value to our germplasm and our products"

2:10pm Dr. Andrew Cromie, Technical Director, Int’l Cattle Breeding Federation (ICBF) "Utilizing genomics to address global challenges facing our agrifood industry"

12:50pm - 3:00pm UgenTec - "Cut Your Genotyping Project Time in Half: Intelligent Software for Automated Genotype Calling & Classification" - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Steven Van Vooren, UgenTec

12:50pm Michiel Reessink, UgenTec, Inc. "State of the Art: Artificial Intelligence for Advanced Genotyping Data Analysis"

1:10pm Wouter Uten, UgenTec, Inc. "Customer Success Story for Diploid Vegetable Seed Genotyping Data Analysis at Scale"

1:30pm Herlien Declerck, UgenTec, Inc. "Software Demonstration: Accelerated Cluster Calling & Result Review with Fastfinder Genotyper"

12:50pm - 3:00pm GeneSeek, A Neogen Company - "GeneSeek Genomic Technologies and Innovation" - ROYAL PALM SALON 3-4 Organizer: Jeremy Walker, GeneSeek

12:50pm Jeremy Walker, Neogen/GeneSeek "Geneseek Genomic Tools Updates"

1:05pm Katherine M. Lytle, Wisdom Health "Decoding Man’s Best Friend: Lessons Learned By Testing 1.5 Million Dogs"

1:30pm Sergio Vela, Akvaforsk Genetics "Development of Genomic Selection Tools in Tilapia and Shrimp"

1:55pm Christopher M. Seabury, Texas A&M University "Genome-Wide Association and Genotype By Environment Interactions for Growth Traits in U.S. Gelbvieh Cattle"

2:20pm Rich Tait Jr., Neogen GeneSeek "Retained Genomic Heterosis: Methods and Effects on Performance in Beef Cattle"

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12:50pm - 3:00pm NCBI Genome Resources - PACIFIC SALON 1 Organizers: Terence D. Murphy, NCBI/NLM/NIH and Francoise Thibaud-Nissen, National Center for Biotechnology Information (NCBI)

12:50pm Ilene Mizrachi, National Center for Biotechnology Information (NCBI/NLM/NIH)

"NCBI Wants Your Sequence Data! How Do I Get It There?" 1:15pm Jinna C. Hoffman, NCBI/NLM/NIH

"Annotation of Eukaryote Genomes at NCBI" 1:35pm Nuala A. O'Leary, NCBI/NLM/NIH

"Accessing Homologous Gene Datasets at NCBI" 1:55pm Kathi Canese, NCBI/NLM/NIH

"The New Pubmed Is Here!" 2:15pm Ben Busby, NCBI/NLM/NIH

"Taxonomy Lookup; Data Retrieval: How to Find and Stream Genomic Data in the Cloud!"

12:50pm - 3:00pm International Sheep Genomics Consortium - EAST 1 Organizers: Shannon Clarke, AgResearch, Invermay Agricultural Centre and Noelle Cockett, Utah State University

12:50pm Shannon M. Clarke, AgResearch Ltd. Invermay Agricultural Centre "International Sheep Genomics Consortium Update"

1:00pm Brenda M. Murdoch, University of Idaho "An Update of the Ovine Faang Project"

1:15pm Shavahn C. Loux, University of Kentucky "High-Quality Sheep Genome Assemblies for White Dorper and Romanov Breeds By F1 Trio Binning"

1:30pm Elizabeth Ross, Queensland Alliance For Agriculture and Food Innovation - University of Queensland

"Genomic Predictions for Enteric Methane Production are improved by Metabolome and Microbiome Data in Sheep (Ovis aries)"

1:45pm Luiz Brito, Purdue University "Across-Population Genomic Predictions in Composite Sheep Populations with Similar Development History"

2:00pm Hasan Khatib, University of Wisconsin Madison "The Effects of Paternal Nutrition on Traits of the Next Generation in Sheep"

2:15pm Badr Benjelloun, LECA, UGA-CNRS-USMB and INRA-Morocco "Whole Genome Neutral and Adaptive Diversity in Traditional Sheep Breeds: Case of Morocco"

2:30pm Christian J Posbergh, Cornell University "Chasing Colors: Identifying the Genetic Variants Responsible for Coat Color Variation in Sheep"

2:45pm Sarah Helen Dias dos Santos, University of Alberta "Whole Genome Sequence Data and Analysis from Wild Thinhorn Sheep"

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12:50pm - 3:00pm KeyGene - Translating Genomics Innovations into Agriculture. Biotic Interactions with Crops & Beyond - SAN DIEGO Organizer: Jimmy Zumba, KeyGene

12:50pm Walter Nelson, KeyGene USA "Translating Breakthroughs in Crop Innovation"

1:10pm Marcel Prins, KeyGene "Trait Development for Aboveground Pests and Pathogens: Novel Sources of Resistance Against Whitefly-Transmitted Geminiviruses"

1:30pm Kanwarpal S. Dhugga, INTERNATIONAL CENTER FOR MAIZE AND WHEAT IMPROVEMENT

"Genetic and Molecular Approaches to Improve Resistance Against Maize Lethal Necrosis in Africa"

1:50pm Jay Scott Angle, National Institute of Food and Agriculture "Recent and Future Changes at the National Institute of Food and Agriculture (NIFA)"

2:10pm Amit Vas, Joyn Bio "Engineering Better Microbes for Agriculture"

2:30pm Irina Calic, KeyGene "Integrated Technology Platforms Providing Innovative Solutions to Soil-Borne Pathogens"

12:50pm - 3:00pm MatMaCorp - "Emerging Customizable Technology for SNP and Target Detection" - ROYAL PALM SALON 5-6 Organizer: Seth Lewin, MatMaCorp

12:50pm Seth Lewin, MatMaCorp "Welcome and Introductions"

12:55pm Abe Oommen, MatMaCorp "Core Technologies at MatMaCorp"

1:05pm Michael Carrié, MatMaCorp "An Enhanced Algorithm for Real-Time Genotyping"

1:15pm Cindy Orser, DigiPath Labs "A Simple Assay to Genetically Distinguish Hemp from THC Cannabis"

1:35pm Arryn Craney, Weill Cornell Medicine "Molecular Detection of Antibiotic Resistance in Mycobacterium abscessus"

1:55pm Michael P. Heaton, USDA, ARS, U.S. Meat Animal Research Center (USMARC)

"Genetic Association with Bovine Congestive Heart Failure in Feedlot Cattle"

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12:50pm - 3:00pm Integrated Breeding Platform: Tools, Databases and Applications for Plant Breeding - GOLDEN BALLROOM Organizer: Graham McLaren,

12:50pm Graham McLaren, Integrated Breeding Platform "The Breeding Management System - Development and Deployment"

1:10pm David R Jordan, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland

"Modernizing Plant Breeding Programs in Ethiopia" 1:30pm Zakaria Kehel, International Center for Agriculture Research in the Dry

Areas ICARDA "Informatics Support for Plant Breeding Programs at Icarda"

1:50pm Fred A. van Eeuwijk, Wageningen University & Research - Biometris "Modern Analytical Tools for Plant Breeding and their Integration into Information Management Systems"

2:10pm Cathrine Ziyomo, BECA-ILRI hub "Experiences of the Integrated Genotyping Service and Support (IGSS) in Modernizing Plant Breeding in Africa"

2:30pm Jean-Marcel Ribaut, Integrated Breeding Platform "10 Years to Digitize Breeding Programs in Sub-Saharan Africa: Achievements, Lessons Learned and Perspective"

12:50pm - 3:00pm Arbor Biosciences - "Advances in Visualizing Genome Organization - from Haplotypes to Chromosomal Barcoding" - ROYAL PALM SALON 1-2 Organizer: Matthew Hymes, Arbor Biosciences

12:50pm James A. Birchler, University of Missouri "Haplotype Specific Chromosomal Paints in Maize"

1:25pm Kai Wang, Fujian Agriculture and Forestry University "Characterization of Genome Structure and Evolution in Sugarcane Using Oligo-FISH"

1:50pm Takayoshi Ishii, Arid Land Research Center, Tottori university "RNA-Guided Endonuclease – in Situ Labelling (RGEN-ISL): CRISPR-Based Imaging of Genomic Sequences in Plants and Animals"

75


12:50pm - 3:00pm Plant Transgene Genetics - TERRACE ROOM - HANDLERY HOTEL Organizers: Yi Li, Univ. of Connecticut and Gan-Yuan Zhong, USDA-ARS

12:50pm Qiudeng Que, Syngenta "Simultaneous Gene Editing and Haploid Induction for Direct Editing in Broad Elite Crop Germplams"

1:15pm Yunde Zhao, Section of Cell and Developmental Biology, University of California, San Diego

"On Improving Gene Targeting in Plants" 1:40pm Gözde S. Demirer, Department of Chemical and Biomolecular

Engineering "Carbon Nanomaterials Enable Plant Genome Engineering without Transgene Integration"

2:05pm Katie Higginbottom, University of Bristol "A Simple Method for Spray-on Gene Editing in Planta."

2:30pm Satoko Nonaka, Tsukuba Plant Inovation Resarch Center, Faculty of Life and Environmental Sciences, University of Tsukuba

"Modification of Agrobacterium Tumefaciens for Improving the Transformation Frequency in Crops"

2:55pm James Thomson, USDA-Agriculture Research Service "Transgene Stacking in Potato Using the Gaantry System"

12:50pm - 3:00pm Digital Tools and Resources Session 2 - CALIFORNIA Organizers: Brian Smith-White, and Monica C. Munoz-Torres, Translational and Integrative Sciences Lab, Oregon State University

12:50pm Jeremy Destin, URGI, INRA, Université Paris-Saclay "FAIDARE, a Federation of Plant Data Repositories to Facilitate the Access to Genotype and Phenotype Data."

1:10pm Peifen Zhang, Phoenix Bioinformatics "PhyloGenes, a New Online Phylogenetics Resource for Plant Gene Function Inference"

1:30pm Mélanie Buy, URGI, INRA "GnpIS, a Multispecies Integrative Information System for Plant and Fungi"

1:50pm Yang Hu, Dept. of Crop and Soil Science, Washington State University "GridFree: A Python Package of Image Analysis for Object Counting and Measuring without Grid Restriction"

2:10pm Chunpeng James Chen, Washington State University "GRID: A Python Package for Aerial High-Throughput Phenotyping"

2:30pm Anthony Greenberg, Bayesic Research "Population Structure Inference using Phenotype Data"

3:00pm - 5:00pm Coffee Break - GRAND EXHIBIT HALL

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4:00pm - 5:30pm Pragmatic solutions for scaling your analysis: Machine Learning, Imaging, Containers, Clouds and APIs - Organizers: Jason Williams, Cold Spring Harbor Laboratory and Nirav Merchant, CyVerse

4:00pm BOF Discussion and Tutorials

4:00pm - 6:10pm AgriPlex Genomics Presents: PlexSeq™: A Focused NGS Platform For Mid-Density SNP Genotyping - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Scott Weigel, AgriPlex Genomics

4:00pm Alexander Miron, AgriPlex Genomics "Agriplex Genomics Presents: Plexseq™: A Focused NGS Platform for Mid-Density SNP Genotyping"

4:00pm - 6:10pm Population and Conservation Genomics 2 - PACIFIC SALON 3 Organizer: Om P. Rajora, University of New BrunswickChair: Om P. Rajora, University of New Brunswick

4:00pm Klaus-Peter Koepfli, Center for Species Survival, Smithsonian's National Zoological Park and Conservation Biology Institute

"Genomic Impact of Founder History on Populations of the Critically Endangered Dama Gazelle (Nanger dama)"

4:20pm Megan A. Supple, University of California, Santa Cruz "Mountain Lion Genomes Provide Insights into the Genomic Consequences of Inbreeding and Genetic Rescue"

4:40pm Yong-Bi Fu, Plant Gene Resources of Canada "What We Can Learn from Wild Emmer Wheat in Response to 28 Years of Global Warming"

5:00pm Jonas Aguirre, University of California, Irvine "Modelling Local Adaptation and Migration Potential Predict the Vulnerability of Populations of Wild Maize to Climate Change"

5:20pm Jesse Lasky, Pennsylvania State University "Genomics of Sorghum Local Adaptation to a Parasitic Plant"

5:40pm Harly J. Durbin, Division of Animal Sciences, University of Missouri "Leveraging Genotype-By-Environment Interactions across Discrete Environmental Regions to Select More Sustainable Beef Cattle"

6:00pm Filippos Aravanopoulos, Aristotle University of Thessaloniki "Population Genetic and Epigenetic Monitoring: An Approach to Evaluate the Genetic Resources across Time and Space"

77


4:00pm - 6:10pm Arbor Biosciences - "Complete Wheat Exome Analysis - From DNA to Variant Calling" - ROYAL PALM SALON 1-2 Organizer: Matthew Hymes, Arbor Biosciences

4:00pm Ute Baumann, The University of Adelaide "Diversity and Mutant Analyses Using Exome Capture of Wheat - a Pilot Study"

4:20pm Burkhard Steuernagel, The Sainsbury Laboratory and John Innes Centre "Rapid Cloning of Resistance Genes Using Targeted Sequence Capture"

4:40pm Shawn Quinn, Curio Genomics "Extending the Curio Platform for the Wheat Research Community; DNA Sequences to Analysis Results"

4:00pm - 6:10pm Integrated DNA Technologies - Case Studies on the Development and Application of Economical PCR-based Assays - GOLDEN WEST Organizer: Kelsi Ludvicek, Integrated DNA Technologies, Inc.

4:00pm Mitchell Gore, Integrated DNA Technologies "Case Studies on the Development and Application of Economical PCR-Based Assays for 1) SNP Genotyping and Hemizygote Selection in Cotton and 2) Conversion of GWAS-Discovered SNPs to MAS Markers in Wheat"

4:20pm David M. Stelly, Texas A&M University, Texas A&M Agrilife Research "Case Studies on the Development and Application of Economical PCR-Based Assays for 1) SNP Genotyping and Hemizygote Selection in Cotton and 2) Conversion of GWAS-Discovered SNPs to MAS Markers in Wheat"

4:40pm Robert Vaughn, Texas A&M University, Texas A&M Agrilife Research "Case Studies on the Development and Application of Economical PCR-Based Assays for 1) SNP Genotyping and Hemizygote Selection in Cotton and 2) Conversion of GWAS-Discovered SNPs to MAS Markers in Wheat"

5:00pm Emmanuel Adeyemo, University of Minnesota "Case Studies on the Development and Application of Economical PCR-Based Assays for 1) SNP Genotyping and Hemizygote Selection in Cotton and 2) Conversion of GWAS-Discovered SNPs to MAS Markers in Wheat"

5:20pm John Holme, 3CR Bioscience "Case Studies on the Development and Application of Economical PCR-Based Assays for 1) SNP Genotyping and Hemizygote Selection in Cotton and 2) Conversion of GWAS-Discovered SNPs to MAS Markers in Wheat"

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4:00pm - 6:10pm iGenomX, TGEN, University of Nebraska Lincoln - "Next-Generation Genotyping in Plants, Animals & Humans: 10x more genetic variants for 10x less the cost of microarrays" - ROYAL PALM SALON 3-4 Organizer: Justin Kermack, iGenomX

4:00pm Keith Brown, iGenomX "Next Generation Genotyping (NGG) for Population Scale Genomic Studies using Riptide™ DNA Library Preparation"

4:20pm David L. Hyten, University of Nebraska-Lincoln "Generating High Density, Low Cost Genotype Data in Soybean with Next Generation Genotyping (NGG)"

4:40pm James C Schnable, Department of Agronomy and Horticulture, University of Nebraska-Lincoln

"Mapping Recombination Breakpoints in Sorghum using Highly Multiplexed Whole Genome Shotgun Sequencing"

5:00pm Matt J. Huentelman, Translational Genomics Research Institute "Genetic Variants Associated with Canine Idiopathic Pulmonary Fibrosis in the West Highland White Terrier"

4:00pm - 6:10pm Rice Functional Genomics - PACIFIC SALON 2 Organizers: Yulin Jia, USDA-ARS, Hiroyuki Tsuji, Kihara Inst. Biol. Res., Yokohama City Univ. and Xuewei Chen, Sichuan Agricultural University

4:00pm Yulin Jia, USDA-ARS "Identification of Critical Amino Acid Residues in Ptr mediated Plant Innate Immunity"

4:17pm Kanako Bessho-Uehara, Carnegie Institution " Independent Gene Selection for Rice Awn Development in Asia and Africa"

4:34pm Taiji Kawakatsu, Institute of Agrobiological Sciences, NARO "Rice Transcription Factor Binding Atlas"

4:51pm Xiaoquan Qi, Institute of Botany, Chinese Academy of Sciences, China "Diversity and Function of Triterpenoid Pathways in Rice"

5:08pm Letian Chen, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University

"An Asymmetric Genome Interaction Drives Allele Transmission Bias in Interspecific Rice Hybrids"

5:25pm Qingyun Bu, Institute of Geography and Agroecology, Chinese Academy of Sciences

"WRKY53 Integrates the Classic BR Signaling and Mitogen-Activated Protein Kinase Pathway to Regulate Rice Architecture and Seed Size"

5:42pm Rod Wing, Arizona Genomics Institute, University of Arizona "The International Oryza Map Alignment Project (IOMAP) from a Platinum Reference Genome Sequence (PSRefSeq) Perspective"

79


4:00pm - 6:10pm Strawberry Genomics - CALIFORNIA Organizers: Patrick Edger, and Zhongchi Liu,

4:02pm Sook Jung, Washington State University "Resources for Strawberry Genomics, Genetics and Breeding Research in GDR, Genome Database for Rosaceae"

4:18pm Sachiko Isobe, Kazusa DNA Research Institute "Strawberry Genomics: Whole Genome Assembly and Structure Analysis in Japanese Strawberry"

4:34pm Mitchell J. Feldmann, of California, Davis "Genomic Prediction of Hybrid Performance in Strawberry"

4:50pm Zhongchi Liu, Dept. of Cell Biology and Molecular Genetics, University of Maryland

"Genomic and Genetic Resources in Wild Strawberry and its Application Toward Understanding Mechanisms of Fruit and Stolon Development"

5:06pm Seonghee Lee, University of Florida "Genomic Approaches to Improve Disease Resistance and Fruit Quality in Octoploid Strawberry"

5:22pm Elizabeth Alger, Michigan State University "Transposable Elements Shape the Transcriptional Landscape in Woodland Strawberry"

5:38pm Amèlia Gaston, INRA "Identification of New Actors Influencing the Balance between Flowering and Runnering in Strawberry"

5:54pm Chunying Kang, Huazhong Agricultural University "Dissection of Key Genes Controlling Important Agricultural Traits by using the Diploid Strawberry Fragaria vesca"

4:00pm - 6:10pm Seed Genomics - GARDEN 1 - HANDLERY HOTEL Organizers: Adel Zayed, NA and Vijay Sharma, Benson Hill

4:00pm Ramin Yadegari, University of Arizona "Gene Regulatory Networks of Maize Endosperm"

4:20pm Jaspreet Sandhu, University of Nebraska, Lincoln "Temporal Dynamics of Heat Stress Response during Early Seed Development in Rice"

4:40pm Hiro Nonogaki, Department of Horticulture/Oregon State University "A Novel Regulator of Seed Reserve Accumulation"

5:00pm Qingshun Quinn Li, Xiamen University "Vivipary in Mangrove: Germination with a Developing Embryo"

5:20pm Mathew G. Lewsey, La Trobe University "Integrated Multi-Omic Framework of the Plant Response to Jasmonic Acid"

5:40pm Yong-Qiang Charles An, USDA-ARS Plant Genetics Research Unit, Donald Danforth Plant Science Center

"Discover Soybean Seed Quality Trait Genes, Allele and Germplasm using a Big-Data Driven Technology Platform"

80


4:00pm - 6:10pm RAPiD Genomics - Fast, Focused, Flexible : High-Throughput Genotyping Solutions for Livestock & Agriculture - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Leandro Neves, RAPiD Genomics

4:00pm Itaraju Brum, CTC "Solving Challenges of Polyploid Genotyping: Using Capture-Seq for Commercial Sugarcane Breeding at CTC"

4:35pm Leandro G. Neves, RAPiD Genomics "High-Throughput SNP and Haplotype Genotyping with Flex Seq Ex-L for Breeding, Population Genetics and Other Applications"

5:05pm Adam Payton, RAPiD Genomics "Ultra-High-Throughput Genotyping for Animal Breeding with Flex Seq Ex-L: Examples in Pigs and Cattle"

5:35pm Leandro G. Neves, RAPiD Genomics "Addition By Subtraction: Repeat Depletion for Skim Sequencing in Maize"

4:00pm - 6:10pm Bayer Crop Science - "Breeding for Climate Change and Sustainability" - ROYAL PALM SALON 5-6 Organizers: Florian Jupe, Bayer Crop Science and Shilpa Swarup, Bayer Crop Science

4:00pm Mike Graham, Bayer U.S. Crop Science "Global Breeding Efforts at Bayer Crop Science"

4:30pm Shilpa Swarup, Bayer Crop Science "Conventional Breeding- Perceptions and Science behind It"

5:00pm Jennifer Spindel, Bayer CropScience "Scaling GWAS for an Industrial Breeding Pipeline"

5:30pm Ed M. Allen, Bayer CropScience "Stewardship Best Practices for Field Testing of Pre-Commercial Plant Genome Editing Material"

6:00pm Joseph A Bedell, Bayer CropScience "Searching for the Needles: Combing through Metagenomic Haystacks for New Weapons in the Fight Against Plant Pests"

81


4:00pm - 6:10pm Its More than Just Genomics: Understanding How Societal, Economic and Regulatory Factors Influence the Application of Genomics in Plants and Animals - TERRACE ROOM - HANDLERY HOTEL Organizer: Kate E. Harland, Genome British Columbia

4:00pm Alison Van Eenennaam, University of California "How Regulatory Factors Influence the Application of Genomics in Animals"

4:10pm Loren Rieseberg, University of British Columbia "Opportunities, Risks, and Benefits of Genetic Modification: Sunflower As a Case Study"

4:20pm Steven H. Strauss, Oregon State University "Applying Genomic Knowledge to Forest Trees by Gene Editing and Transformation: A Case Study of Scientist Efforts to Resolve Market and Regulatory Obstacles to Field Research and Breeding"

4:30pm Jason Delborne, Genetic Engineering and Society Center, North Carolina State University

"Public and Stakeholder Engagement in the Governance of Emerging Biotechnologies"

4:40pm Terre Satterfield, University of British Columbia

4:00pm - 6:10pm Bionano Genomics - Generating accurate de novo assemblies with Bionano Optical Mapping - EAST 2 Organizer: Yashashree Joshi, Bionano Genomics

4:00pm Todd Michael, J. Craig Venter Institute "Assembling Complex Plant Genomes"

4:20pm Michael Hiller, Max Planck Institute of Molecular Cell Biology and Genetics

"Reference-Quality Genomes of 6 Bats Illuminate Genomic Determinants and Evolution of Unique Adaptations in Bats"

4:40pm Victor Llaca, Corteva Agriscience "Optical Mapping of Different Genome Architectures in a Highly Diverse Pipeline"

5:00pm Geoff Waldbieser, USDA-ARS Warmwater Aquaculture Research Unit "Improvement of North American Catfish Genome Assemblies Using Optical Mapping"

82


4:00pm - 6:10pm Phase Genomics - Platinum Genomes, Hologenomes, Metagenomes: Enabling the Next Era of Genomics with Proximity Ligation Technology - SAN DIEGO Organizers: Kayla Young, Phase Genomics and Ivan Liachko, Phase Genomics

4:00pm Fritz J. Sedlazeck, Baylor College of Medicine, Human Genome Sequencing Center

"Why so Pale and Wan: Comparative Genomics Based on a Platinum Cavefish Genome"

4:20pm Stephen Schauer, KeyGene "Translating Innovations in Reference Genome Phasing into Crop Improvement"

4:40pm Ben Auch, University of Minnesota "It Came from Planet Earth: The Genome of the Aquatic Invasive Zebra Mussel, Dreissena polymorpha"

5:00pm Cristian Gallardo-Escárate, Interdisciplinary Center for Aquaculture Research (INCAR), Department of Oceanography, University of Concepción

"Free Two Birds with One Key: Chromosome Assembly and Metagenomes using Proximity-Ligation in the Sea Louse Caligus rogercresseyi"

5:20pm Derek M. Bickhart, Dairy Forage Research Center, USDA-ARS "Assignment of Virus and Antimicrobial Resistance Genes to Microbial Hosts in a Complex Microbial Community by Combined Long-Read Assembly and Proximity Ligation"

5:40pm Ivan Liachko, Phase Genomics "Connecting the Plasmidome, Resistome, and Virome to the Microbiome"

4:00pm - 6:10pm NRGene - Accelerating Crop Research with High-Quality Genome Assemblies - PACIFIC SALON 1 Organizer: Daphna Tako, NRGene

4:00pm Assaf Distelfeld, School of Plant Sciences and Food Security, Tel Aviv University "Pangenomic View of Wheat Domestication Loci"

4:25pm Patricio R. Munoz, University of Florida "Better Genome Assembly, Better Plant Breeding"

4:50pm Gil Ronen, NRGene "Capturing Diversity "

5:15pm Joseph D. Clarke, Syngenta Biotechnology Inc. "Pangenome Enhance, Haplotype Enabled Genotyping through Genomagic: Population Level Insights "

83


4:00pm - 6:10pm Meiotic Recombination - EAST 1 Organizer: Raphael Mercier, Max Planck Institute for Plant Breeding Research

4:00pm Ian Henderson, University of Cambridge "ASY1 acts as a Dosage-Dependent Antagonist of Telomere-Led Recombination via Crossover Interference in Arabidopsis"

4:20pm Piotr A. Ziolkowski, Adam Mickiewicz University "Natural Variation in Recombination Frequency Reveals SNI1 as a New Regulator of Meiotic Crossovers"

4:40pm Petra Bulankova, VIB-UGent Center for Plant Systems Biology "Inter-Homolog Mitotic Recombination is Enhanced in Diatoms and Contributes to High Haplotype Diversity in Clonal Populations"

5:00pm Korbinian Schneeberger, Max Planck Institute for Plant Breeding Research "Generating Haplotype-Resolved, Chromosome-Level Genome Assemblies using Single-Cell Genome Sequencing of Recombined Gametes"

5:20pm James David Higgins, University of Leicester "A Genotype-Phenotype Association for Autopolyploid Meiosis Stabilisation"

6:20pm - 8:30pm Single Cell Genomics - SAN DIEGO Organizer: Parwinder Kaur, UWA School of Agriculture and Environment, The University of Western AustraliaCo-Organizer: Anthony Bosco, Telethon Kids Institute

6:20pm Anthony Bosco, Telethon Kids Institute "Exploring New Frontiers for Systems Immunology at Single Cell Resolution. "

6:40pm Mathew G. Lewsey, La Trobe University "Tissue and Cell-Specific Regulation of the Genome during Seed Germination"

7:00pm Jong Kyoung Kim, DGIST "Transdifferentiation of Arabidopsis Abscission Zone Cells at Single Cell Resolution"

7:20pm Marc Libault, University of Nebraska Lincoln "A Multiomic Approach at the Single Cell Level to Better Understand the Transcriptional Regulation of Plant Genes"

7:40pm Jason F Kim, 10x Genomics "Accelerating Biology at True Resolution with Single Cell Analyses and Spatial Transcriptomics"

7:40pm Sylva Donaldson, University of Toronto / CAGEF "Expression Profiling Resources at the Bio-Analytic Resource: Scrna-Seq Efp Browser and More"

8:00pm Jason Kim, 10x genomics "Accelerating Biology at True Resolution with Single Cell Analyses and Spatial Transcriptomics"

84


6:20pm - 8:30pm Mammalian Cloning. Process, Progress and Pitfalls, Practicality, Preservation and Potential of Cloning and other Advanced Genetic and Reproductive Technologies - GOLDEN WEST Organizer: Heather Koshinsky, STEIR

6:20pm - 8:30pm Gene Mapping by Segregation - PACIFIC SALON 3 Organizer: Zhiwu Zhang, Dept. of Crop and Soil Science, Washington State University

6:20pm Zhiwu Zhang, Dept. of Crop and Soil Science, Washington State University

"Gene Mapping in Era of High-Throughput Phenotyping" 6:25pm Jean-Luc Jannink, USDA-ARS

"RNA Polymerase Mapping in Plants Identifies Enhancer Candidates Enriched in Causal Variants"

6:50pm Long-Xi Yu, USDA-ARS Plant Germplasm Introduction and Testing Research

"Genomic Approach for Enhancing Abiotic Stress Resilience in Alfalfa (Medicago sativa L.)"

7:15pm Alex C Ogbonna, Cornell University and Boyce Thompson Institute "Genetic Architecture and Gene Mapping of Cyanogenic Glucoside in Cassava"

7:40pm Yang Hu, Dept. of Crop and Soil Science, Washington State University "High Throughput Image Techniques in Breeding"

8:05pm Iulian Gabur, Department of Plant Breeding, Justus Liebig University "Mapping Gene Presence-Absence in a Recent Complex Polyploid Crop Genome"

6:20pm - 8:30pm Application of Genetics and Genomics for Large-scale Breeding Programs - ROYAL PALM SALON 1-2 Organizer: Florian Jupe, Bayer CropScience


6:25pm T Lynne Reuber, Two Blades Foundation "Developing Durable Disease Resistance"

6:45pm Christian R. Werner, University of Edinburgh, The Roslin Institute "Data Driven Plant Breeding"

7:05pm Fabiana Mokry, Genus ABS "A New Paradigm for Beef Cattle Genetic Improvement"

7:25pm Andrew Walker, Cibus US LLC "Development of Cibus’ Trait Machine™ to Efficiently Apply Gene Editing"

7:45pm Radu Totir, Corteva "Use of Advanced Technologies to Digitally Engineer Seed Products at Corteva Agriscience"


85


6:20pm - 8:30pm Cloud Computing for Genomics Data Analysis - PACIFIC SALON 2 Organizer: Avjinder Kaler, Benson Hill

6:20pm Xinshuai Qi, Benson Hill "Cloud Computing Bridges Big Biological Data and AI to Accelerate Research and Application in Plant Genomics"

6:20pm Thomas G. Doak, National Center for Genome Analysis "National Center for Genome Analysis Support (NCGAS): Genomics and other Science in the NSF-Funded Jetstream Cloud"

6:20pm Jason Williams, Cold Spring Harbor Laboratory "Reproducibility in the Clouds - Harnessing the in Nube Paradigm"

6:20pm Arkarachai Fungtammasan, DNAnexus "Scalable Genome Assembly on the Cloud: From One Hundred to Seventy Thousand Species"

6:20pm Rob Long, Bayer Crop Science "Industrializing Genotype Data on Public Cloud Infrastructure"

6:20pm - 8:30pm BER Plant Genomic Science - ROYAL PALM SALON 3-4 Organizer: Jeremy Schmutz, DOE Joint Genome InstituteCo-Organizer: Robert W. Cottingham, Oak Ridge National Laboratory

6:20pm Robert W. Cottingham, Oak Ridge National Laboratory "Introduction and Overview of KBase and Joint Genome Institute Plant Program"

6:34pm Daniel Jacobson, Oak Ridge National Laboratory "Exascale Networks for Arabidopsis in Kbase"

6:52pm Karolina Heyduk, Yale University "Understanding the Regulation of Crassulacean Acid Metabolism through a New Genomic Model in Yucca (Asparagaceae)"

7:10pm Xiaohan Yang, Biosciences Division, Oak Ridge National Laboratory "Comparative Genomics Analysis of Drought Response between CAM and C3 Photosynthesis Plants"

7:28pm Alice H. MacQueen, University of Texas at Austin "Genetics of Genotype-by-Environment Interactions in the Switchgrass Diversity Panel"

7:46pm Janaka N. Edirisinghe, Argonne National Laboratory "Fungal Modeling in KΒase: Automated Reconstruction, Manual Curation, Evaluation and Comparison of Diverse Genome-Scale Fungal Metabolic Models"

8:04pm Jerry Jenkins, HudsonAlpha Institute for Biotechnology "Plant Genomic References of the Future"

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6:20pm - 8:30pm Arabidopsis Informatics - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Tanya Z. Berardini, Phoenix Bioinformatics


6:24pm Yi-Jing Zhang, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

"Plant Regulomics: A Data-Driven Interface for Retrieving Upstream Regulators from Plant Multi-Omics Data."

6:42pm Wen-Biao Jiao, Max Planck Institute for Plant Breeding Research "Chromosome-Level Assemblies of Multiple Arabidopsis Genomes Reveal Hotspots of Rearrangements with Altered Evolutionary Dynamics"

7:00pm Andrew Farmer, National Center for Genome Resources (NCGR) "Exploring Arabidopsis and Brassicaceae Genomes with the Genome Context Viewer"

7:18pm Larry Wu, Michigan State University "Identification of Novel Translated ORFs using Enhanced Super-Resolution Ribosome Profiling in Arabidopsis"

7:36pm Sylva Donaldson, University of Toronto / CAGEF "The Bio-Analytic Resource for Plant Biology – Thalemine and 2019 Updates"

7:54pm Muhammad Waqas Khokhar, Canterbury Christ Church University "Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana"

8:12pm Sabarinath Subramaniam, Phoenix Bioinformatics "Improvements and New Features at the Arabidopsis Information Resource (TAIR)"

6:20pm - 8:30pm Data Resource Sustainability and Funding - EAST 1 Organizer: Eva Huala, Phoenix Bioinformatics

6:20pm Introduction - Eva Huala

6:25pm Eva Huala, Phoenix Bioinformatics "Sustainability Approaches for Biological Databases and Tools"

6:37pm Charles E Cook, Global Biodata Coalition "Global Core Data Resources and the Global Biodata Coalition"

6:49pm Susan Russo Gelbart, Harvard University "Flybase Community Financial Support"

7:01pm Sarah C. R. Elgin, Washington University in St. Louis "Working Toward Sustainability for the Genomics Education Partnership"

7:13pm Jessica Kissinger, University of Georgia, IOB, CTEGD & Genetics "Eukaryotic Pathogen, Vector & Host Informatics Resources (VEuPathDB) - a Merged International Approach Towards Achieving Sustainability"

7:25pm M.J. Woodward-Greene, USDA-ARS, National Agricultural Library "Sustainability for USDA’s Ag Data Commons Catalog and Repository"

7:37pm Peter McCartney, National Science Foundation "Database and Resource Sustainability from the NSF Viewpoint"

7:49pm Panel Discussion - all speakers

87


6:20pm - 8:30pm Decadal Vision for Plant Systems Science: Challenges and Breakthroughs - EAST 2 Organizers: Brett Tyler, Oregon State University and Sreekala Chellamma, Corteva Agriscience™

6:20pm Rebecca Grumet, Department of Horticulture, Michigan State University "Overview of the Plant Science Research Network and the Psrn Decadal Vision"

6:35pm Katie Rogers, American Society of Plant Biologists "Reimagining the Workplace to Nurture and Support Adaptive and Diverse Scientists"

6:55pm Pamela S. Soltis, University of Florida "Harnessing Plant Systems for Planetary Resilience."

7:15pm Gerardus W. van der Heijden, Corteva Agriscience "The Role of Science in Future Farming"

7:35pm Sreekala Chellamma, Corteva Agriscience™ "Panel Discussion"

6:20pm - 8:30pm Potato Genomics - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: David Douches, Michigan State University

6:20pm Martina Stromvik, Department of Plant Science - McGill University "Genome Sequencing of 12 Taxonomically Diverse Potato Species of Varying Ploidy"

6:40pm Dan Milbourne, Teagasc, Crop Science Department, Carlow "Developing Pathways for Practical Deployment of DNA-Based Selection Strategies in Potato Breeding"

7:00pm Natalie R Kirkwyland, Michigan State University "Insect Resistance in Potato"

7:20pm Eric M Magembe, International Potato Center "3-R-Gene Potato for Late Blight Resistance"

7:40pm Corentin C.R. Clot, Plant Breeding, Wageningen University and Research "The Origin and Widespread Occurrence of Sli based Self-Compatibility in Potato"

8:00pm Jeffrey B. Endelman, University of Wisconsin "Joint QTL Analysis of a Tetraploid Potato Diallel Population"

6:20pm - 8:30pm NimaGen - Next generation genotyping: GreenoType® accelerates potato breeding - ROYAL PALM SALON 5-6 Organizer: Walter van der Vliet, Nimagen bv

6:20pm Welcoming Remarks 6:25pm Introductory Remarks 6:35pm Pieter van der Vlies, HZPC

"Next Generation Genotyping: Greenotype® Accelerates Potato Breeding"


7:00pm - 7:30pm Coffee Break - ATLAS FOYER

88

Tuesday - January 14, 2020







8:00am - 8:45am Plenary Lecture: Kimberly Cooper - TOWN & COUNTRY BALLROOM Chair: Christopher K. Tuggle, Animal Science, Iowa State University

8:00am Kimbery Cooper, UCSD, Cooper Lab "Super-Mendelian Inheritance Mediated by CRISPR–Cas9 in the Female Mouse Germline"

8:45am - 9:30am Plenary Lecture: Zach Lippman - TOWN & COUNTRY BALLROOM Chair: Christopher K. Tuggle, Animal Science, Iowa State University

8:45am Zach Lippman, Cold Spring Harbor Laboratory "Structural Variant Landscapes in Plant Genomes and their Impact on Evolution, Domestication, and Breeding"

9:30am - 10:30am Coffee Break - GRAND EXHIBIT HALL

9:30am - 3:00pm Exhibits Open - GRAND EXHIBIT HALL

10:30am - 12:40pm Brachypodium Genomics - PACIFIC SALON 2 Organizer: David F. Garvin, USDA-ARS, Plant Science Research Unit

10:30am Justin O. Borevitz, The Australian National University "Extending the Genotype in Brachypodium By Including DNA Methylation Reveals a Joint Contribution with Genetics Adaptive Traits"

10:55am Samuel Holden, The Sainsbury Laboratory "From Brachypodium to Ecdeiocolea: The Origin, Expansion, and Diversity of the NLR Integrated Domains in the Grasses"

11:20am Jared Streich, Oak Ridge National Laboratory "Genome Assembly Variation and Time-Series Association in Brachypodium Species"

11:45am Karen Sanguinet, Washington State University "The Role of the Buzz Kinase in Post-Initiation Root Hair Growth"

12:35pm John Vogel, DOE Joint Genome Institute "Developing Ecofabs As a Reproducible System to Study the Root Microbiome"

89


10:30am - 12:40pm Genomics-Assisted Breeding - TOWN AND COUNTRY Organizer: Rajeev K Varshney, ICRISAT and University of Western Australia

10:30am Sarah Hearne, International Maize and Wheat Improvement Center (CIMMYT)

"Smart Targeting of Germplasm Bank Exploration" 10:50am Silvio Salvi, University of Bologna, Bologna

"Combining Mutant Analysis and Genome Wide Association for Root Genetics Dissection in Barley"

11:10am Yuanyuan Zhang, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences

"Breeding Pedigrees Demonstrate Asymmetrical Subgenome Recombination and Selection in Polyploid Brassica napus"

11:30am Kai Voss-Fels, The University of Queensland "Predicting a Path for Increased Genetic Gain in Wheat Using Artificial Intelligence"

11:50am Nadim Tayeh, INRAE, UMR1347 Agroécologie "Taking Cool-Season Grain Legume Breeding to the Next Level: The Key Role of the Pea Genome Sequence"

12:10pm Pasupuleti Janila, ICRISAT "Genomic Tools for Early Generation Selection Delivers Improved Peanut Cultivars for Cultivation."

10:30am - 12:40pm International Phytomedomics and Nutriomics Consortium (ICPN) 1 - ROYAL PALM SALON 3-4 Chair: Chittaranjan Kole, ICAR-National Institute for Plant Biotechnology Co-Organizer: Yong Pyo Lim, Chungnam National University

10:30am Chittaranjan Kole, ICAR-National Institute for Plant Biotechnology "Phytomedomics and Nutriomics for Health Security"

10:45am Massimo Iorizzo, Plants for Human Health Institute, Department of Horticulural Science, North Carolina State University

"Diversity in Metabolites and Fruit Quality Traits in Blueberry Enables Ploidy and Species Differentiation and Establishes a Strategy for Genetic Studies on Bioactive Traits"

11:00am Cheng-Ruei Lee, National Taiwan University "The Bitter Gourd (Momordica charantia) Genome Reveals the Genomic Architecture of Domestication"

11:15am Li Li, Cornell University "Harness Carotenoid Metabolism for the Development of Nutrient-Enriched Crops"

11:30am Sachiko Isobe, Kazusa DNA Research Institute "Whole Genome Sequencing and Genetic Diversity Analysis in Atractylodes lancea and Ephedra sinica"

11:45am Michael Baum, ICARDA

12:00pm Kathleen Hefferon, University of Toronto

90


10:30am - 12:40pm Compositae - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Richard Michelmore, The Genome Center, University of California and Jennifer Mandel, University of Memphis

10:30am Annabelle Damerum, University of California "CRISPR Lettuce? Manipulating Lettuce Shelf Life Using Genome Editing"

10:51am Ramhari Thapa, University of Memphis "Phylogenomics Yields Insights into the Evolution and Biogeography of the Complex Genus Antennaria"

11:12am Sariel Hübner, Galilee research institute (MIGAL) "The Cultivated Sunflower Pan-Genome Provides Evidence That Introgression from Wild Species Shaped the Gene Repertoire and Enhanced Disease Resistance"

11:33am Rong Tao, Huazhong Agricultural University and The Genome Center, University of California

"Characterization of Seven Polymorphic Genes Controlling Red Leaf Color in Lettuce and their Applications in Lettuce Improvement"

11:54am Zoé Le Bihan, INRA Bordeaux University, Biology and Fruit Pathology / Oviatis "Stevia rebaudiana : Cultivated and Landraces Phenotypic and Genotypic Diversity, Towards Yield Components Mapping"

12:15pm Bort Edwards, Smithsonian Institute, NMNH "The Importance of Phylogenomics in Understanding the Evolution of North American Compositae"

10:30am - 12:40pm Genome Variation and Somatic Cell Breeding - ROYAL PALM SALON 5-6 Organizer: Xiyin Wang, North China University of Science and TechnologyCo-Organizer: Valérie Poncet, IRD UMR DIADE


10:35am Xiyin Wang, North China University of Science and Technology "Reconstruction of Cell Karyotypes and Chromosome Evolutionary Trajectories of Plants"

10:55am Xiaoming Song, North China University of Science and Technology "Deciphering the High Quality Genome Sequence of Coriander"

11:15am Yanbin Yin, University of Nebraska-Lincoln "The Reductive Genome of Zygnema Circumcarinatum Provides New Insights into Plant Terrestrialization"

11:35am Weijian Zhuang, Fujian Agriculture and Forestry University "The Arachis hypogaea Genome Provides Insight into the Polyploid Origin and Subgenomes Differential Evolution"

11:55am Chaobo Tong, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences

"Expression Patterns and Epigenetic Regulation under Subgenomic Interaction in Brassica napus"

12:15pm Valérie Poncet, IRD UMR DIADE "Patterns of Adaptive Genetic Variation across Coffea canephora"

91


10:30am - 12:40pm Bioinformatics - GOLDEN WEST Organizer: Aleksey Zimin, University of Maryland

10:30am Sergey Koren, Genome Informatics Section, NHGRI, NIH "A Novel Approach for Assembly of High-Fidelity Pacbio Hifi Reads Resolves Large Segmental Duplications and Haplotypes"

10:50am Mikhail Kolmogorov, UC San Diego "Long-Read Assembly: Are Metagenomes Easier Than Diploid Genomes?"

11:10am Jason Chin, DNAnexus "Speeding up Genome Assembly with Sparse and Hierarchical Minimizer Indices"

11:30am Ivan Liachko, Phase Genomics "Beyond Binning: Combining Proximity-Ligation and Metagenomic Deconvolution Algorithms Significantly Improves the Quality and Quantity of Genomes Extracted from Complex Microbiome Samples"

11:50am Igor Rogozin, National Institutes of Health "Ubiquitous Mutational Footprints of Aid/Apobec Deaminases in Human Cancer Genomes: Application of Nucleotide Weight Matrices"

12:10pm Alexandre Lomsadze, Georgia Institute of Technology "Eukaryotic Gene Prediction By Genemark-EP+ with Support from Homologous Proteins"

10:30am - 12:40pm BBSRC/NSF/ERA-CAPS - EAST 2 Organizer: Anne Sylvester, NATIONAL SCIENCE FOUNDATION

10:30am - 12:40pm Farm Animal Genome Editing - SAN DIEGO Organizer: Bruce Whitelaw, The Roslin Institute and R(D)SVS, University of Edinburgh


10:40am Daniel F. Carlson, Recombinetics, Inc. "From Barn to Bedside - Genome Editing in Livestock for Food and Biomedicine"

10:55am Rachel J. Hawken, Cobb-Vantress "Opportunities for Gene Editing in Poultry"

11:10am Elena Rice, Genus plc "Gene Editing for Healthier Animals and Sustainable Food System"

11:25am Andrea Doeschl-Wilson, The Roslin Institute, University of Edinburgh "Modelling Feasibility of Eradicating PRRS with Genome Editing"

11:40am Wenfang Spring Tan, the Roslin Institute "Genome Wide CRISPR Knockout Screen Identifies Host Factors Important for Bovine Herpes Virus Type 1 Replication"

92


11:55am Christopher J. Davies, Utah State University and Center for Integrated

BioSystems, Utah State University "Type I Interferon Receptor Knockout Sheep: A Model for Viral Immunology and Reproductive Signaling"

12:10pm Stefanie Kurtz, Institute for Farm Animal Genetics, Friedrich-Loeffler-Insitute "The Knockout of the HMG Domain of the Porcine SRY Gene by CRISPR/Cas RNP Microinjection Causes Sex Reversal in Gene-Edited Pigs"

12:25pm Bruce Whitelaw, The Roslin Institute and R(D)SVS, University of Edinburgh "Public Attitudes Towards Genome Edited Meat"

10:30am - 12:40pm Genomics of Phytoremediators, Metal Accumulators and Relatives - PACIFIC SALON 1 Organizers: Adel Zayed, Seed Production Information, Bayer and Sensei and Bjoern Pietzenuk, Ruhr-University Bochum

10:30am Qingqing Xie, Division of Biological Sciences Cell and Developmental Biology Section & Ctr for Mol. Genetics

"Identification of Functionally Redundant Genes in Heavy Metal Tolerance and Accumulation"

10:30am Robert Tournay, University of Washington "The Genomics of Endophytic Biofilms in the Phytoremediation of Arsenic"

10:30am Pramod Pantha, Louisiana State University "Understanding High Potassium Stress Responses of the Extremophyte, Schrenkiella Parvula Using Systems Biology Approaches"

10:30am Kieu-Nga T Tran, Louisiana State University "Extremophyte Arabidopsis Relatives Thrive in Soils with Toxic Concentrations of Sodium"

10:30am - 12:40pm Hybridization, heterosis and balancing selection - TERRACE ROOM - HANDLERY HOTEL Organizers: Jianming Yu, Iowa State University and Xianran Li, Iowa State University

10:30am James A. Birchler, University of Missouri "Is the Magnitude of Heterosis Correlated with Transcriptome Size?"

11:00am Xuehui Huang, Shanghai Normal University "Heterosis Dissection"

11:25am Kathleen Newton, University of Missouri "Changes in Total and Mitochondrial Proteomes Associated with Different Levels of Heterosis in Maize"

11:50am Samantha Snodgrass, Iowa State University "Gene Expression and Heterosis"

12:15pm David R Jordan, The University of Queensland "Towards Better Exploitation of Heterosis in Commercial Hybrid Grain Sorghum"

93


10:30am - 12:40pm BreedBase and SGN: Genomics and Breeder Data Management and Analyses Tools - EAST 1 Organizers: Isaak Y. Tecle, Boyce Thompson Institute, Cornell University and Lukas Mueller, Boyce Thompson Institute for Plant Research

10:30am Lukas A. Mueller, Boyce Thompson Institute "Introduction"

10:35am Agbona Afolabi, International Institute of Tropical Agriculture (IITA) "Improving Quality in Africa RTB Crop Breeding Programs: A Database Management System Approach"

10:55am Isaak Y. Tecle, Boyce Thompson Institute "BreedBase: Genomic Selection Analysis and Decision Support Tools"

11:15am Nicolas Morales, Boyce Thompson Institute and Cornell University "Aerial Drone Imagery Database and Prediction of End-of-Season Traits in Maize"

11:35am Jeremy Edwards, Dale Bumpers National Rice Research Center "Ricebase: A Breedbase Implementation for Rice with Tools for Gene Discovery and Marker Development"

11:55am Prashant S Hosmani, Boyce Thompson Institute "A Symphony of N. sylvestris and N. tomentosiformis Sub-Genomes in the Allotetraploid Genome of N. tabacum"

10:30am - 12:40pm Systems Genomics - GARDEN 1 - HANDLERY HOTEL Organizers: Hong-Bin Zhang, Department of Soil and Crop Sciences, Texas A&M University and Meiping Zhang, Department of Soil and Crop Sciences, Texas A&M University

10:30am Nathan M. Springer, University of Minnesota "Maize Hybrids over-Express Chloroplast Digenomic Protein Complexes"

10:50am Chi Zhang, University of Nebraska - Lincoln "Network-Based Feature Selection Associates Gene Modules in Co-Expression Network to Phenotypic Data"

11:10am Yoseph Beyene Aydagn, CIMMYT "Empirical Comparison of Tropical Maize Hybrids Selected through Genomic and Phenotypic Selections"

11:30am Libin Wei, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, China

"Long-Read RNA Sequencing Reveals Transcriptome Complexity in Sesamum Indicum L."

11:50am Camila Urbano Braz, Division of Animal Sciences, University of Missouri "Exploring Alternative Genome-Wide Approaches to Analyze SNP Data for Complex Traits in Beef Cattle"

12:10pm Hongbin Zhang, Department of Soil and Crop Sciences, Texas A&M University "The Genes Controlling a Quantitative Trait Are Multiple-Fold More Likely to Form a Co-Expression Network in Plants"

94


10:30am - 12:40pm Proteomics - PACIFIC SALON 3 Organizers: Madan K. Bhattacharyya, and Michael A. Djordjevic,

10:30am S.P. Dinesh-Kumar, Department of Plant Biology and The Genome Center, University of California Davis,

"Turboid-Based Proximity Labeling for in Planta Identification of Protein Interaction Networks"

10:50am Shahid Mukhtar, University of Alabama at Birmingham "Getting to the Edge of Plant-Pathogen Interaction Networks"

11:10am Xiao-Ning Zhang, St Bonaventure University "Quantitative Proteomics Reveals Tissue-Specific Preferences for a Splicing Regulator, Serine/Arginine-RICH 45, in Arabidopsis thaliana"

11:30am Dennis V. Lavrov, Iowa State University "Evolution of Mitochondrial Proteome in Animals"

11:50am Abhinav Upadhyay, UNIVERSITY OF CONNECTICUT "Efficacy of Phytochemicals on Campylobacter jejuni Biofilms on Common Food Processing Surfaces and their Effect on Proteome of C. jejuni"

12:10pm Savithiry Natarajan, USDA-ARS "Fast Neutron Mutagenesis Alters Seed Protein Content in Soybean "

10:30am - 12:40pm Digital Tools and Resources Session 3 - CALIFORNIA Organizers: Brian Smith-White, and Monica C. Munoz-Torres, Translational and Integrative Sciences Lab, Oregon State University

10:30am Taner Z. Sen, USDA-ARS "GrainGenes: Small Grain Resources, Tools, and Sharing"

10:50am Kenji K. Kojima, Genetic Information Research Institute "Repbase: A Comprehensive Database of Eukaryotic Repeat Sequences and Transposons"

11:10am Tao Tao, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health

"NCBI Blast: Enhanced Web Usability through New Result Page, and Effective Genomic Data Access"

11:30am Arthur Korte, Center for Computational and Theoretical Biology, University Wuerzburg

"AraPheno and the AraGWAS Catalog 2020: A Major Database Update including RNA-Seq and Knockout Mutation Data for Arabidopsis thaliana"

11:50am Katharina J. Hoff, Institute for Mathematics and Computer Science, University of Greifswald and Center for Functional Genomics of Microbes, University of Greifswald

"MakeHub: Creating Individual Assembly Hubs for Display with the UCSC Genome Browser"

95


10:30am - 12:40pm Banana Genomics - PACIFIC SALON 6-7 (2ND FLOOR) Organizers: Mathieu Rouard, Bioversity International and Angelique D'Hont, CIRAD, UMR AGAP

10:30am Michael F Seidl, Utrecht University "Global Epidemic of Panama Disease on Banana is caused by a New Fungal Species Originating from Southeast Asia"

10:50am Allan Brown, International Institute of Tropical Agriculture "Advancements Toward Molecular Breeding and Genomics in the ‘Breeding Better Bananas’ Project in East Africa"

11:10am Angelique D'Hont, CIRAD "Two Large Reciprocal Translocations and Their Impact on Chromosome Segregation Characterized in Musa Acuminata Burmannica"

11:30am Eli Khayat, Rahan Meristem (1998) LTD "In-vitro Activation of Retro-Transposable Elements as an Effective Mode of mutagenesis in Musa"

11:50am Mathieu Rouard, Bioversity International "The Complex Story of Intergenomic Recombination in ABB Allotriploid Bananas"

12:10pm Valentine Nakato, International Institute of Tropical Agriculture, "New Insight for Banana Resistance to Xanthomonas vasicola pv. musacearum"

10:30am - 12:40pm Soybean Genomics - ROYAL PALM SALON 1-2 Organizer: Suk-Ha Lee, Seoul National UniversityChair: Suk-Ha Lee, Seoul National University

10:30am Prem L Bhalla, The University of Melbourne "Genomic of Floral Transition in Soybean"

10:45am Yoshihiro Ohmori, The University of Tokyo "Ionome As an Intermediate Phenotype of Soybean and Its Possible Use for Genomic Prediction"

11:00am Hao-Xun Chang, National Taiwan University "Characterizationof Soybean STAY-Green Genes in Susceptibility to Foliar Chlorosis of Sudden Death Syndrome"

11:15am Soon-Chun Jeong, Korea Research Institute of Bioscience and Biotechnology "A Map of Genetic Variation from 781 Soybean Genomes"

11:30am Xuelu Wang, Huazhong Agricultural University "Global Gene Coexpression Networks Give Insight into the Evolution of Nodulation in Non-Legumes and Legumes"

11:45am Jian Zhao, Anhui Agricultural University "Lipidomic and Transcriptomic Profiling of Developing Nodules Reveal the Essential Roles of Active Glycolysis and Fatty Acid and Membrane Lipid Biosynthesis in Soybean Nodulation"

12:00pm Tri D. Vuong, University of Missouri "Integrative Approach Using RNA-Seq and Whole-Genome Resequencing Data to Detect Causal Variants Underlying Cool Temperature Stable High Protein in Soybean"

12:15pm Yan Li, National Center for Soybean Improvement, Nanjing Agricultural Univ. "Genetic Variation Underlying Seed Oil Content in Soybean"

96


12:30pm - 1:30pm Lunch - EXHIBIT HALL, LION COURT & ROYAL PALM COURT

1:30pm - 3:40pm BGI Americas - Advanced NGS Technologies for Phylodiversity Research, Agricultural Trait Discovery and Molecular Breeding. - GOLDEN WEST Organizer: David Fahmy, BGI Americas

1:30pm Gane Ka-Shu Wong, University of Alberta "From 1,000 Plant Transcriptomes to 10,000 Plant Genomes: Phylodiverse Sequencing in the 21st Century"

2:00pm David D. Fang, Cotton Fiber Biosciences Research Unit, USDA-ARS-SRRC "Whole Genome Sequencing of a MAGIC Population Identified Genomic Loci and Candidate Genes for Major Fiber Quality Traits and Envoke® Herbicide Tolerance in Cotton "

2:30pm Joseph K. Pickrell, Gencove Inc "Low-Pass Sequencing As an Alternative for Genotyping Arrays in Agricultural and Companion Animal Genetic Applications"

1:30pm - 3:40pm Agilent Technologies: Automated Nucleic Acid Analysis Tools to Accelerate Plant and Animal Research - ROYAL PALM SALON 1-2 Organizer: Karen Brown, Agilent Technologies Inc.

1:30pm Jana Molitor, Agilent Technologies "Standardize Your Sample Quality Control"

1:30pm Whitney A. Pike, Agilent Technologies "Automated High Throughput Fragment Analysis with the Agilent Zag DNA Analyzer System"

1:30pm Fábio Yamashita Barletta, Sakata Seed Sudamerica Ltda "Use of Automated Capillary Electrophoresis System at Sakata Seed Sudamerica"

97


1:30pm - 3:40pm Beyond Drosophila: Genomic advances in non-model Diptera - GARDEN 1 - HANDLERY HOTEL Organizers: Sheina Sim, USDA-ARS and Scott Geib, USDA-ARS

1:30pm Megan E. Williamson, North Carolina State University "Conditional Transgenic Male-Only System Development in the Sheep Blowfly, Lucilia Cuprina"

1:50pm Alaine C. Hippee, University of Iowa "Host Shifting and Host Sharing in a Genus of Specialist Flies Diversifying alongside their Sunflower Hosts"

2:10pm Haynes Heaton, Wellcome Sanger Institute "New Approaches to Generate Single Insect Haplotype Assemblies"

2:30pm Nikolay Kandul, University of California, San Diego "Precision Guided Sterile Insect Technique (pgSIT): A Novel Environmentally Friendly Technology for Insect Population Suppression"

2:50pm Kelsey A. Coffman, University of Georgia "Genomic Insights into Beneficial Virus Evolution within Fruit Fly Parasites"

3:10pm Alistair Darby, University of Liverpool "Chromosome Level Assemblies of Arthropod Pests and Vectors for Genetic Control"

1:30pm - 3:40pm Corteva Agriscience - "Enriching Lives Through Genomic Innovations" - PACIFIC SALON 3 Organizer: Gregory D. May, Corteva Agriscience

1:30pm Welcoming Remarks 1:31pm Doane Chilcoat, Corteva Agriscience

"An Introduction to Corteva Agriscience" 1:41pm Matthew B. Hufford, Iowa State University

"Uncovering Novel Variation Relevant to Maize and Sorghum Breeding through Genome Assembly of Diverse Lines and Crop Wild Relatives"

2:01pm Kevin Fengler, Corteva Agriscience "Maize Reference Genome Assembly in a Day "

2:21pm Doreen Ware, Cold Spring Harbor Laboratory "Moving from a Single Genome to Population-Based References Assemblies of Plants"

2:41pm Eli Rodgers-Melnick, Corteva Agriscience "Making the Most of Our Molecules - a Computational Framework for Unified Germplasm Characterization and Inference"

3:01pm Kathy Munkvold, Corteva Agriscience "Building Successful Collaborations through Open Innovation"

3:16pm Mat Muller, Corteva Agriscience "Improving the Lives of Small-Holder Farmers through Genomic Innovation"

98


1:30pm - 3:40pm QTL Cloning - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Roberto Tuberosa, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy


1:35pm Jorge Dubcovsky, University of California "Map-Based Cloning of a QTL for Spikelet Number per Spike in Wheat"

1:55pm Rajeev K Varshney, ICRISAT "Novel Insights into Physiological and Molecular Mechanisms of Drought Tolerance in Chickpea"

2:15pm Harkmal Walia, University of Nebraska, Lincoln "Genetic and Molecular Analysis of Rice Grain Yield Under High Temperature Stress"

2:35pm Heng Ye, University of Missouri "Map-Based Cloning of a Major QTL Associated with Waterlogging Tolerance in Soybean Involved in Regulation of Root System Architecture"

2:55pm Pauline Duriez, UBC "A Receptor-like Kinase Enhances Sunflower Resistance to Orobanche cumana by Preventing Plant-Plant Interaction"

3:15pm Soodeh Tirnaz, University of Western Australia, Perth, WA "Identification of Candidate Resistance Genes Against Blackleg in Brassica napus"

1:30pm - 3:40pm Gramene: Unifying Comparative Genomics and Pathway Resources for Plant Communities - CALIFORNIA Organizers: Doreen Ware, USDA-ARS, Cold Spring Harbor Laboratory, Sushma Naithani, Oregon State University and Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory

1:30pm Doreen Ware, Cold Spring Harbor Laboratory "Introduction to Gramene Workshop"

1:45pm Nancy George, European Bioinformatics Institute (EMBL-EBI) "Single Cell RNA-Sequencing in Plants: EMBL-EBI's Resources for Data Submission, Archival and Visualization"

2:00pm Zhanguo Xin, USDA ARS "NGS-Enabled Fast Gene Discovery from Sorghum Pedigreed Mutant Library"

2:15pm Shujun Ou, Iowa State University "Effect of Sequence Depth and Length in Long-Read Assembly of the Maize Inbred NC358"

2:30pm Rebecca L. Seipelt-Thiemann, Middle Tennessee State University "Investigating the Maize Genome with Undergraduate Researchers"

2:45pm Liya Wang, Cold Spring Harbor Laboratory "Accessing the Maizecode Data from Gramene and Sciapps"

99


3:00pm Andrea Braeutigam, Bielefeld University

"Gene Regulatory Network Construction Based on Machine Learning Enables Phylogenetic Comparisons in the Monocots"

3:15pm Justin Preece, Dept. of Botany and Plant Pathology, Oregon State University "Plant Reactome 2020: A Plant Pathway Knowledgebase"


1:30pm - 3:40pm Oxford Nanopore - Closing the Gap in Plant and Animal Genomics with nanopore technology - SAN DIEGO Organizers: Kim Cowan, Oxford Nanopore Technologies Ltd and Iain MacLaren, Oxford Nanopore Technologies Ltd

1:30pm Iain MacLaren, Oxford Nanopore Technologies Ltd "Advancements in Nanopore Technology"

2:00pm Maximilian Schmidt, ANSES

“using the Ont Sequencing Technology for Generating Chromosome Scale Plant De Novo Genome Assemblies”

2:20pm Anna Cusco, Vetgenomics 2:35pm Harmeet Singh Chawla, Department of Plant Breeding, Justus Liebig

University 2:50pm Brad Abramson, J. Craig Venter Institute 3:05pm Loan Nguyen, Queensland Alliance for Agriculture and Food Innovation

- University of Queensland 3:25pm Iain MacLaren, Oxford Nanopore Technologies Ltd

"Closing Remarks"

1:30pm - 3:40pm Root Nodule Symbiosis: Genetics, Evolution, and Engineering for Future Crops - TERRACE ROOM - HANDLERY HOTEL Organizers: Shifeng Cheng, BGI-Genomics Douglas E. Soltis, University of Florida

1:30pm Daniel Conde, University of Florida "Chromatin Accessibility Characterization of the Gene Regulatory Network Controlling Nodulation Factors Response in Medicago Truncatula"

1:50pm Thomas Irving, University of Wisconsin-Madison "Insights & Engineering of Symbiotic Nitrogen Fixation in Poplar"

2:10pm Tatiana Vernie, LRSV "Evolution of Symbiotic Gene Regulatory Networks"

2:30pm Shifeng Cheng, Agricultural Genome Institute at Shenzhen, CAAS "Capturing the Conserved Cis-Regulatory Elements and Gene Expression Complexity of Root Nodule Symbiosis within the N-Fixing Clade"

2:50pm Rene Geurts, Wageningen University "Parasponia As a Comparative System to Identify Genetic Changes Causal to the Evolution of Root Nodule Symbiosis"

3:10pm Ryan A. Folk, Mississippi State University "Challenging Soil Environments and the Origins of Nitrogen-Fixing Symbioses"

100


1:30pm - 3:40pm Perennial Grasses - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Christian Tobias, USDA-ARS, Western Regional Research Center

1:30pm Nejc Stopnisek, Michigan State University "Prioritizing Core Microbiome Members on Switchgrass to Inform Assembly and Host-Microbe Interactions"

1:50pm Viviana Echenique, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) Universidad Nacional del Sur-CONICET and Dpto. Agronomía, Universidad Nacional del Sur (UNS)

"Novel Genomic Resources for the Polyploid Forage Grass Eragrostis Curvula"

2:10pm Jonathan Willis, USDA-Agriculture Research Service "Controlling Transgene Gene Flow via Pollen Biocontainment and Herbicide Mitigation in Panicum virgatum"

2:30pm Yiwei Jiang, Department of Agronomy, Purdue University "Genetic Control of Flowering Time and Plant Biomass Traits in Switchgrass"

2:50pm Serge Edme, USDA-ARS Wheat, Sorghum, and Forage Research Unit "Optimizing Selective Breeding in Switchgrass (Panicum virgatum) Combining Genetics and Genomics"

3:10pm Acer VanWallendael, Michigan State University "Large-Effect QTLs for Rust Fungus Resistance in Switchgrass are Effective in Northern, but NOT Southern Locations"

1:30pm - 3:40pm DoveTail Genomics - Advances in De Novo Genome Assembly with Dovetail Genomics – Methods, Applications, and Some Pretty Cool Science! - TOWN AND COUNTRY Organizer: Nicole Holder, Dovetail Genomics

1:30pm Beth Shapiro, University of California, Santa Cruz "An Omni-C Library Enables High Coverage of the Dodo Genome and Brings Us One Step Closer to Dodo De-Extinction"

2:00pm Peter J. Maughan, Brigham Young University "A Highly Contiguous Reference Genome for Cheatgrass (Bromus tectorum)"

2:30pm Oliver Ryder, San Diego Zoo Institute for Conservation Research "Opportunities and Obstacles in the Practical Application of Conservation Genomics"

3:00pm Mark Daly, Dovetail Genomics "New Applications from Dovetail Genomics"

101


1:30pm - 3:40pm Drone Data In The Plant Breeding Software: Integrating High Throughput Phenotyping Information To A Central Research IT System - Joint Presentation by HIPHEN-PLANT and DORIANE - EAST 2 Organizers: Tristan Duminil, Doriane and Romain Royer, Doriane

1:30pm Alexis Comar, HiPhen "Insights of Using Drones for Plant Breeding Departments"

2:10pm Tristan Duminil, Doriane SAS "Trial Setting up and Data Capture Preparation"

2:50pm Alexis Comar, HiPhen "From Flight Preparation and Trial Mapping to image Analysis and Index Models"

3:30pm Tristan Duminil, Doriane SAS "Drone Data Centralization and Analysis - Benefits of Integrating High Phenotyping Throughput with Genetical Data and Deep Multi-Platform Analysis"

1:30pm - 3:40pm Weedy and Invasive Plant Genomics - EAST 1 Organizers: Patrick Tranel, University of Illinois and C. Neal Stewart Jr., Department of Plant Sciences, University of Tennessee

1:30pm Johanne Brunet, USDA-ARS "Introgression of Cultivar Genes into Wild Carrot Populations"

1:50pm Stéphane Muños, Laboratoire des Interactions Plantes Micro-organismes (LIPM) - INRAE/CNRS/Université de Toulouse

"The Whole Genome Sequence of the Obligate Root Parasitic Plant Orobanche Cumana (sunflower broomrape)"

2:10pm Martin Laforest, Agriculture and Agrifood Canada "Canada Fleabane Genome Sequence"

2:30pm Jefferson F. Paril, The University of Melbourne "Genome-Wide Association and Genomic Prediction of Herbicide Resistance in Annual Ryegrass (Lolium rigidum) using Pool Sequencing Data"

2:50pm Christopher A. Saski, Clemson University "The eccDNA Replicon, Adaptive Potential, and Functional Genomics in Amaranthus palmeri"

3:10pm Satoshi Iwakami, Kyoto University "Role of CYP81A P450s in Metabolism-Based Cross-Resistance in Echinochloa phyllopogon"

102


1:30pm - 3:40pm Crop Genomics for Global Food Security - GOLDEN BALLROOM Organizers: Antonio Costa De Oliveira, and Henry T. Nguyen, University of Missouri & National Center for Soybean Biotechnology

1:30pm Revathi Ponnuswamy, Crop Improvement-Hybrid rice section ICAR - Indian Institute of Rice Research (IIRR)

"Identification and Mapping of Heterotic Loci (HLs) from Oryza Rufipogon to Enhance Yield Potential of Hybrid Rice Parental Lines"

1:50pm Yongfu Tao, The University of Queensland "Comparison of 16 Wild and Domesticated Sorghum Genomes Reveals Extensive Variation in the Sorghum Pan-Genome"

2:10pm Robert J. Henry, University of Queensland/QAAFI and Queensland Alliance for Agriculture and Food Innovation

"Capturing Cereal Biodiversity for Food Security" 2:30pm Manish Roorkiwal, ICRISAT

"Genomic Prediction to Accelerate the Rate of Genetic Gain in Chickpea for Providing Nutritional Food Security"

2:50pm Guangchao Sun, University of Nebraska-Lincoln and Center for Plant Science Innovation

"Genomic, Metabolic, and Transcriptomic Responses of the Extremophile Grass Paspalum Vaginatum to Nutrient Deficit Stress"

1:30pm - 3:40pm New England Biolabs: Enabling transformative crop science through innovative molecular biology - PACIFIC SALON 1 Organizer: Kari Goodwin, New England Biolabs, Inc.

1:30pm Sarah K. Bowman, Directed Genomics "A Highly Multiplexed, Targeted NGS Approach for High-Throughput and Cost-Effective Genotyping"

1:30pm Bjoern Textor, New England Biolabs GmbH "Automation of Nebnext Direct Genotyping Solution on the Biomek i7 Automated Workstation"

1:30pm Bart Brugmans, GenNovation "Evaluation of the Nebnext Direct Genotyping Solution for Molecular Breeding of Ornamentals"

1:30pm Deyra N. Rodriguez, New England Biolabs "Enhancing Transcript Detection across Species: Removing Abundant RNAs from Plants and Other Species of Interest."

1:30pm Karen R. McKay, New England Biolabs "Nebnext® Ultra™ II FS DNA: A Robust, DNA Library Preparation Method Compatible with Plant Samples"

103


1:30pm - 3:40pm International Phytomedomics and Nutriomics Consortium (ICPN) 2 - ROYAL PALM SALON 3-4 Chair: Chittaranjan Kole, ICAR-National Institute for Plant Biotechnology Co-Organizer: Haiyang Zhang, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, China

1:30pm Yong Pyo Lim, Chungnam National University "A Genome Wide Association Approach Combined with Quantitative Trait Loci Analysis Reveals the Genetic Architecture of Glucosinolate Biosynthesis in Brassica rapa L. Leaves"

1:48pm Umesh K. Reddy, West Virginia State University "Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon"

2:06pm Chang Liu, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences&Peking Union Medical College

"Progress and Applications of the 1000 Medicinal Plant Genomes Project (1KMPG)"

2:24pm Hongmei Miao, Henan Sesame Reserach Center, Henan Academy of Agricultural Sciences

"Genome Evolution and Regulation of Oil Biosynthesis of a Model Oilseed Crop Sesame"

2:42pm Mei Jiang, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences&Peking Union Medical College

"A Whole Genome Association Study in Salvia miltiorrhiza" 3:00pm Desalegn D. Serba, Kansas State University

"Towards Genomics-Enabled Breeding in Pearl Millet: a Climate Resilient and Nutrient Dense Cereal Crop"

3:18pm Amit Dhingra, Molecular Plant Sciences, Washington State University "Concomitant Phytonutrient and Transcriptome Analysis of mature Fruit and Leaf Tissues of Tomato grown Using Organic and conventional Fertilizer"

1:30pm - 3:40pm Perkin Elmer - Maximize Your Agricultural Genomics Workflows - ROYAL PALM SALON 5-6 Organizer: Andrea Feher, PerkinElmer

1:30pm Charlie Johnson, Texas A&M AgriLife: Genomics and Bioinformatic Service

"Maximize Your Agricultural Genomics Workflows"

1:50pm Noel O.I. Cogan, Agriculture Victoria, AgriBio, Centre for AgriBioscience

"Maximize Your Agricultural Genomics Workflows"

2:10pm Penny Riggs, Department of Animal Science, Texas A&M University "Maximize Your Agricultural Genomics Workflows"

104


1:30pm - 6:10pm IWGSC – Wheat Genome Manual and Functional Annotation - PACIFIC SALON 2 Organizers: Frederic Choulet, INRA GDEC and Kellye Eversole, IWGSC

1:30pm Alex Mahlandt, University of Maryland "Impact of Wheat Refseq v1.0: Translational Research to Increase Wheat Yield By Isolating Sink Controlling Genes"

1:50pm Yong Q. Gu, USDA ARS, Western Regional Research Center "Annotation of the Wheat Prolamins"

2:10pm Sandip Mallikarjun Kale, Leibniz Institute of Plant Genetics and Crop Plant Research

"Genebank Genomics: Paving Way to Identify Candidate Genes for Disease Resistance in Wheat"

2:30pm Frédéric Choulet, GDEC, INRA, UCA "Iwgsc Refseq Annotation v2.0"

2:50pm Shawn Quinn, Curio Genomics "Alignment, Analysis, and Visualization of Wheat NGS Samples in Curio"

3:10pm Anne-Francoise Adam-Blondon, URGI, INRA, Université Paris-Saclay "JBrowse & Apollo for Manual Annotation of Wheat"

3:30pm Xi Wang, BASF "Applying Network Biology and Deep Learning Approach for Large-Scale Characterization of Gene Function in Wheat"

3:50pm Marco Maccaferri, University of Bologna, Bologna "Durum Wheat Pan-Transcriptome As a Bridge to Unravel Tetraploid and Hexaploid Wheat Gene Function and Evolution"

4:10pm Tanya Z. Berardini, Phoenix Bioinformatics "Applying Machine Learning to Plant Literature: Augmenting Human Curation"

4:30pm Kellye Eversole, IWGSC "Iwgsc Phase II Activities: Moving from Structural to Functional Wheat Genomics"

4:50pm Song Weining, Northwest A&F University "IWGSC Proteomics Project"

2:00pm - 3:00pm Coffee Break - GRAND EXHIBIT HALL

4:00pm - 5:00pm Brachypodium Community Organizational Meeting - POOLVIEW - HANDLERY Organizer: John Vogel, DOE Joint Genome Institute

105


4:00pm - 6:10pm Simulation of Genetic and Genomic Systems - ROYAL PALM SALON 1-2 Organizers: Justin N Vaughn, USDA-ARS/University of Georgia and Robert Christopher Gaynor, University of Edinburgh, The Roslin Institute

4:00pm Vivi N. Arief, The University of Queensland "QuLinePlus: A Versatile Module of QU-GENE for Plant Breeding Simulation"

4:20pm Justin N Vaughn, USDA-ARS/University of Georgia "Simulation using Crossword Defines Gene-Discovery Potential of QTL-Seq"

4:40pm Robert Christopher Gaynor, University of Edinburgh, The Roslin Institute "Alphasimr: An R-Package for Breeding Program Simulations"

5:00pm Yanlin Liao, Wageningen University and Research "GenoSim: A User-Friendly Simulation Tool for Sequence Reads and SNP Array Genotyping Data in Polyploid Species"

5:15pm Samuel B Fernandes, University of Illinois at Urbana-Champaign "simplePHENOTYPES: SIMulation of Pleiotropic, Linked and Epistatic PHENOTYPES in R"

4:00pm - 6:10pm Components of Apomixis - PACIFIC SALON 3 Organizer: Emidio Albertini, University of Perugia

4:00pm Emidio Albertini, University of Perugia "Introduction to the New Era of Clonal Seeds Production"

4:20pm Kejian Wang, China National Rice Research Institute "Synthetic Apomixis in Hybrid Rice"

4:40pm Imtiyaz Khanday, University of California-Davis "Synthetic Apomixis for Hybrid Crop Propagation"

5:00pm John G. Carman, Utah State University "Meiosis to Apomeiosis Switching Is Metabolically Inducible in Angiosperms"

5:20pm Bharti Parihar, California State University East Bay "Evolution of Ectopic Plantlet Formation in Kalanchoe"

5:40pm Viviana Echenique, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS) Universidad Nacional del Sur-CONICET and Dpto. Agronomía, Universidad Nacional del Sur (UNS)

"Water Stress, Apomixis and Gene Expression in the Diplosporous Grass Eragrostis curvula"

106


4:00pm - 6:10pm African Orphan Crops - EAST 2 Organizer: Allen Van Deynze, University of California


4:05pm Rita H. Mumm, University of Illinois and African Plant Breeding Academy

"Aiming for Excellence in Training and Sustaining African Plant Breeders"

4:25pm Prasad Hendre, WORLD AGROFORESTRY (ICRAF) "Development of a Genomics-Based Breeding and Improvement Programme for Moringa Oleifera in Kenya"

4:45pm Damaris Achieng Odeny, The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)

"Draft Genome Sequence of the African Eggplant" 5:05pm Xin Liu, Beijing Genomics Institute-Shenzhen

"Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis) Provide Insight into Starch Metabolism"

5:25pm Bernice Waweru, KALRO "African-Led Genome Sequencing of Lablab and African Yam Bean Orphan Crops Genomes to Unveil Pathways Underlying Key Traits"

5:45pm Erick Mikwa, ICRISAT "Re-Sequencing of Eleusine species"

4:00pm - 6:10pm Yam Genomics - GARDEN 1 - HANDLERY HOTEL Organizer: Ranjana Bhattacharjee,

4:00pm Graham Thiele, CGIAR Research Program on Roots, Tubers and Bananas (RTB), led by CIP

"Varietal Change and Consumer Preferences in Roots, Tubers and Bananas: Yams in Côte D'ivoire"

4:15pm Asrat Asfaw Amele, IITA "Phenotypic and Genetic Variability in a Panel of White Guniea Yam (Dioscorea rotundata) Genotypes Based on Joint Analysis of Morphological and Molecular Diversity"

4:30pm Patrick Olusanmi Adebola, IITA Ibadan Nigeria "Plant Sex Prediction in White Guinea Yam (Dioscorea rotundata)"

4:45pm Morufat O. Balogun, International Institute of Tropical Agriculture /University of Ibadan

"Genetic Fidelity of Yam Planting Materials Produced with Novel High Ratio Propagation Technologies Based on Morphological, Ploidy and SSR Markers "

5:00pm Ranjana Bhattacharjee, International Institute of Tropical Agriculture "Effect of Ploidy Levels on Flowering Behavior in Yams (Dioscoreaspp.) "

107


5:15pm Jessica B. Lyons, University of California, Berkeley "Development of Genomic and Genetic Resources for Water Yam, Dioscorea Alata L."

5:30pm Angelot Paterne AGRE, International Institute of Tropical Agriculture (IITA/IBADAN)

"Genome-Wide Association Mapping of Tuber Flesh Oxidation and Dry Matter Content in Water Yam (Dioscorea alata) Panel"

5:45pm Norbert Godonou Maroya, International Institute of Tropical Agriculture (IITA) "Effect of Vine Position of Aeroponics Mother-Plant on the Performance of Seed Yam Production "

6:00pm Venkatramana Pegadaraju, Agribody Technologies "Expanding Global Food Supply By Improving Shelf Life of Perishable Produce Using Patented Gene Technology"

4:00pm - 6:10pm Cannabis Diversity: Genomics and Phenomics - TOWN AND COUNTRY Organizer: C J Schwartz, Sunrise Genetics

4:00pm Marie Turner, Sunrise Genetics Inc. "Sources of Variation: Steps Towards Understanding GxE and Development of Important Hemp Chemotypes over Time"

4:20pm Lawrence B. Smart, Horticulture Section, School of Integrative Plant Science, Cornell University

"Genotypic and Phenotypic Evaluation of Hemp Cultivars for Cannabinoid Production in New York"

4:40pm Brian Campbell, Phylos Bioscience "Trait Plasticity and Genetic Diversity in Cannabis"

5:00pm Todd Michael, J. Craig Venter Institute "Sorting Assemblies"

5:20pm Sophie Watts, Dalhousie University "Cannabis’ indica/sativa Dilemma: Clarity from Genomics and Chemistry"

5:40pm Oori Weisshaus, NRGene "cannabis Genome Arrangement - Comparison of Multiple Heterozygous Genomes"

4:00pm - 6:10pm Host-Microbe Interactions - TERRACE ROOM - HANDLERY HOTEL Organizer: Christopher Barker, Global Institure for Food Security (GIFS)

4:00pm David A. Baltrus, School of Plant Sciences, University of Arizona "Are All Pseudomonas Syringae infections the Same? What Plant Responses Can Tell Us about Taxonomy and Diversity within a Single Microbial 'species'."

4:30pm Daniel Kliebenstien, University of California, Davis "Genome Wide Association Mapping of Co-Transcriptome Variation in the Interaction of Botrytis cinerea with Eudicots"

5:00pm Anatoliy M Trokhymchuk, Prairie Diagnostic Services "Rapid Metagenomics for Livestock Antimicrobial Use Decisions"

108


4:00pm - 6:10pm Gene Expression Analysis - PACIFIC SALON 1 Organizers: David W. Galbraith, BIO5 Institute & School of Plant Sciences, University of Arizona and Gregory D. May, Pioneer HiBred

4:00pm Michael K. Deyholos, University of British Columbia "Insights into Plant Transcriptomes from the 1KP Project"

4:20pm Donat Wulf, Bielefeld University "Machine Learning Based Comparative Analysis of Gene Regulatory Networks in Monocots"

4:40pm Shivraj Braich, Agriculture Victoria Research "Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis"

5:00pm Amanda P Cavanagh, University of Illinois at Urbana-Champaign "Lowering the Cost of Photorespiration Using Synthetic Biology"

5:20pm Benjamin J. Cole, DOE-Joint Genome Institute "Integrative Analysis of Plant Single-Cell Transcriptomes"

5:40pm Jason Kim, 10x genomics "Analysis Considerations for Handling Single Cell Transcriptomic Data"

4:00pm - 6:10pm Animal Epigenetics - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Hasan Khatib, University of Wisconsin Madison

4:00pm Jessica R. Powell, The Roslin Institute "Profiling the Immune Epigenome across Global Cattle Breeds"

4:15pm Cong-jun Li, ARS, USDA "Systematic Discovery and Characterization of Chromatin States and Butyrate-Induced Variations for Cattle Genome Functional Annotation"

4:30pm Ryan J. Corbett, Genetics & Genome Sciences Graduate Program, Michigan State University

"Developmental and Allele-Specific Methylation Patterns in Fetal Liver of Pigs Derived from White Composite x Meishan Reciprocal Crosses"

4:45pm Kimberly M. Davenport, University of Idaho "Hitting the Mark: Characterizing Four Histone Modifications in Ovine Liver and Spleen"

5:00pm Jessica L. Petersen, University of Nebraska-Lincoln "Discovery of Regions of Genome Regulation in the Horse"

5:15pm Katy Kesler, Michigan State University and CentralStar Cooperative "Identification of Epigenetic Markers Predictive of Late Embryonic Mortality in Bovine Milk"

5:30pm Christopher M. Ashwell, North Carolina State University "Diet Impacts the Avian Epigenome for Generations"

5:45pm Brittni P. Littlejohn, Texas A&M AgriLife Research & Extension Center, Texas A&M University

"Prenatal Transportation Stress Alters Genome-Wide Methylation of DNA in Leukocytes from Brahman Bull Calves"

109


4:00pm - 6:10pm Galaxy: An Open Platform for Data Analysis and Integration - CALIFORNIA Organizer: Dave Clements, Johns Hopkins UniversityCo-Organizer: Mo Heydarian, Johns Hopkins University

4:00pm Dave Clements, Johns Hopkins University "Introduction to Galaxy and the Galaxy Ecosystem"

4:20pm Star Yanxin Gao, Cornell University "Galaxy for Excellence in Breeding"

4:50pm Dave Clements, Johns Hopkins University "Galaxy Demo: Genomic Selection and Genome Wide Association Study (GWAS) Analysis with Excellence in Breeding Tools"

4:00pm - 6:10pm Root Genomics - PACIFIC SALON 6-7 (2ND FLOOR) Organizer: Antonio Costa De Oliveira, Universidade Federal de Pelotas

4:00pm Samir Alahmad, Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Australia

"A Major Root Angle QTL in Durum Wheat Improves Yield in Drought and Crown Rot Environments"

4:20pm Gilad Gabay, University of California Davis "Characterization of a 1RS Chromosome with a 1BS Introgression Associated with Seminal Root Length and Root Development in Wheat"

4:40pm Roberto Tuberosa, University of Bologna, Bologna, Italy "GWAS Reveals the QTLome Complexity Governing Different Root Types in Adult Durum Wheat Plants"

5:00pm Philip N. Benfey, Duke University and Howard Hughes Medical Institute "Monitoring Root System Dynamics"

5:20pm Jack Christopher, The University of Queensland - Leslie Research Facility "Genomics of Root and Stay-Green Traits to Improve Wheat Adaptation to Late Season Drought"

5:40pm Jinrong Wan, University of Missouri "Novel Genetic Resources and Genes for Root Parasitic Nematodes"

4:00pm - 6:10pm Illumina - Translating Nature’s Secrets – Using Genomics to Increase Food Security and Sustainability - GOLDEN WEST Organizer: William O'Bannon, Illumina, Inc.

4:00pm Mark Blaxter, Wellcome Sanger Institute "Darwin Tree of Life Project"

4:30pm Bob Wayne, UCLA - Department of Ecology & Evolutionary Biology "California Conservation Genomics Program"

5:30pm Matt Hayden, La Trobe University and Agriculture Victoria Scientist "Multi-Species Iselect XT Bead Chip Array Delivers Accurate Imputation to Wheat Exome and Barley Whole Genome Density"

110


4:00pm - 6:10pm L7 Informatics - "Advancing the Game: Next-Generation Seed Company Revolutionizing Plant Breeding Readies for Expansion with Streamlined and Optimized Operations" - EAST 1 Organizer: Jessica Tobey, L7 Informatics

4:00pm Robert Zeigler, Ph.D., L7 Informatics Inc. "Robert Zeilger"

4:30pm Christopher Bagley, Inari Agriculture "Chris Bagley"

4:00pm - 6:10pm Avian Genomics - Going Wild! - ROYAL PALM SALON 5-6 Organizer: Robert H. S. Kraus, Max Planck Institute of Animal Behavior

4:00pm Alain Vignal, GenPhySE, INRAE, ENVT, ENSAT "Avian Genomics in Animal Breeding: do we still need model organisms?"

4:20pm Bernice Sepers, The Netherlands Institute of Ecology (NIOO-KNAW) and Wageningen University & Research (WUR)

"Avian Ecological Epigenetics: Pitfalls and Promises" 4:40pm Veronika N. Laine, The Netherlands Institute of Ecology (NIOO)

"The Hidden Information of Unmapped Reads in a Wild Songbird" 5:00pm Sadye Paez, The Rockefeller University

"The Role of Genomics in Conserving Biodiversity during the Sixth Mass Extinction"

5:20pm Paul B. Frandsen, Brigham Young University "Conservation Genomics of the Critically Endangered Red Siskin (Spinus cucullata)"

5:40pm Philip Lavretsky, University of Texas at El Paso "Landscape Level Genetic Consequences of Game-Farm Mallard Releases in North America: Domestic Mallards Gone-Wild!"

111

Wednesday - January 15, 2020

7:00am - 8:00am Continental Breakfast - GARDEN BALLROOM





8:00am - 8:45am Plenary Lecture: Anne Stone - TOWN & COUNTRY BALLROOM Chair: Catherine Feuillet, Inari Agriculture

8:00am Anne C. Stone, School of Human Evolution and Social Change, Arizona State University

"Using Ancient DNA to understand the Evolutionary History of M. tuberculosis in Humans and other Animals"

8:45am - 9:30am Plenary Lecture: Raphael Mercier - TOWN & COUNTRY BALLROOM Chair: Catherine Feuillet, Inari Agriculture

8:45am Raphael Mercier, Max Planck Institute for Plant Breeding Research "Tinkering with Meiosis: To Mix, or Not to Mix"

9:30am - 10:30am Coffee Break - ATLAS FOYER

10:30am - 12:40pm Plant long non-coding RNAs - PACIFIC SALON 2 Organizer: Andrew Nelson, Boyce Thompson Institute

10:30am Jiri Fajkus, Institute of Biophysics, CAS, v.v.i. "Characterisation of Plant Telomerase RNAs"

10:45am Marianne Kramer, University of Pennsylvania "Elucidating the Function of a Novel Long Non-Coding RNA during Arabidopsis development"

11:00am Rebecca Murphy, Centenary College of Louisiana "MINE the Gap: LncRNA Identification as a Bridge between Computational and Bench Approaches in the Undergraduate Classroom"

11:15am Sateesh Peri, Genetics Graduate Interdisciplinary Group, University of Arizona "Comparison of lncRNAs identified through Nanopore and short read RNA-sequencing strategies"

11:30am Larry Wu, Michigan State University "The Landscape of Coding and Non-Coding RNAs Defined by Enhanced Super-Resolution Ribosome Profiling"

11:45am Eve Syrkin Wurtele, Iowa State University "Targets of Opportunity: The Birth of Orphan Genes, Exemplified in Yeast, Arabidopsis, Maize and Humans"

112


10:30am - 12:40pm Cassava Genomics - PACIFIC SALON 6-7 (2ND FLOOR) Organizers: Steve Rounsley, Genus plc and Chiedozie Egesi, National Root Crops Research Institute (NRCRI), Umudike

10:30am Linda Hanley-Bowdoin, North Carolina State University "Mobilization of Host DNA Sequences during Cassava Mosaic Disease"

10:50am Ben N. Mansfeld, Donald Danforth Plant Science Center "Resolving the Cassava Haploid Genomes"

11:10am Jason Gardiner, University of California, Los Angeles "Building Targeted DNA Methylation Tools for Cassava"

11:30am Jessica B. Lyons, University of California, Berkeley "Engineering Cyanide-Free Cassava using CRISPR-Cas9"

11:50am Guillaume J. Bauchet, Boyce Thompson Institute "population Structure and Linkage Disequilibrium in Brazilian Cassava: Insights into Crop Diversification and Domestication."

12:10pm Alfred Ozimati, NaCRRI, Uganda "Genetic Gain for Cassava Brown Streak Disease in White and Yellow Fleshed Cassava Breeding Populations in East Africa"

10:30am - 12:40pm ChIP-seq: Challenges and Ideas - PACIFIC SALON 4-5 (2ND FLOOR) Organizer: Claire P. Prowse-Wilkins, Agriculture Victoria

10:30am Claire P. Prowse-Wilkins, The University of Melbourne "Searching for Causal Variants in Functional Regions of the Bovine Genome"

11:00am Colin Kern, Department of Animal Science, University of California "Exploring the Effect of Signal-to-Noise Ratio on ChIP-Seq Analysis and the Ability of Downsampling to Improve Comparisons between Samples"

11:30am Yahui Gao, Animal Genomics and Improvement Laboratory, USDA-ARS; The University of Maryland

"Integrative Analyses of Multi Omics Data accelerate the understanding of the Genetic Basis underlying in vivo Rumen Development in Dairy Cattle"

113


10:30am - 12:40pm Animal Genomics and Adaptation to Climate Change - ROYAL PALM SALON 1-2 Organizer: Susan J. Lamont, Iowa State University

10:30am Gary A. Rohrer, USDA, ARS, U.S. MEAT ANIMAL RESEARCH CENTER

"Genetic Factors Associated with Changes in Feeding Behavior Due to Elevated Temperature"

11:00am Jin-Hyoung Kim, Korea Polar Research Institute "Understanding of Genomic Properties and Development of Useful Genomic Resources from Polar Organisms: Antarctic Blackfin Icefish Genome Reveals Adaptations to Extreme Environments"

11:30am John C. Hsieh, Department of Animal Science, Iowa State University "Microbiome of Heat-Stressed Layer Hens"

11:50am M. Walugembe, Department of Animal Science, Iowa State University "Detection of Selection Signatures among Chicken Population under Different Climatic Conditions"

12:10pm Androniki Psifidi, Royal Veterinary College, University of London "Poultry Genomic Projects in Low and Middle Income Countries"

10:30am - 12:40pm UCSC Genome Browser - tools and visualizations for all organisms - EAST 1 Organizers: Brian Lee, Univ. Calif. Santa Cruz and Robert Kuhn, UCSC Genome Browser

10:30am Robert Kuhn, UCSC Genome Browser "UCSC Genome Browser History and Overview"

11:00am Brian Lee, Univ. Calif. Santa Cruz "Assembly Hubs and New API Data Access"

10:30am - 12:40pm Digital Tools and Resources Session 4 - CALIFORNIA Organizers: Brian Smith-White, and Monica C. Munoz-Torres, Translational and Integrative Sciences Lab, Oregon State University

10:30am Bhavya Papudeshi, Indiana University "Mining Microbial Genomes from Datasets on the Sequence Read Archive"

10:50am Deborah A. Triant, University of Missouri "FAANGMine: Genomic Data Mining Tools for Domesticated Animal Species"

11:10am Xinbin Dai, Noble Research Institute "LegumeIP V3: Empowering Comparative Genomics, Transcriptomics, and Phylogenomics in Legumes"

11:30am Naveen Duhan, Utah State University "CitSATdb: Genome-Wide Simple Sequence Repeats (SSR) Marker Database of Citrus Species for Germplasm Characterization and Crop Improvement"

11:50am Ben Busby, NCBI/NLM/NIH "Federated Cloud Access to Datasets through Indexing and/or Graphs!"

114


10:30am - 12:40pm Flax Genomics – East 2 Organizers: Bourlaye Fofana, Agriculture and Agri-Food Canada and Braulio J. Soto-Cerda, Centro de Genómica Nutricional Agroacuícola (CGNA)

10:30am Michael K. Deyholos, University of British Columbia "Comparative Transcriptomics of Root Responses to Pathogenic (Fusarium oxysporum f. sp. lini) and Non-Pathogenic (Rhizoglomus irregulare) Fungi"

10:50am Christopher Cullis, Case Western Reserve University "Can Flax 'edit' its Genome"

11:10am Manisha Sharma, ICAR-National Institute of Plant Biotechnology "Gene Expression Analysis Associated with Salinity Stress in Flax/Linseed (Linum usitatissimum)"

11:30am Bradley J. Till, Centro de Genómica Nutricional Agroacuícola (CGNA) "Genomic Improvement of Flax using Natural Variation and Induced Mutations"

11:50am Sylvie Cloutier, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada

"Insights into Genetic Structure and Genomic Prediction of Powdery Mildew Resistance in Flax (Linum usitatissimum L.)"

10:30am - 12:40pm Rhinoceros Genomics Studies: tools for conservation - ROYAL PALM SALON 5-6 Organizer: Oliver Ryder, San Diego Zoo Institute for Conservation Research

10:30am Alfred L. Roca, University of Illinois at Urbana-Champaign "Genetic Analysis and Marker Development in the Sumatran Rhinoceros (Dicerorhinus sumatrensis)"

10:50am Love Dalén, Swedish Museum of Natural History "Conservation Genomics of the Sumatran Rhinoceros"

11:10am Aryn Wilder, San Diego Zoo Institute for Conservation Research "Deleterious Genetic Variation and the Prospects for Genetic Restoration of White Rhinos"

11:30am Iñigo Valiente-Alandi, San Diego Zoo Institute for Conservation Research "Omics Characterization of Northern White Rhinoceros Induced Pluripotent Stem Cells"

115


10:30am - 12:40pm Exploring Phytobiomes - ROYAL PALM SALON 3-4 Organizers: Isabelle Caugant, International Phytobiomes Alliance, Kellye Eversole, International Phytobiomes Alliance and Jan E. Leach, Colorado State University

10:30am Kellye Eversole, International Phytobiomes Alliance "Phytobiomes Research for Enhancing the Sustainable Production of Food, Feed, and Fiber"

10:50am John Fellers, USDA ARS "Wheat Virus Identification using Oxford Nanopore Technology"

11:10am Andrea Marino, Advanced Biological Marketing "Trichoderma-Derived Seed Treatments Stabilize Yields and Provide Drought Resilience to Zea mays by Modulating Host Gene Expression during Periods of Osmotic Stress."

11:30am Yiheng Hu, The Australian National University "Pathogen Detection and the Role of Microbial Communities in the Phyllosphere during Fungal Infection of Wheat"

11:50am Betsy Alford, University of California-Davis "Variability and Plasticity of the Wild Chickpea Microbiome"

12:10pm Imtiaz Ahmad, Department of Entomology, Pennsylvania State University "Mighty Microbes: The Tri-Trophic Interactions of Endophytic Metarhizium in Maize"

10:30am - 12:40pm IRIC: Rice Informatics for the Global Community - PACIFIC SALON 1 Organizer: Kenneth L. McNally, International Rice Research Institute

10:30am Rod Wing, Arizona Genomics Institute, University of Arizona "The International Oryza Map Alignment Project (IOMAP) from a Platinum Reference Genome Sequence (PSRefSeq) Perspective"

10:50am Michael D. Purugganan, New York University "A Fitness Consequence Map for the Rice Genome"

11:10am Manuel Ruiz, CIRAD, UMR AGAP "South Green Resources to Manage Rice Big Genomics Data"

11:30am Laurel Cooper, Dept. of Botany and Plant Pathology, Oregon State University "Planteome: Ontologies and Resources for Integrative Plant Genomics"

11:50am Update on IRIC and SNP-Seek

12:10pm Community Forum and Discussion with Focus on SNP-Seek Sustainability

116


10:30am - 12:40pm Plant Disease Resistance - PACIFIC SALON 3 Organizers: Zhanao Deng, University of Florida and Awais Khan, Plant Pathology and Plant-Microbe Biology, Cornell University


10:32am Yulin Jia, USDA-ARS "Co-Evolutionary Mechanisms of the Oryza sativa and Magnaporthe oryzae Pathosystem"

10:52am Nidhi Rawat, University of Maryland "Mechanistic Insights into the Broad-Spectrum Resistance of a Wheat Pore-Forming Toxin-like Gene"

11:12am Samuel F. Hutton, University of Florida, GCREC "Characterization and Mapping of Resistance to Target Spot (Corynespora cassiicola) in Tomato"

11:32am Dustin G. Wilkerson, Horticulture Section, School of Integrative Plant Science, Cornell University

"Salix purpurea eQTL for Response to Infection by Willow Leaf Rust, Melampsora americana"

11:52am Ina Schlathoelter, Breeding Research, Research Division Plant Breeding, Agroscope and Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich

"Cisgenesis As Tool to Improve Disease Resistance in Apple - from the Lab to the Field"

12:12pm Zhonglin Mou, University of Florida "The Function of Extracellular Pyridine Nucleotides and their Receptors in Plant Immunity"

12:30pm - 1:30pm Lunch – LION COURT & ROYAL PALM COURT

1:30pm - 3:40pm Farmed Insects to Feed Future Populations - ROYAL PALM SALON 3-4 Organizers: Brenda Oppert, USDA ARS CGAHR and Aaron T. Dossey, All Things Bugs LLC

1:30pm Aaron T. Dossey, All Things Bugs LLC "Workshop Introduction"

1:40pm Guillem Ylla, Harvard University "Genome Assembly and Annotation of the Cricket Gryllus Bimaculatus"

2:04pm Brenda Oppert, USDA ARS CGAHR "Reference Genomes for Two Cricket Species"

2:28pm Fu-Chyun Chu, All Things Bugs LLC "Developing Insects for Food, Feed and Bioproduction: White-Eye Marker for CRISPR/Cas9 in Crickets and Mealworms"

2:52pm Arpita Kulkarni, Harvard University "Techniques for Quantitative and Functional Genetic Analyses in the Cricket Gryllus bimaculatus"

117


1:30pm - 3:40pm Honeybee Genomics - PACIFIC SALON 4-5 (2ND FLOOR) Organizers: Sonia Eynard, GenPhySe, INRAE, ENVT, ENSAT and Alain Vignal, GenPhySE, INRAE, ENVT, ENSAT

1:30pm Alain Vignal, GenPhySE, INRAE, ENVT, ENSAT "European Honeybee Subspecies Genomes at the Individual and Population Levels"

1:50pm Gertje Petersen, AbacusBio "16andBee - Using Genomics to Unravel Unknown Family Relationships in Honeybees"

2:10pm Brock Harpur, Purdue University "Reproductive Variation and Admixture in Honeybee Populations of the United States"

2:30pm Maeva Angelique Techer, Okinawa Institute of Science and Technology Graduate University

"Facing the War between Honey Bee and Mites: Genomic Insights into Varroa Global Success"

2:50pm Perot Saelao, USDA-ARS Honey Bee Breeding, Genetics, and Physiology lab and USDA-ARS

"Genome-Wide Patterns of Genetic Differentiation of U.S. Commercial Honey Bee Stocks"

3:10pm Sonia Eynard, GenPhySe, INRAE, ENVT, ENSAT "Statistical Imputation of Queen Genotype from Pool Sequencing of Workers"

1:30pm - 3:40pm Duckweed Research and Applications - EAST 2 Organizers: Todd Michael, J. Craig Venter Institute and Eric Lam, Department of Plant Biology, Rutgers, the State University of New Jersey

1:30pm Buntora Pasaribu, Department of Plant Biology, Rutgers, the State University of New Jersey

"The Secret of Duckweed Survival: Molecular Characterization of Turion Formation in Spirodela polyrhiza"

1:50pm Shifra Ben-Dor, Weizmann Institute of Science "A Gene-Centric View of the Genomes of Lemnaceae"

2:10pm Erin Baggs, Department of Plant and Microbial Biology UC Berkeley "Developing Duckweed as a Model System to Study Plant-Pathogen Interactions"

2:30pm Uwe Heinig, Weizmann Institute of Science "The Metabolome of the Duckweed Family – Metabolic Diversity and Biosynthetic Pathway Discovery"

118


1:30pm - 3:40pm Genomics of Crop Ecosystem Services - ROYAL PALM SALON 1-2 Organizer: Andrew H. Paterson, Plant Genome Mapping Laboratory, University of Georgia

1:30pm Tara Maireid Conway, Plant Genome Mapping Laboratory, UGA "Towards a Viable Perennial Grain Sorghum through Integrated Genetic and Economic Analysis"

1:50pm Jared Crain, Kansas State University "Applied Genomics to Improve IWG Breeding Efficiency"

2:10pm Andy Raduski, University of Minnesota "Silphium Population Genomics: Progress and Applications to Breeding Programs"

2:30pm Matthew Rubin, Donald Danforth Plant Science Center "High Throughput Phenotyping and Population Genomics of Lupinus polypyllus"

1:30pm - 3:40pm Sweetpotato Genomics - ROYAL PALM SALON 5-6 Organizers: Dorcus C. Gemenet, International Potato Center (CIP) and Craig Yencho, North Carolina State University

1:30pm Welcome Remarks

1:35pm Zhangjun Fei, Boyce Thompson Institute, Cornell University "Toward a Hexaploid Sweetpotato Pan-Genome"

1:55pm Marcelo Mollinari, North Carolina State University "Characterization of Sweetpotato Inheritance using Ultradense Multilocus Genetic Map"

2:10pm G. Craig Yencho, North Carolina State University (NCSU) "Identification of QTL for Storage Root α-and β-Amylase Activity in Sweetpotato at Harvest and during Post-Harvest Storage"

2:25pm Phillip A. Wadl, USDA, ARS, U.S. Vegetable Laboratory "Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collection"

2:40pm Dorcus C. Gemenet, International Potato Center (CIP) "Breeding 3.0 in Sweetpotato: Advances Towards Genome-Enabled Breeding in Sub-Saharan Africa"


119


1:30pm - 3:40pm Linkage and Deletion Mapping - EAST 1 Organizer: Charles F. Crane, USDA-ARS and Department of Botany and Plant Pathology, Purdue University

1:30pm Beth Rowan, University of California, Davis "High-Density Genetic Linkage Maps: Methods and Applications"

1:50pm Kyle Fletcher, The Genome Center, University of California "Assembly-Free, High-Density Linkage Map Construction from Whole Genome Sequencing Data"

2:10pm Amanda M. Hulse-Kemp, USDA, North Carolina State University "Needs for Future Genetic Mapping Analyses Learned after Five Years of the CottonSNP63K Array"

2:30pm Yanlin Liao, Wageningen University and Research "Using Probabilistic Genotypes in Linkage Analysis of Polyploids"

2:50pm Joyce Njuguna, Dept of Crop Sciences, University of Illinois "Bayesian Genotype Calling in Polyploids, and a Novel Statistic to Infer Marker Quality from Read Depth Distribution I"

3:00pm Wittney D. Mays, University of Illinois, Dept of Crop Sciences "Bayesian Genotype Calling in Polyploids, and a Novel Statistic to Infer Marker Quality from Read Depth Distribution II"

3:10pm Charles F. Crane, USDA-ARS, Purdue University "Holistic Genotyping of Amplicon Panels with Spades and Blastn"

1:30pm - 3:40pm Biotech 101 – a.k.a. Navigating the U.S. Regulatory System for Products of Biotechnology - PACIFIC SALON 3 Organizer: Traci Kantarski, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Biotechnology Regulatory Services

1:30pm Neil Hoffman, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Biotechnology Regulatory Services

"Neil Hoffman: USDA" 1:50pm Mike Mendelsohn, U.S. Environmental Protection Agency

"Mike Mendelsohn: EPA" 2:10pm Patrick Cournoyer, U.S. Food and Drug Administration

"FDA Oversight of Food from New Plant Varieties"

7:00pm - 11:59pm Closing Banquet Dinner - GRAND EXHIBIT HALL

120

Corporate Sponsors

Thanks to our Corporate Sponsors for their support of the PAG XXVIII Conference:

Arbor Biosciences Mobile App AUM LifeTech Portfolio Bags / Mobile App Bayer CropScience Coffee Break Sponsor Corteva Agriscience Mobile App Limagrain Mobile Device Charging Stations

Oxford Nanopore Technologies Hospitality Event Thermo Fisher Scientific Aisle Signs & Carpet Logos

Syngenta Wifi Service / Computer Room

Future Meeting Dates

PAG XXIX - January 9-13, 2021 - Town & Country Hotel San Diego, CA

PAG XXX - January 8-12, 2022 - Town & Country Hotel

San Diego, CA PAG XXX1 - January 14-18, 2023 - Town & Country Hotel

San Diego, CA 121

RAMP 5DN.

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LGC, BiosearchTechnologies

SpringerNature

RAPiDGenomics,

LLC

Rijk Zwaan

Synchron

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B.V.WPS

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PersephoneSoftware,

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UgenTec, Inc. IntactGenomics

VHL Genetics

Hudson RiverBiotechnology Golden Helix

AgriPlexGenomics

PSI (PhotonSystems

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PhoenixBioinformatics

PerkinElmer Psomagen,Inc.

ArborBiosciences

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AUMLifeTech,

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Universityof Minnesota

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New EnglandBiolabs, Inc.

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ZymoResearch

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MettlerToledoRainin

L7Informatics

McDonnellGenome

Institute atWashingtonUniversity

AGDIA, INC.

NovogeneCorporation,

Inc.

Syngenta

BioChambersIncorporated

BGI Americas

KeyGene

DovetailGenomics

DOE-NSF-USDAFunding

Information

DOE SystemsBiology

Knowledgebase(Kbase)

GeneSeek

3CRBioscience CyVerse

AuroraBiomed

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OxfordNanopore

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TwistBioscience

PlatformGenetics Inc

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NorgenBiotekCorp

MatMa Corp MiltenyiBiotec Inc.

UniversalSequencingTechnology

MPBiomedicals

ArimaGenomics

PhytoTechLabs Inc. BEX Co., Ltd.

GenevaScientific

Kyazma B.V.

HamiltonCompany

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BeckmanCoulter Life

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BayerCropScienceGencove

Kazusa DNAResearchInstitute

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GrandomicsBiosciences

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AmericanSociety of

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AgilentTechnologies

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20'

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On Hold

On Hold

Plant & Animal Genome ConferenceJanuary 12-14, 2020Town & Country Resort & Convention Center - Grand Exhibit Hall Plotted: Nov 19, 2019

By: MCDERD

File: pgi-2001-towcou.dwg

RESPONSIBILITY OF THE EXHIBITOR TO PHYSICALLY INSPECT THE FACILITYTO VERIFY ALL DIMENSIONS AND LOCATIONS.

THE CONSTRUCTION OR USAGE OF AN EXHIBIT, IT IS THE SOLE ARCHITECTURAL COMPONENTS OF THE FACILITY IS A CONSIDERATION INPLAN. IF THE LOCATION OF BUILDING COLUMNS, UTILITIES, OR OTHEREITHER EXPRESSED OR IMPLIED, ARE MADE WITH RESPECT TO THIS FLOORINFORMATION CONTAINED ON THIS FLOOR PLAN. HOWEVER, NO WARRANTIES,EVERY EFFORT HAS BEEN MADE TO INSURE THE ACCURACY OF ALL

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Town & Country Resort & Convention CenterLower Exhibit Hall

San Diego, CA

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Documents

ProgramBook workFinalScientificProgram RC111 2019 12 21 12 ... · "Translational Genomics of Forage Legumes to Advance Molecular Breeding of Seed Traits in Cover Crop Legumes" 9:40am