Volume 3, Issue 2 April 2011

Dave’s Perspective 1

Last Chance Chips 3

DM Development 4

New WEB Resource 6

Breeders Toolbox 7

Calendar 10

Inside this issue:

SolCAP

Solanaceae Coordinated

Agricultural Project

Project Headquarters

Michigan State University

A372 Plant and Soil Science

East Lansing, Michigan 48824

SolCAP Newsletter Editor:

Kelly Zarka

Phone:

517-355-0271 Ext. 1-111

E-mail: solcap@msu.edu

Web site: http://solcap.msu.edu

SolCAP has it’s 3rd Annual Meeting

Since the last newsletter SolCAP has been genotyping the tomato

panel (480 lines) as well as the potato panel (325 lines) and numer-

ous mapping populations for potato. With Illumina’s Infinium

platform we were able to genotype over 7000 SNPs in tomato and

8300 SNPs in potato, many more than originally planned. We are

also working to have multi-year and multi-environment phenotype

data to align with the SNP marker data for the tomato and potato

panels. We anticipate that the resulting genetic + phenotypic

data, which will be stored and curated at the SolCAP and SGN websites, will serve as a valuable

public resource for the tomato and potato communities.

The SNP “calls” for the tomato and potato panels are posted on the SolCAP website (http://

solcap.msu.edu/potato_genotype_data.shtml and http://solcap.msu.edu/

tomato_genotype_data.shtml). The first SNP calls for potato and tomato were based on three

genotypes (AA, AB and BB). The potato SNP calls were recently expanded to five genotypes

(AAAA, AAAB, AABB, ABBB, BBBB), since most potato cultivars are tetraploid. Over 3500

SNPs were called into 4 or 5 clusters. Being able to score dosage enhances the utility of SNPs in

tetraploid mapping and expands the number of available markers we can access when mapping

in tetraploids. Figure 1 (see page 2) is an example of two ideal SNP markers where dosage can

be scored confidently.

SolCAP is also genotyping several potato populations. In one diploid population (DM1-3 x

84SD22) we identified over 2,500 SNPs segregating. These SNPs are distributed throughout the

genome covering 881 scaffolds. In a tetraploid mapping population (MSG227-2 x Jacqueline Lee)

we have identified over 2700 SNPs segregating as single dose markers (e.g. AAAB x AAAA or

ABBB x BBBB). There are over 2500 SNPs that are heterozygous in both parents. With the abil-

ity to call dosage, we will be now able to expand the SNP markers available (continued on p.2)

Dave D.’s Perspective:

The third annual SolCAP meeting was a success! The meeting which was held in San Diego at

the Town and Country Resort in conjunction with the Plant and Animal Genomics Conference

on January 15th, 2011, once again had excellent attendance and participation.

We focused on our project outcomes, impacts and the resources we developed. The Advisory

Board noted that the SolCAP Team has met and exceeded their objectives in many ways and it has only

been 2 years and 3 months into the 4 year project. SolCAP has developed many tools and resources for

the community. The outputs from SolCAP should help to ensure that the Solanaceae research community

has a bright future. These outputs have raised the profile of Solanaceae research in the USA.

The SolCAP Executive Committee would like to thank the members of the SolCAP Advisory

Board (scientific advisors, stakeholders, education/extension advisors and assessment advisors)

for their participation and input. We are all looking forward to another productive year!

PAGE 2 VOLUME 3, I SSUE 2

Dave D.’s Perspective: (continued from page 1)

for mapping and QTL analyses.

Most of the SNP genotyping has now been completed on

the russet tetraploid mapping population and SolCAP

has collected multi-environment phenotype data in 2009

and 2010. We will complete the phenotyping in 2011.

When the SNP genotyping is completed on the 200 prog-

eny, we will initiate QTL analysis. Two other commu-

nity tetraploid mapping populations from the University

of Wisconsin and North Carolina State University are

also largely genotyped. Later this summer QTL analysis

can be conducted on these populations for processing

quality, specific gravity (tuber dry matter), tuber sugar

levels, internal heat necrosis, vine maturity, tuber cal-

cium, etc.

SolCAP is at a similar point with the potato panel. The

potato panel is composed of the top 50 North American

varieties, historical varieties, advanced breeding clones

from every US and Canadian breeding program, some

germplasm from international colleagues and genetic

stocks. Key traits we have collected data for include spe-

cific gravity, sucrose, glucose, maturity, tuber shape, tu-

ber number, and yield. We will be looking for associations between SNP markers and this phenotypic data. We an-

ticipate that breeders will access germplasm from this panel for crossing based upon SNP polymorphism and linked

QTL of interest, design crosses for complementary QTL and traits, and use marker assisted breeding in early gen-

eration selection. Furthermore, breeders will be able to design crosses to manipulate and select variation within

existing elite populations or introgress novel alleles from wild germplasm. We envision varietal breeding becoming

more predictable and directed for processing and fresh market traits.

Cindy Lawley, Agriculture consortia manager, Illumina, Inc., recently summarized some important information

about the Potato SNP array for its users. I want to share her letter with the broader potato community.

“1. Please find below a link to the cluster file developed by the SolCAP community for this product.

http://solcap.msu.edu/potato_infinium.shtml

The development of this file was an effort by the SolCAP community to support biomarker assisted breeding through

funding of the USDA-NIFA Initiative. Although this is not a commercial product supported through Illumina's Tech-

Support, if you have questions about Infinium or iSelect, please do not hesitate to contact us. If you have questions

specifically about the content on the chip, the SolCAP website is probably the best place to go although I am happy

to receive questions and find the appropriate avenue for answering them.

2. Please keep in mind that the cluster file save feature in GenomeStudio's Genotyping module does not support

more than three expected clusters per locus for diploid loci. For calling genotypes for up to 5 clusters using manual

functionality in GenomeStudio, please download the short video and TechNote from the GenomeStudio portal

(attached is a screen shot illustrating this location) or from the following FTP location: Ftp.illumina.com

Ilmn_temp_05

192MT8h

3. Some of you may be interested in the Sol Newsletter that is distributed by Joyce Van Eck. Below is the link to the

latest issue of the Sol Newsletter:

http://solgenomics.net/static_content/solanaceae-project/docs/SOL_newsletter_Mar_11.pdf

It is also available as a link from the SOL Genomics Network (SGN) homepage at http://solgenomics.net/

4. And, finally, the deadline for all orders for the SolCAP Potato Genotyping tool is July 1, 2011. “ (More informa-

tion is on page 3 of this newsletter)

Lastly, we recently sent out a call to the tomato community, requesting populations to submit for SNP genotyping.

We have received 10 proposals to consider. It is great to have this high level of participation!

Tetraploid Segregation

Yellow = Parents (AABB x AABB)

Red = Population

(1:8:18:8:1

AAAA:AAAB:AABB:AAAB:BBBB)

P2

P1

Yellow = Parents (AABB x BBBB)

Red = Population

(1:4:1 AABB:AAAB:BBBB)

P1

P2

Fig. 1 SNP markers where dosage can be scored confi-

dently.

PAGE 3 VOLUME 3, I SSUE 2

The SolCAP team would like to extend a thank you to our fellow Solanaceae scientists for joining us in a consortium

through Illumina® to develop a potato array and a tomato array for the interrogation of SNPs in the genomes.

The deadline for any new orders or reorders for Bead Chips are as follows:

SolCAP Potato Consortium: July 1, 2011

SolCAP Tomato consortium: October 15, 2011

Through this collaborative effort the Solanaceae community is on the way to seeing

significant advances in research.

For more information please contact:

Cindy Taylor Lawley, the Agriculture Consortia Manager consortiamanager@illumina.com

Illumina, Inc., 25861 Industrial Blvd., Hayward, CA 94545, Tel: 510 670 9478

Last Chance for Special Pricing on

SolCAP’s Illumina Bead Chips

SolCAP Potato Genomics Workshop at PAA

The USDA Solanaceae Coordinated Ag project ( solcap.msu.edu) is hosting the workshop "Using SolCAP pheno-

type and Infinium SNP data in Potato Breeding" in conjunction with the 95th Annual Meeting of the Potato Asso-

ciation of America. The workshop will take place at the Hilton Wilmington Riverside, 301 North Water Street, Wil-

mington, North Carolina on Sunday, August 14, 2011 from 1:00 pm until 5:00 pm.

The workshop 2011 topics include:

Phenotyping the SolCAP potato germplasm panel - Walter De Jong (Cornell University)

Potato Genomics: What's Next? - Robin Buell (Michigan State University)

SNP-based genetic maps: Linkage and QTL analysis - Dave Douches (Michigan State University)

Breeding in a Genomics Era - Dave Francis (The Ohio State University, Wooster)

Developing the Breeder's Toolbox at SGN - Joyce Van Eck (Cornell University)

Who should attend? This workshop is specifically designed for potato breeders, breeding assistants and lab

personnel.

Registration: Registration is free but required to help us keep track of the total number of participants. If you

would like to attend, when registering for the PAA meeting (register at http://paa2011.org/) please select the

SolCAP Workshop option. If you have already registered for the PAA meeting and overlooked the SolCAP

workshop registration please contact Jeanette Martins directly: email:jmartins@ucdavis.edu or phone:

530.752.4984

PAGE 4 VOLUME 3, I SSUE 2

Development of the Double Monoploid Potato

Richard Veilleux Ph.D.

Department of Horticulture

Virginia Tech

After Guha and Maheshwari first published their short astounding reports in the mid 1960s about

the chance discovery that Datura microspores could undergo embryogenesis to become haploid

plants, the plant breeding community was captivated by the new opportunities to derive haploid and doubled haploid

lines of commercial crops. Our intentions for applying the technique to the Haynes adapted phureja population of

potato were motivated by the possibility of deriving homozygous lines as building blocks for hybrid true potato seed.

My dissertation research at the University of Minnesota under the direction of Florian Lauer involved selecting 2n

pollen producing clones from the adapted phureja population, crossing them to potato cultivars and evaluating the

resulting tetraploid 4x-2x hybrids in the field. The high yield and cultivar like appearance of these 4x-2x hybrids was

remarkable, despite the lack of selection on the phureja population for any traits except 2n pollen. Their heterogene-

ity could be attributed to genetic segregation expected to occur both during the formation of megasporocytes in the

tetraploid cultivars as well as the formation of 2n pollen in the diploid phureja selections. We knew from the work of

Wenzel in Germany and Uijtewaal in Holland that inbreeding depression in potato cultivars or (di)haploid breeding

lines was severe, so that even if plants could be obtained, they were too weak to be of much use. However they had

established a protocol for anther culture of potato. We hoped that the adapted phureja population would have greater

tolerance to inbreeding.

Potato ploidy descriptions are confusing and inconsistent. Commercial potato varieties (S. tuberosum) are tetraploid

(2n=4x=48); haploids of cultivated potato (which should really be and sometimes are called dihaploids) are diploid

(2n=2x=24) and heterozygous; Solanum phureja is a diploid (2n=2x=24), primitive, cultivated species that has little genetic

distinction from and is completely cross compatible with S. tuberosum; haploids of S. phureja are called monoploids

(2n=1x=12), or sometimes monohaploids, and have only a single homolog of each chromosome; doubled monoploids are dip-

loid (2n=2x=24) and homozygous.

Wanda Collins had assumed Frank Haynes’ potato breeding position at NC State and agreed to dig into his seed col-

lection to supply me with a diverse set of his phureja seed families selected for tuberization under long days and heat

tolerance. We grew about 1,000 seedlings in the field in Virginia and selected 30 of the

best. Many of the worst had hundreds of tiny tubers per plant or nasty tuber shape. Our

selections produced more than 1.5 kg tubers per plant and had more acceptable tuber size

and shape. We applied the German anther culture protocol on these selections and were

delighted to regenerate some androgenetic plants. Eventually we counted their chromo-

somes and found some monoploids among them. We used flow cytometry to estimate

ploidy in order to process efficiently the growing numbers of anther derived plants, many

of which were diploid due to androgenetic development of unreduced microspores that

abound in the phureja germplasm. We wanted this trait for later application of sexual

polyploidization but it was a nuisance in anther culture because the preponderance of

heterozygous diploid anther-derived plants was not interesting to us. Eventually we iden-

tified several monoploid lines with just 12 chromosomes and, though they were not ex-

actly vigorous, they could be established in the greenhouse and eventually the field to

produce flowers and tubers. Flow cytometry had revealed that endopolyploidization was

rampant among the somatic cells of the leaves of the monoploid plants, so that they

were comprised of mostly diploid and tetraploid cells. The meristems remained mo-

noploid, however, through countless rounds of in vitro propagation. Placing monoploid

leaf segments on a brief callus induction medium, followed by a regeneration medium

provided an easy route to doubling the chromosome number of monoploids spontaneously to regenerate homozygous

doubled monoploids (DMs), the first of our building blocks for hybrid production.

The DMs were somewhat more vigorous than the monoploids and were able to set seed on cross pollination with most

fertile heterozygous diploid potato germplasm. Their progenies exhibited normal vigor and fertility. Pollen develop-

ment in the DMs was variable, with some having only aborted microspores and others with stainable pollen that

could germinate in vitro or yield androgenetic embryos in anther culture. However we have been unable to use DMs

as successful pollinators with other potato germplasm. We tried to increase fertility by subjecting the progenies of

DMs to a second round of anther culture, thinking that the inbreeding depression would not be so severe since half

the genome had already passed through the “monoploid sieve.” Joe Pavek supplied some heterozygous diploid field

Androgenetic embryos

emerging from cultured

anther of Solanum

phureja

PAGE 5 VOLUME 3, I SSUE 2

selections that had overall good appearance and various useful traits

developed through a complex pedigree. We used these selections as polli-

nators on the DMs. Since the response to anther culture is heritable, we

obtained many second cycle DMs from the F1 plants. We were disap-

pointed to find that they were not any better than the first cycle DMs.

There must have been sufficient genetic load in the heterozygous parents

that it did not matter that the female parent was homozygous. Our next

strategy was to fuse protoplasts of distantly related monoploids to create

intermonoploid somatic hybrids that we hypothesized would have little

or no genetic load. All of the somatic hybrids were polyploid. We focused

on the tetraploids and found that they were fertile as male and female

parents. We performed anther culture on the hybrids derived from

crosses between two intermonoploid somatic hybrids, drawing on the

variation contributed by each of four different monoploids. The (di)

haploids obtained were vigorous, flowered abundantly and set some

seeds on cross pollination. We are still trying to reduce these to the mo-

noploid level.

So, how was DM 1-3 516 R44 selected for the sequencing project? Sanwen Huang was complaining to Marc Ghislain on

a visit to China about how difficult the heterozygous RH was to sequence and wondered if there were some homozy-

gous potato germplasm available. Marc and Merideth Bonierbale had visited me

in Virginia some years ago and arranged to have some of my DMs sent to CIP

because Merideth was interested in their breeding potential. They subsequently

did many crosses with them at the CIP breeding station using different diploid

selections as male parents so they were familiar with the material. Marc men-

tioned to Sanwen that they had this germplasm and Sanwen contacted me for

permission to sequence a DM. Shortly afterwards, Robin Buell independently

requested homozygous DM germplasm from me for exactly the same reason. I

mentioned to her that Sanwen was already using it, sent her the same clone and

the Consortium shifted its focus after verifying that the DM was truly homozy-

gous and that both Sanwen and Robin were working with the same clone. Me-

rideth had selected DM 1-3 516 R44 from among the five DMs because it was

the most fertile in her crossing block. It was derived from BARD 1-3, one of the

original selections made in the field from Frank Haynes’ material. Its BARD

designation derives from my participation in the 1980s in a Binational Agricul-

tural Research and Development research project with David Levy in Israel to

develop heat tolerant potato. BARD provided much of the early support for my

research. USDA has also sponsored several related research projects.

It becomes obvious from the names mentioned throughout

this report that the potato community has contributed to

many aspects of this research. I am hardly one man working

alone. In addition to those already mentioned, numerous

graduate students and technicians at Virginia Tech have

provided me with a talented workforce to be able to persist

in this project. The Department of Horticulture at Virginia

Tech has generously supported my program with assistant-

ships, laboratory space, greenhouse space and field plots. I

am happy to have provided DM 1-3 516 R44 to the potato

community for generating a draft genome sequence, even if I

still do not have the homogeneous, hybrid TPS progenies

that I envisioned when I first set on this course. The het-

erozygous progenitor, BARD 1-3, its monoploid derivative, 1-

3 516 and DM 1-3 516 R44 (GS224, GS395 and GS225, re-

spectively) are all available freely through the Potato intro-

duction Station, Sturgeon Bay, Wisconsin (http://www.ars-

grin.gov/nr6/).

Tubers of DM 1-3 516 R44 (pink,

upper left), RH tubers (white,

lower ) and and F1 hybrid be-

tween DM x RH (red, middle)

Monoploid (left) and isogenic doubled

monoploid (right) of adapted Solanum

phureja

Richard Veilleux, Professor, Suzanne Piovano, Re-

search Specialist, Jeff Burr, Greenhouse manager.

PAGE 6 VOLUME 3, I SSUE 2

New Plant Breeding and Genomics

Web Resource Available!

Led by SolCAP, a group of researchers and educators from U.S. land-grant universities, government agencies and

industry have created the first internet resource aimed at quickly putting basic research on crop genomes on the web

to support plant breeding programs. The resource is new at eXtension (pronounced E-extension), http://

www.extension.org and can be found at http://www.extension.org/plant breeding genomics

This resource is for students and professionals involved with plant breeding, and for agricultural producers who util-

ize the new varieties resulting from traditional and emerging plant breeding methods. This is a growing collection of

educational information, collaboratively authored and reviewed by our community of researchers, educators, and

eXtension personnel who have experience and expertise in plant breeding and genomics topics and crop production

topics.

The Goals of the Plant Breeding and Genomics Resource Help put genomics research and tools in to practice through plant breeding by:

Presenting unbiased science-based information in a variety of media formats

Sharing the most current, relevant, and accurate information available on techniques, procedures, and bioinfor-

matics software

Being a reliable resource that is responsive to the changing needs of the plant breeding industry and agricul-

tural producers

Fostering collaboration among members

of the plant breeding and genomics com-

munity

Plant Breeding and Ge-

nomics Tools You Can Use

Feature Articles: Our feature articles keep

you up to date in this rapidly emerging field

and cover everything from the basics of popu-

lation development and molecular markers to

the latest plant breeding and genomics re-

search and technologies and crop production

information.

Tutorials: Our tutorials, in the form of webi-

nars, interactive animations, and self-paced

lessons, walk you through the details of how

to make use of plant breeding and genomics

research and resources in your breeding pro-

gram.

Aggregation: Partnering with other educa-

tional efforts, our experts have organized

links to other excellent genomics, plant

breeding and agricultural production re-

sources.

Ask an Expert: eXtension’s Ask an Expert tool allows you to submit specific questions to the community’s plant

breeding and genomics experts.

As eXtension and its plant breeding and genomics community grow, our content will grow. Look for additional oppor-

tunities to connect with other plant breeders and service providers.

Contact Us Please join us! If you have experience and expertise in plant breeding and genomics or crop production and would

like to be a part of our community, create an account with eXtension and indicate your interest in joining our plant

breeding and genomics community at https://people.extension.org

PAGE 7 VOLUME 3, I SSUE 2

Breeders Toolbox on SGN

The SOL Genomics Network (SGN; http://solgenomics.net) is a Clade Oriented Database

(COD) containing genomic, genetic, phenotypic and taxonomic information for plant genomes.

SGN originally concentrated on the Euasterid clade, including the families Solanaceae (e.g.

tomato, potato, eggplant, pepper and petunia) and Rubiaceae (coffee), but the scope of the database is being ex-

panded to include additional related families.

The Breeders Toolbox (http://solgenomics.net/breeders/index.pl) on SGN is dedicated solely to the resources that

would be of the most interest to breeders, which will help save time figuring out where to start a search on SGN.

The resources available on SGN include but are not

limited to 1) various types of markers, 2) search ca-

pabilities for information on markers, 3) search capa-

bilities for information on phenotypes, trait ontolo-

gies, and QTLs, 4) SNP data that will be available

soon, and 5) tomato genome sequence, assembly, and

annotation.

Currently, the toolbox page includes portals for

doing trait and marker searches, a QTL tool, and a

SNP tool that is under development (Figure 1).

These portals provide quick access to the many mo-

lecular, genetic, and genomic resources available on

SGN that can help to efficiently target breeding pro-

grams toward the traits of interest. As a result, the

application of these resources has the potential to

reduce both the amount of time and financial input

needed to achieve breeding goals. The toolbox is a

work in progress and tools will be added in the future

based on breeder community needs and the availabil-

ity of data.

In order to guide users through the features on the

toolbox page, tutorials will be available at eXtension

(http://www.extension.org), which will be accessible

by links associated directly with each tool icon. At

this time, the toolbox contains links for tutorials for the Tomato Genome Browser and designing a CAPS marker

from a SNP using the SGN CAPS Designer.

If you have suggestions for additions and/or improvements to the toolbox, send an e-mail to

sgn-feedback@solgenomics.net or Joyce Van Eck (jv27@cornell.edu).

The Breeders Toolbox on SGN

(http://solgenomics.net/breeders/index.pl) on SGN

Journal Highlights :

Li, Wentao. and R.T. Chetelat (2010). A Pollen Factor Linking Inter- and Intraspecific Pollen Rejection in To-

mato. Science 330: 1827-1830.

Zhangjun Fei,1,2* Je-Gun Joung,1 Xuemei Tang,1 Yi Zheng,1 Mingyun Huang,1 Je Min Lee,1 Ryan

McQuinn,1 Denise M. Tieman,3 Rob Alba,1 Harry J. Klee,3 and James J. Giovannoni1,2. (2011) Tomato

Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genom-

ics. Nucleic Acids Res. 39(Database issue): D1156–D1163 .

Urbany C, Stich B, Schmidt L, Simon L, Berding H, Junghans H, Niehoff KH, Braun A, Tacke E, Hofferbert

HR, Lübeck J, Strahwald J, Gebhardt C. Association genetics in Solanum tuberosum provides new insights

into potato tuber bruising and enzymatic tissue discoloration. BMC Genomics. 2011 Jan 5;12:7.

PAGE 8 VOLUME 3, I SSUE 2

Applications for Plant Breeding Academy in Europe

Class II, starting Fall 2011, are now available!

Apply Here

The Seed Biotechnology Center at the University of California, Davis has organized a professional development

course to teach the principles of plant breeding to seed industry personnel. This two-year course addresses the

reduced numbers of plant breeders being trained in academic programs. Participants meet for six, 6

day sessions over two years in various locations. Readings and exercises continue between sessions via internet

to allow participants to maintain their current positions while being involved in the course.

PBA in Europe Class II (2011-2013 Course)

PBA in Europe Class I (2009-2011 Course)

Instructors and Curriculum

Policies & Procedures

Tuition & Fees

FAQs

For information on current and past participants, please see PBA Participants

For more information about the PBA, please contact Joy Patterson at jpatterson@ucdavis.edu or 530-752-4414.

Chetelat, Li identify gatekeeper for tomato pollination Published in: PLANT SCIENCES WEEKLY NEWSLETTER – Dec. 29, 2010

Tomato plants use similar biochemical mechanisms to reject pollen from their own flowers as well as pollen from for-

eign but related plant species, thus guarding against both inbreeding and cross-species hybridization, according to re-

search by Roger Chetelat, director and curator of the Charles M. Rick Tomato Genetics Resource Center, and Wentao

Li, a postdoctoral researcher. Their findings are reported in the Dec. 24 issue of the journal Science

(http://www.sciencemag.org/content/330/6012/1827.short). The researchers identified a tomato pollen gene that en-

codes a protein that is very similar to a protein thought to function in preventing self-pollination in petunias. The to-

mato gene also was shown to play a role in blocking cross-species fertilization, suggesting that similar biochemical

mechanisms underlie the rejection of a plant’s own pollen as well as foreign pollen from another species. Their discov-

ery will likely find application in plant breeding, particularly for California’s $1.5 billion tomato industry, and in de-

veloping a better basic understanding of the biology of pollination. “Flowering plants have several types of reproduc-

tive barriers to prevent accidental hybridization between species in nature,” Chetelat said. “We have identified one

piece of this puzzle, a gene that helps control whether or not tomato pollen is recognized and rejected by flowers of re-

lated wild species. “Understanding and manipulating these reproductive barriers might help breeders access desired

traits found in wild tomatoes,” he said. More information about Chetelat’s research group is available at

http://irbtomato.org.

PAGE 9 VOLUME 3, I SSUE 2

Affordable SNP genotyping facility at

Michigan State University

A high throughput Single Nucleotide Polymorphism (SNP) genotyping lab has been set up in the Plant and Soil Sci-

ences Building at Michigan State University . The lab is equipped with an Illumina iScan system and the associated

facilities to run Illumina high throughput assays. We have been successfully running the Infinium Assay using the sys-

tem. In an Infinium assay, a sample can be genotyped with 3,000-1,200,000 SNP markers, depending on the format of

the BeadChips. We are making the MSU high throughput SNP genotyping system available to Tomato and Potato Com-

munities for their population genotyping. The following table shows the estimated cost for processing Illumina 24-

sample BeadChips. The costs include labor, equipment maintenance and consumables for the lab procedures.

This cost is for processing of the Infinium chips only. Infinium BeadChips must be purchased separately from Illumina

and shipped to Infinium SNP genotyping lab c/o Dr. Dave Douches, A499 Plant and Soil Sciences Building, Department

of Crop and Soil Sciences, East Lansing, MI 48824-1325.

There are specific requirements needed when submitting samples. Contact the lab to receive specific instructions before

preparing and sending your samples.

The data needs to be processed with Genome Studio software. The software is installed on a computer in the SNP Geno-

typing lab. If you need a license of the Genome Studio software, you need to purchase the license from Illumina directly

(www.illumina.com). A new module of Genome Studio is now available to call up to 5 genotypes.

For more information contact Dr. David Douches, Michigan State University, douchesd@msu.edu or 517-355-0271

Cost for processing Illumina BeadChips

No. of BeadChips 2 4 6 8

Total No. of samples for 24-sample chips 48 96 144 192

Per sample cost $27 $13.50 $10 $8

Calling Polyploid Genotypes with GenomeStudio®

Software v2010.3/v1.8

GenomeStudio Data Analysis Software is a highly visual and intuitive platform for analyzing data generated from Illu-

mina® assays. Illumina’s GenomeStudio Software works seamlessly with Illumina’s sequencing and genotyping platforms

to support a diverse range of data analysis needs. Primary analyses, such as raw data normalization, clustering, and

genotype calling of GoldenGate® and Infi nium® Genotyping Assay data, are performed using algorithms in the Genotyp-

ing (GT) Module. Illumina has used some of SolCAP’s data to create a document that provides best practices for using the

GenomeStudio GT Module v2010.3/v1.8 to assign genotypes for up to five clusters in tetraploid genomes. The document

can be viewed by following the “calling polyploidy link found here: http://solcap.msu.edu/tutorials.shtml

May 23-25, 2011, 5th Annual National Association of Plant Breeders

Meeting, Texas A&M University, College Station, TX.

http://www.plantbreeding.org/napb/Meetings/pbccmeeting2011.html

June 4-8, 2011, In Vitro Biology Meeting, The Raleigh Marriott City Center, Raleigh, NC.

http://www.sivb.org/meetings.asp

August 6-11, 2011, Plant Biology 2011, Minneapolis, MN. http://my.aspb.org/?

page=Meetings_Annual

August 14-18, 2011, Potato Association of America, Hilton Wilmington Riverside, Wil-mington, NC. Note: The SolCAP Workshop will be held at that location on Sunday, Au-

gust 14, 2011 from 1:00 pm until 5:00 pm. http://paa2011.org/

September 25-28, 2011, American Society of Horticultural Science Annual Conference,

Hilton Waikoloa, Village, HI. http://www.ashs.org

November 28-Dec 1, 2011, The SOL & ICuGI 2011 joint conference will be held at the

Kobe Convention Center, 6-9-1 Minatojima-nakamichi, Chuo-ku, Kobe, Japan.

Calendar of Events:

SolCAP

Solanaceae Coordinated Agricultural Project

Michigan State University

A372 Plant and Soil Science Building

East Lansing, Michigan 48824

SolCAP Newsletter Editor:

Kelly Zarka

Phone: 517-355-0271 Ext. 1-111

E-mail: solcap@msu.edu

Visit us on the web:

http://solcap.msu.edu

PAGE 10 VOLUME 3, I SSUE 2

This project is supported by the Agriculture and Food Research Initia-

tive (AFRI) of USDA’s National Institute of Food and Agriculture

(NIFA)