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New resources and strategies for genome-wide mapping in sorghum Geoff Morris Research Assistant Professor Kresovich Lab University of South Carolina

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Why do we need gene-resolution mapping (or causal variants)? More accurate marker-assisted selection, in breeding programs and from germplasm Leverage knowledge from other crops and model plant species

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Genotyping- by-sequencing identified 265,000 SNP markers

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An atlas of genomic variation in 1000 sorghum accessions Genetic Variation: Recombination rates:

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Mapping genes underlying trait variation using genome-wide association studies (GWAS) * Causative A T Phenotype Tallest Taller Tall Short Shorter Shortest p < 10 -8 p = 10 -0 Quantitative trait locus (Candidate gene) Height T A Linked SNP G C C G Unlinked SNP G C G C G C G

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GWAS reveals multiple loci controlling panicle branch length CLV1 APO1 SP1 ID1 LUG BDE1,ID1 TCP,TLK GDD 1 THE1 LOM3 DFL2 F-box protein in rice (Ikeda et al. 2005 Dev Biol) Receptor-like kinase in maize (Lunde and Hake 2009 Genetics) Peptide transporter in rice (Li et al. 2009 Plant J) Aberrant panicle organization1 ortholog Short panicle1 homolog Thick tassel dwarf1 homolog

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Back to basics: Pigmentation

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Testing GWAS with validated flavonoid genes The classical testa gene B2 was cloned as Tannin1 G/T polymorphism found in GBS data Positive control for GWAS in sorghum Wu et al. PNAS 2012

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Mapping testa (presence/absence) in an association panel GLM and CMLM (K, Q+K) identify the locus but not the gene

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Synthetic associations can prevent gene-level resolution in GWAS tan1-a allele Synthetic associations MAF=20% MAF=46% Orozco et al. 2010 Caused by multiple independent mutations in the same gene:

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Gene-resolution mapping of Tannin1 GLM (Q) and MLM (K) do map Tannin1 precisely

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Precise mapping of Tannin1 in recombinant inbred lines One day of scratch tests + GBS data = Precise mapping of Tannin1 Stem borer mapping population (n=263)

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Pericarp pigmentation in the sorghum association panel Ibraheem et al. 2010 Yellow seed1 cloned by Chopra lab

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Basal seedling (coleoptile) pigmentation mapped in a RIL Arabidopsis TT8 Maize B1

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Adult plant pigmentation (tan vs. purple) mapped in a RIL Colocalizes with classical P locus Maps to cluster of DFR (Maize A1)

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Lessons learned Higher-density genotyping will yield more useful mapping results Genotyping-by-sequencing gets the most out of existing investments in RILs GWAS can provide gene-resolution mapping but signals may be complex/indirect Best of both worlds: Nested Association Mapping (NAM) Regional Mapping (RegMap)

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Mapping climate-associated alleles in a high-resolution global diversity panel 700,000 SNPs genotyped in 2,500 source-identified accessions of African and Asian origin

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More info: www.morrislab.org Starting November 1 Assistant Professor Sorghum Genetics and Genomics Department of Agronomy

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Project team University of South Carolina Stephen Kresovich, Davina Rhodes, Zachary Brenton Cornell University/Institute for Genomic Diversity/USDA-ARS SNP pipeline: Ed Buckler, Jeff Glaubitz, James Harriman Genotyping: Sharon Mitchell, Charlotte Acharya International Crops Research Institute for the Semi-Arid Tropics (ICRISAT Patancheru, India) Punna Ramu* Germplasm: Tom Hash, Oscar Riera-Lizarazu, Hari Upadhyaya, Santosh Deshpande, Vinayan Madhumal Bioinformatics: Trushar Shah University of Illinois Phenotypes: Patrick Brown Iowa State University Jianming Yu Funding NSF/Gates-Basic Research to Enable Agricultural Development USDA-Feedstock Genomics