New resources and strategies for genome-wide mapping in sorghum

Geoff MorrisResearch Assistant Professor

Kresovich LabUniversity of South Carolina

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

Genotyping-by-sequencing identified 265,000 SNP markers

An atlas of genomic variation in 1000 sorghum accessions

Genetic Variation:

Recombination rates:

Mapping genes underlying trait variation using genome-wide association studies (GWAS)

*

Causative AAATTT

PhenotypeTallestTallerTall

ShortShorterShortest

p < 10-8 p = 10-0

Quantitative trait locus(Candidate gene)

Height

T A

Linked SNPGGGCCC

C G

Unlinked SNPGCGCGG

C G

GWAS reveals multiple loci controlling panicle branch length

CLV1APO1SP1

ID1ID1

LUGBDE1,ID1TCP,TLK GDD

1

THE1

LOM3DFL2

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 organization1ortholog

Short panicle1homolog

Thick tassel dwarf1homolog

Back to basics: Pigmentation

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

Mapping testa (presence/absence) in an association panel

• GLM and CMLM (K, Q+K) identify the locus but not the gene

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:

Gene-resolution mapping of Tannin1

• GLM (Q) and MLM (K) do map Tannin1 precisely

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)

Pericarp pigmentation in the sorghum association panel

Ibraheem et al. 2010

Yellow seed1 cloned by Chopra lab

Basal seedling (coleoptile) pigmentation mapped in a RIL

Arabidopsis TT8

Maize B1

Adult plant pigmentation (tan vs. purple) mapped in a RIL

• Colocalizes with classical P locus

• Maps to cluster of DFR (Maize A1)

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)

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

More info:www.morrislab.org

Starting November 1Assistant ProfessorSorghum Genetics and GenomicsDepartment of Agronomy

Project teamUniversity of South Carolina

Stephen Kresovich, Davina Rhodes, Zachary BrentonCornell University/Institute for Genomic Diversity/USDA-ARS

SNP pipeline: Ed Buckler, Jeff Glaubitz, James HarrimanGenotyping: 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 MadhumalBioinformatics: Trushar Shah

University of Illinois

Phenotypes: Patrick BrownIowa State University

Jianming YuFunding

NSF/Gates-Basic Research to Enable Agricultural DevelopmentUSDA-Feedstock Genomics