new resources and strategies for genome-wide mapping in sorghum
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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. Why do we need gene-resolution mapping (or causal variants)?. - PowerPoint PPT PresentationTRANSCRIPT
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