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2/26/2014 Wide adaptation and diffusion in the cereal crop sorghum (Sorghum bicolor) Genomic Signatures of Climate and Soil Adaptation in a Widely-diffused Crop Durra: Semiarid climate Guinea: Humid climate • Extreme differentiation in: • Architecture • Phenology • Secondary metabolites Geoffrey Morris, Department of Agronomy, Kansas State University PAG XXII – Population and Conservation Genomics From diverse germplasm to crop improvement From diverse germplasm to crop improvement Diverse Crop Germplasm Diverse Crop Germplasm Genotyping-By-Sequencing (GBS) Genotype-Phenotype Map for Adaptive Trait Legend: Decades and decades of painstaking work by plant breeders Genome Wide Association Studies (GWAS) Genomic Selection (GS) New Crop Varieties Better Adapted to Current and Future Environments Genetic Basis of Adaptive Traits New Crop Varieties Better Adapted to Current and Future Environments Genotyping-By-Sequencing based dissection of agroclimatic traits in sorghum Functional alleles have striking distributions Maturity1 (Morris et al. 2013 PNAS) Inflorescence architecture, plant height, flowering time (Morris et al. 2013 PNAS) LUG Determines flowering: - Photoperiod sensitive in tropics - Photoperiod insensitive in subtropics THE1 SP1 DFL2 LOM 3 ID TCP,TLK CLV1 1 ID 1 BDE1,ID1 GDD 1 APO 1 Functional allele from Murphy et al. 2011 PNAS Can we identify functional alleles using geographic distributions? Tannin1 (Morris et al. 2013 G3) Inner seed coat tannins, Seed pigmentation, Plant pigmentation (Morris et al. 2013 G3) Grain tannins defend against: - Grain mold (wet, warm) - Pre-harvest sprouting (wet, warm) Tannin1 Functional allele from Wu et al. 2011 PNAS Ibraheem et al. 2010 Genetics 1 2/26/2014 Can we identify signals of environmental adaptation directly (without phenotype)? From diverse germplasm to crop improvement Diverse Crop Germplasm • In wild accessions of Arabidopsis thaliana, alleles found in a particular environment GBS predict fitness in that environment – Hancock et al. 2011 Science Genotype-Phenotype Map for Adaptive Traits – Fournier-Level et al. 2011 Science Genome by Environmentof-Origin (GEO) association map GEO-GWAS GWAS • What if an environmentally-adaptive trait can’t GS be phenotyped? GEO-GS Genetic Basis of Adaptive Traits – Challenge phenotyping in the appropriate environment – Genotyping gets easier everyday, field- New Crop Varieties Better Adapted to Current and Future Environments based phenotyping remains very challenging ICRISAT, Sudan Genotyping-by-Sequencing (GBS) of global source-identified sorghum accessions Genome by Environment-of-Origin (GEO) associations to predict adaptation Neutral: Adaptive : >400,000 SNPs genotyped in >2,000 source-identified accessions of African and Asian origin GEO-GS (Identify adapted line) GEO-GWAS (Identify adaptive allele) Charlotte Acharya, Katie Hyma, Sharon Mitchell, Ed Buckler (Cornell) Analogous to the “Common-Disease Common-Variant” hypothesis of GWAS Punna Ramu, Hari Upadhyaya, Tom Hash, Santosh Deshpande (ICRISAT) Genebanks: GRIN, ICRISAT. GIS data: WorldClim, Global Agro-Ecological Zones (GAEZ). GEO-GWAS maps the Tannin1 gene from “Precipitation in the Warmest Quarter” How much genotypic variation can be explained by climate? Arabidopsis Sorghum N accessions = 1819 Space Climate N locations = 1468 Space Jesse Lasky Columbia University Climate colinear with Space Climate colinear with Space Lasky et al. (2012) Molecular Ecology 4th highest peak at Tannin1 Climate • • More variation is explained by “Climate colinear with Space” Space diffusion Climate Ç Space Climate Rapid of sorghum along similar agroclimatic zones? 2 2/26/2014 Is the climate-associated genomic variation adaptive? Explained by climate Explained by climate independent of space • Aluminum toxicity is a serious limitation to crop Al-tolerant Al-sensitive 1.020 yields on acidic soils worldwide 1.02 • A major effect Al-tolerance locus (AltSB) is cloned in sorghum (Magalhaes et al. 2007 Nature 1.01 1.010 Genetics) 1.00 – Does a genome scan for alleles associated with high-Al soils reveal AltSB (GEO-GWAS)? 0.99 1.000 • 0.98 0.990 Fold enrichment Can GEO associations with soil Aluminum predict Aluminum tolerance? Worldwide sorghum diversity has been phenotyped for Al-tolerance (Caniato et al. 2011, PLoS ONE) Intergenic Synonymous n=39,310 n=311,942 – Do alleles from high-Al soils predict observed Non-synonymous n=53,375 Al-tolerance phenotypes (GEO-GS)? Magalhaes et al. 2004, Genetics Method of Lasky et al. (2012) Molecular Ecology GEO-GWAS: Does a genome scan for alleles associated with high-Al soils reveal AltSB? GEO-GS: Do alleles from high-Al soils predict observed Al-tolerance phenotypes? 11th SNP is 75kb from AltSB Aluminum Tolerance GWAS • Relative Net Root Growth (RNRG) in Root growth phenotypes from Caniato et al. 2011 (n=166) Spearman ρ = 0.33 P < 10-5 Al-solution (n=166) • Prediction made without phenotypes, Observed Al-Tolerance or environment-oforigin for Aluminum Toxicity GEO-GWAS phenotyped lines 47th SNP is 120kb from AltSB GEO-GS prediction Can GEO associations predict response to terminal drought stress? Sudan India Terminal Drought Stress Experiment at UT-Austin GEO-GS and GEO-GWAS: Flowering time plasticity under terminal drought stress Reduced seed set 3200 plants in rain-out shelter (400 accessions ) Observed Flowering Plasticity • Spearman ρ = 0.15 P < 0.014 Terminal drought stress is typical for Well-watered many sorghum growing regions • Adapted varieties may show: Terminal Drought Senescence – Stay-green (non-scenescent) – Stable grain fill (yield) Planting GEO-GS prediction Flowering Grain Fill Harvest – Early or delayed flowering Tom Juenger, Jason Bonnette (UT-Austin) Stephen Kresovich, Zachary Brenton (Clemson) Jesse Lasky GEO-GWAS for Growing Season Length 3 2/26/2014 From diverse germplasm to crop improvement Project team Diverse Crop Germplasm GBS Genome by Environmentof-Origin (GEO) association map Integration GEO-GWAS Genotype-Phenotype Map for Adaptive Traits GWAS GS Stephen Kresovich, Zach Brenton Ed Buckler, Katie Hyma, Sharon Mitchell, Charlotte Acharya Punna Ramu, Tom Hash, Hari Upadhyaya, Santosh Deshpande GEO-GS Genetic Basis of Adaptive Traits New Crop Varieties Better Adapted to Current and Future Environments Jesse Lasky Crop conservation Tom Juenger, Jason Bonnette NSF/Gates – Basic Research to Enable Agricultural Development (BREAD) We’re Hiring, Come talk to me! www.MorrisLab.org 4