Genomic Signatures of Climate and Soil Adaptation in a Widely-diffused Crop

In widely-distributed plants the patterns of genomic diversity carry signatures of adaptation to local climates and stressors. To gain insight into the genetic basis of environmental adaptation in sorghum and guide germplasm conservation and utilization, we characterized a worldwide sample of ~2,000 source-identified landraces at >400,000 SNPs using genotyping-by-sequencing. Using this global SNP diversity map, we characterized the associations of alleles with bioclimatic and soil variables, and identified climate-SNP association peaks that co-localize with SNPs associated with agroclimatic traits. We found that climate variation among sites of origin explained a substantial portion of total genomic variation independent of geographical distance among accessions. Additionally, we found that non-synonymous SNPs were enriched for climate associations while intergenic SNPs were under-enriched compared to genome-wide averages. Finally, we found that climate-associated SNPs could be used to predict genotype-by-environment effects on accession performance in common gardens under normal versus drought conditions.