Environmental association identifies candidates for tolerance to low temperature and drought

Abstract

Barley is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (~30 - 40˚ N) primarily at low elevation, < 1500 m. Adaptation to the range of cultivation has occurred over ~8,000 years. The genetic basis of this adaptation is amenable to study through environmental association. Using genotyping from 7,864 SNPs in 784 barley landraces, we perform mixed model association analysis relative to bioclimatic variables and analysis of allele frequency differentiation across multiple partitions of the data. Using resequencing data from a subset of the landraces, we test for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. We identify seven loci previously reported to contribute to adaptive differences to flowering time and abiotic stress in barley and four loci previously identified in other plant species. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well characterized genes may provide new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.