RT Journal Article
SR Electronic
T1 Environmental association identifies candidates for tolerance to low temperature and drought
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 405399
DO 10.1101/405399
A1 Li Lei
A1 Ana M. Poets
A1 Chaochih Liu
A1 Skylar R. Wyant
A1 Paul J. Hoffman
A1 Corey K. Carter
A1 Richard M. Trantow
A1 Brian G. Shaw
A1 Xin Li
A1 Gary J. Muehlbauer
A1 Fumiaki Katagiri
A1 Peter L. Morrell
YR 2019
UL http://biorxiv.org/content/early/2019/02/15/405399.abstract
AB Barley (Hordeum vulgare ssp. vulgare) 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 (< 1,500 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 803 barley landraces, we performed 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 these landraces, we tested for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. Six loci previously reported to contribute to adaptive differences in flowering time and abiotic stress in barley and six loci previously identified in other plant species were identified in our analyses. 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.