Environmental association identifies candidates for tolerance to low temperature and drought

Li Lei, Ana M. Poets, Chaochih Liu, Skylar R. Wyant, Paul J. Hoffman, Corey K. Carter, Brian G. Shaw, Xin Li, Gary J. Muehlbauer, Fumiaki Katagiri, Peter L. Morrell

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

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 adaptation is amenable to study through environmental association. An advantage of environmental association in a well-characterized crop is that many loci that contribute to climatic adaptation and abiotic stress tolerance have already been identified. This provides the opportunity to determine if environmental association approaches effectively identify these loci of large effect. Using published genotyping from 7,864 SNPs in 803 barley landraces, we examined allele frequency differentiation across multiple partitions of the data and mixed model associations relative to bioclimatic variables. Using newly generated 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 a 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.

Original languageEnglish (US)
Pages (from-to)3423-3438
Number of pages16
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number10
DOIs
StatePublished - Oct 1 2019

Bibliographical note

Funding Information:
We would like to thank A Proulx and R Trantow for annotation of physical positions of 9K SNPs. E Vonderharr assisted with National Center for Biotechnology Information's Sequence Read Archive (NCBI SRA) submissions. T Kono provided helpful comments that improved the manuscript. This study was supported by the U.S. NSF Plant Genome Program (IOS-1339393) to PLM and the USDA Triticeae Coordinated Agricultural Project 2011-68002-30029 to GJM and PLM, and NSF (MCB-1518058) to FK. This research was carried out with hardware and software support provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota.

Funding Information:
We would like to thank A Proulx and R Trantow for annotation of physical positions of 9K SNPs. E Vonderharr assisted with National Center for Biotechnology Information’s Sequence Read Archive (NCBI SRA) submissions. T Kono provided helpful comments that improved the manuscript. This study was supported by the U.S. NSF Plant Genome Program (IOS-1339393) to PLM and the USDA Triticeae Coordinated Agricultural Project 2011-68002-30029 to GJM and PLM, and NSF (MCB-1518058) to FK. This research was carried out with hardware and software support provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota.

Publisher Copyright:
Copyright © 2019 Lei et al.

Keywords

  • Adaptation
  • Allele frequency differentiation
  • Barley
  • Cold
  • Drought
  • Mixed model association

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