Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought
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...
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ftcdlib:oai:escholarship.org:ark:/13030/qt0p33r1zh 2024-06-23T07:50:43+00:00 Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought Lei, Li Poets, Ana M Liu, Chaochih Wyant, Skylar R Hoffman, Paul J Carter, Corey K Shaw, Brian G Li, Xin Muehlbauer, Gary J Katagiri, Fumiaki Morrell, Peter L 3423 - 3438 2019-10-01 application/pdf https://escholarship.org/uc/item/0p33r1zh unknown eScholarship, University of California qt0p33r1zh https://escholarship.org/uc/item/0p33r1zh public G3: Genes, Genomes, Genetics, vol 9, iss 10 Biological Sciences Genetics Adaptation Biological Alleles Cold Temperature Cross-Over Studies Databases Genetic Droughts Environment Gene Frequency Genetic Association Studies High-Throughput Nucleotide Sequencing Molecular Typing Plant Physiological Phenomena Plants Polymorphism Single Nucleotide Stress Physiological cold drought barley allele frequency differentiation mixed model association Biochemistry and cell biology Statistics article 2019 ftcdlib 2024-06-05T00:31:59Z 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. Article in Journal/Newspaper Arctic University of California: eScholarship Arctic |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Biological Sciences Genetics Adaptation Biological Alleles Cold Temperature Cross-Over Studies Databases Genetic Droughts Environment Gene Frequency Genetic Association Studies High-Throughput Nucleotide Sequencing Molecular Typing Plant Physiological Phenomena Plants Polymorphism Single Nucleotide Stress Physiological cold drought barley allele frequency differentiation mixed model association Biochemistry and cell biology Statistics |
spellingShingle |
Biological Sciences Genetics Adaptation Biological Alleles Cold Temperature Cross-Over Studies Databases Genetic Droughts Environment Gene Frequency Genetic Association Studies High-Throughput Nucleotide Sequencing Molecular Typing Plant Physiological Phenomena Plants Polymorphism Single Nucleotide Stress Physiological cold drought barley allele frequency differentiation mixed model association Biochemistry and cell biology Statistics Lei, Li Poets, Ana M Liu, Chaochih Wyant, Skylar R Hoffman, Paul J Carter, Corey K Shaw, Brian G Li, Xin Muehlbauer, Gary J Katagiri, Fumiaki Morrell, Peter L Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
topic_facet |
Biological Sciences Genetics Adaptation Biological Alleles Cold Temperature Cross-Over Studies Databases Genetic Droughts Environment Gene Frequency Genetic Association Studies High-Throughput Nucleotide Sequencing Molecular Typing Plant Physiological Phenomena Plants Polymorphism Single Nucleotide Stress Physiological cold drought barley allele frequency differentiation mixed model association Biochemistry and cell biology Statistics |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Lei, Li Poets, Ana M Liu, Chaochih Wyant, Skylar R Hoffman, Paul J Carter, Corey K Shaw, Brian G Li, Xin Muehlbauer, Gary J Katagiri, Fumiaki Morrell, Peter L |
author_facet |
Lei, Li Poets, Ana M Liu, Chaochih Wyant, Skylar R Hoffman, Paul J Carter, Corey K Shaw, Brian G Li, Xin Muehlbauer, Gary J Katagiri, Fumiaki Morrell, Peter L |
author_sort |
Lei, Li |
title |
Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
title_short |
Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
title_full |
Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
title_fullStr |
Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
title_full_unstemmed |
Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought |
title_sort |
environmental association identifies candidates for tolerance to low temperature and drought |
publisher |
eScholarship, University of California |
publishDate |
2019 |
url |
https://escholarship.org/uc/item/0p33r1zh |
op_coverage |
3423 - 3438 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
G3: Genes, Genomes, Genetics, vol 9, iss 10 |
op_relation |
qt0p33r1zh https://escholarship.org/uc/item/0p33r1zh |
op_rights |
public |
_version_ |
1802641631123341312 |