Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

Joanne Russell, Martin Mascher, Ian K Dawson, Stylianos Kyriakidis, Cristiane Calixto, Fabian Freund, Micha Bayer, Iain Milne, Tony Marshall-Griffiths, Shane Heinen, Anna Hofstad, Rajiv Sharma, Axel Himmelbach, Manuela Knauft, Maarten van Zonneveld, John W S Brown, Karl Schmid, Benjamin Kilian, Gary J Muehlbauer, Nils Stein & 1 others Robbie Waugh

Research output: Contribution to journalArticleResearchpeer-review

62 Citations (Scopus)

Abstract

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

Original languageEnglish
Pages (from-to)1024-1030
Number of pages7
JournalNature Genetics
Volume48
Issue number9
DOIs
Publication statusPrint publication - 1 Sep 2016
Externally publishedYes

Fingerprint

Exome
Hordeum
Genome
Genes
Geography
Haplotypes
Temperature

Keywords

  • Adaptation
  • Environment
  • Exome
  • Plant genetics
  • Genetic variation
  • Genotype
  • Geography
  • Hordeum
  • Phenotype

Cite this

Russell, Joanne ; Mascher, Martin ; Dawson, Ian K ; Kyriakidis, Stylianos ; Calixto, Cristiane ; Freund, Fabian ; Bayer, Micha ; Milne, Iain ; Marshall-Griffiths, Tony ; Heinen, Shane ; Hofstad, Anna ; Sharma, Rajiv ; Himmelbach, Axel ; Knauft, Manuela ; van Zonneveld, Maarten ; Brown, John W S ; Schmid, Karl ; Kilian, Benjamin ; Muehlbauer, Gary J ; Stein, Nils ; Waugh, Robbie. / Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. In: Nature Genetics. 2016 ; Vol. 48, No. 9. pp. 1024-1030.
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abstract = "After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.",
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Russell, J, Mascher, M, Dawson, IK, Kyriakidis, S, Calixto, C, Freund, F, Bayer, M, Milne, I, Marshall-Griffiths, T, Heinen, S, Hofstad, A, Sharma, R, Himmelbach, A, Knauft, M, van Zonneveld, M, Brown, JWS, Schmid, K, Kilian, B, Muehlbauer, GJ, Stein, N & Waugh, R 2016, 'Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation', Nature Genetics, vol. 48, no. 9, pp. 1024-1030. https://doi.org/10.1038/ng.3612

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. / Russell, Joanne; Mascher, Martin; Dawson, Ian K; Kyriakidis, Stylianos; Calixto, Cristiane; Freund, Fabian; Bayer, Micha; Milne, Iain; Marshall-Griffiths, Tony; Heinen, Shane; Hofstad, Anna; Sharma, Rajiv; Himmelbach, Axel; Knauft, Manuela; van Zonneveld, Maarten; Brown, John W S; Schmid, Karl; Kilian, Benjamin; Muehlbauer, Gary J; Stein, Nils; Waugh, Robbie.

In: Nature Genetics, Vol. 48, No. 9, 01.09.2016, p. 1024-1030.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Russell, Joanne

AU - Mascher, Martin

AU - Dawson, Ian K

AU - Kyriakidis, Stylianos

AU - Calixto, Cristiane

AU - Freund, Fabian

AU - Bayer, Micha

AU - Milne, Iain

AU - Marshall-Griffiths, Tony

AU - Heinen, Shane

AU - Hofstad, Anna

AU - Sharma, Rajiv

AU - Himmelbach, Axel

AU - Knauft, Manuela

AU - van Zonneveld, Maarten

AU - Brown, John W S

AU - Schmid, Karl

AU - Kilian, Benjamin

AU - Muehlbauer, Gary J

AU - Stein, Nils

AU - Waugh, Robbie

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N2 - After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

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KW - Environment

KW - Exome

KW - Plant genetics

KW - Genetic variation

KW - Genotype

KW - Geography

KW - Hordeum

KW - Phenotype

U2 - 10.1038/ng.3612

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M3 - Article

VL - 48

SP - 1024

EP - 1030

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

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