Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley

Daniela Bustos-Korts, Ian K. Dawson, Joanne Russell, Alessandro Tondelli, Davide Guerra, Chiara Ferrandi, Francesco Strozzi, Ezequiel L. Nicolazzi, Marta Molnar-Lang, Hakan Ozkan, Maria Megyeri, Peter Miko, Esra Çakır, Enes Yakışır, Noemi Trabanco, Stefano Delbono, Stylianos Kyriakidis, Allan Booth, Davide Cammarano, Martin Mascher & 7 others Peter Werner, Luigi Cattivelli, Laura Rossini, Nils Stein, Benjamin Kilian, Robbie Waugh, Fred A. van Eeuwijk

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Abstract

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

Original languageEnglish
Pages (from-to)1172-1191
Number of pages20
JournalPlant Journal
Volume99
Issue number6
Early online date20 May 2019
DOIs
Publication statusPublished - 13 Sep 2019

Fingerprint

Exome
Hordeum
field experimentation
barley
Climate Change
Genotype
crops
genotype
Circadian Clocks
Geography
climate change
prioritization
Haplotypes
Genes
Breeding
crop models
geography
breeding lines
heading
phenotypic variation

Keywords

  • H. vulgare ssp. vulgare
  • adaptation
  • barley
  • common garden trials
  • exome sequence haplotypes
  • genetic diversity
  • genotype-by-environment interactions

Cite this

Bustos-Korts, D., Dawson, I. K., Russell, J., Tondelli, A., Guerra, D., Ferrandi, C., ... van Eeuwijk, F. A. (2019). Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. Plant Journal, 99(6), 1172-1191. https://doi.org/10.1111/tpj.14414
Bustos-Korts, Daniela ; Dawson, Ian K. ; Russell, Joanne ; Tondelli, Alessandro ; Guerra, Davide ; Ferrandi, Chiara ; Strozzi, Francesco ; Nicolazzi, Ezequiel L. ; Molnar-Lang, Marta ; Ozkan, Hakan ; Megyeri, Maria ; Miko, Peter ; Çakır, Esra ; Yakışır, Enes ; Trabanco, Noemi ; Delbono, Stefano ; Kyriakidis, Stylianos ; Booth, Allan ; Cammarano, Davide ; Mascher, Martin ; Werner, Peter ; Cattivelli, Luigi ; Rossini, Laura ; Stein, Nils ; Kilian, Benjamin ; Waugh, Robbie ; van Eeuwijk, Fred A. / Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. In: Plant Journal. 2019 ; Vol. 99, No. 6. pp. 1172-1191.
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abstract = "Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.",
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author = "Daniela Bustos-Korts and Dawson, {Ian K.} and Joanne Russell and Alessandro Tondelli and Davide Guerra and Chiara Ferrandi and Francesco Strozzi and Nicolazzi, {Ezequiel L.} and Marta Molnar-Lang and Hakan Ozkan and Maria Megyeri and Peter Miko and Esra {\cC}akır and Enes Yakışır and Noemi Trabanco and Stefano Delbono and Stylianos Kyriakidis and Allan Booth and Davide Cammarano and Martin Mascher and Peter Werner and Luigi Cattivelli and Laura Rossini and Nils Stein and Benjamin Kilian and Robbie Waugh and {van Eeuwijk}, {Fred A.}",
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Bustos-Korts, D, Dawson, IK, Russell, J, Tondelli, A, Guerra, D, Ferrandi, C, Strozzi, F, Nicolazzi, EL, Molnar-Lang, M, Ozkan, H, Megyeri, M, Miko, P, Çakır, E, Yakışır, E, Trabanco, N, Delbono, S, Kyriakidis, S, Booth, A, Cammarano, D, Mascher, M, Werner, P, Cattivelli, L, Rossini, L, Stein, N, Kilian, B, Waugh, R & van Eeuwijk, FA 2019, 'Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley', Plant Journal, vol. 99, no. 6, pp. 1172-1191. https://doi.org/10.1111/tpj.14414

Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. / Bustos-Korts, Daniela; Dawson, Ian K.; Russell, Joanne; Tondelli, Alessandro; Guerra, Davide; Ferrandi, Chiara; Strozzi, Francesco; Nicolazzi, Ezequiel L.; Molnar-Lang, Marta; Ozkan, Hakan; Megyeri, Maria; Miko, Peter; Çakır, Esra; Yakışır, Enes; Trabanco, Noemi; Delbono, Stefano; Kyriakidis, Stylianos; Booth, Allan; Cammarano, Davide; Mascher, Martin; Werner, Peter; Cattivelli, Luigi; Rossini, Laura; Stein, Nils; Kilian, Benjamin; Waugh, Robbie (Lead / Corresponding author); van Eeuwijk, Fred A. (Lead / Corresponding author).

In: Plant Journal, Vol. 99, No. 6, 13.09.2019, p. 1172-1191.

Research output: Contribution to journalArticle

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T1 - Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley

AU - Bustos-Korts, Daniela

AU - Dawson, Ian K.

AU - Russell, Joanne

AU - Tondelli, Alessandro

AU - Guerra, Davide

AU - Ferrandi, Chiara

AU - Strozzi, Francesco

AU - Nicolazzi, Ezequiel L.

AU - Molnar-Lang, Marta

AU - Ozkan, Hakan

AU - Megyeri, Maria

AU - Miko, Peter

AU - Çakır, Esra

AU - Yakışır, Enes

AU - Trabanco, Noemi

AU - Delbono, Stefano

AU - Kyriakidis, Stylianos

AU - Booth, Allan

AU - Cammarano, Davide

AU - Mascher, Martin

AU - Werner, Peter

AU - Cattivelli, Luigi

AU - Rossini, Laura

AU - Stein, Nils

AU - Kilian, Benjamin

AU - Waugh, Robbie

AU - van Eeuwijk, Fred A.

N1 - Funding: European Union's Seventh Framework Programme (FP7/ 2007-2013) under the grant agreement n°FP7-613556.

PY - 2019/9/13

Y1 - 2019/9/13

N2 - Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

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KW - H. vulgare ssp. vulgare

KW - adaptation

KW - barley

KW - common garden trials

KW - exome sequence haplotypes

KW - genetic diversity

KW - genotype-by-environment interactions

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Bustos-Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C et al. Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. Plant Journal. 2019 Sep 13;99(6):1172-1191. https://doi.org/10.1111/tpj.14414