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 MascherPeter 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

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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., Strozzi, F., Nicolazzi, E. L., Molnar-Lang, M., Ozkan, H., Megyeri, M., Miko, P., Çakır, E., Yakışır, E., Trabanco, N., Delbono, S., Kyriakidis, S., Booth, A., Cammarano, D., ... 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