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

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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Figure 1: Principal-components analysis of diversity in the barley collection.
Figure 2: Chromosome-level profiles for different groups of barley accessions.
Figure 3: Geographical partitioning of diversity.
Figure 4: Common garden experiments.
Figure 5: Molecular and spatial variation in HvCEN and HvPPD-H1.

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European Nucleotide Archive

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Acknowledgements

We specifically thank B. Thomas and A. Booth for helpful discussions around the common garden experiments. We would like to acknowledge funding from the Scottish Government Research Program to R.W., J.R., I.K.D., M.B. and I.M. and from the European Union Framework Programme 7 WHEALBI project to J.R., R.W., N.S., I.K.D., S.K. and B.K. M.v.Z. has been supported by the CGIAR Climate Change, Agriculture and Food Security (CCAFS) program. The work would not have been possible without funding from BBSRC grant BB/I00663X/1 to R.W., German Science Foundation (DFG) SPP1530 grant KI1465/6-1 to B.K. and BMBF TRITEX 0315954 A to N.S. Funding to G.J.M. was provided by the US Department of Agriculture–National Institute of Food and Agriculture (USDA-NIFA) as part of the Triticeae Coordinated Agricultural Project (TCAP), grant 2011-68002-30029. Analysis carried out by F.F. and K.S. was mainly performed on the computational resource bwUniCluster funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany, within the framework program bwHPC.

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Authors

Contributions

R.W., G.J.M., N.S. and B.K. conceived the study. B.K. selected the germplasm for inclusion and purified lines by two rounds of SSD. B.K., R.S., G.J.M., S.H., A. Hofstad and J.R. conducted the common garden experiments and analyzed the data. M.K., A. Himmelbach and N.S. generated the exome sequence data. J.R., I.K.D., K.S., F.F., M.M., S.K., C.C., M.B., J.W.S.B., M.v.Z., T.M.-G. and I.M. analyzed the data and provided information included in the supplementary files. R.W., M.M., I.K.D., J.R., F.F., N.S. and G.J.M. wrote the manuscript.

Corresponding author

Correspondence to Robbie Waugh.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Table 2–4 and 6, and Supplementary Figures 1–31. (PDF 7631 kb)

Supplementary Table 1

Information on 267 exome-captured barley accessions. (XLSX 146 kb)

Supplementary Table 5

Polymorphisms in flowering-associated genes. (XLSX 92 kb)

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Russell, J., Mascher, M., Dawson, I. et al. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48, 1024–1030 (2016). https://doi.org/10.1038/ng.3612

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