Hidden variation in polyploid wheat drives local adaptation
- Laura-Jayne Gardiner1,
- Ryan Joynson1,
- Jimmy Omony2,
- Rachel Rusholme-Pilcher1,
- Lisa Olohan3,
- Daniel Lang2,
- Caihong Bai4,
- Malcolm Hawkesford4,
- David Salt5,
- Manuel Spannagl2,
- Klaus F.X. Mayer2,6,
- John Kenny3,
- Michael Bevan7,
- Neil Hall1,8 and
- Anthony Hall1,8
- 1Earlham Institute, Norwich, NR4 7UZ, United Kingdom;
- 2HelmholtzZentrum München, German Research Center for Environmental Health, Munich, 85764, Germany;
- 3Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom;
- 4Rothamsted Research, Harpenden, AL5 2JQ, United Kingdom;
- 5University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, United Kingdom;
- 6Wissenschaftszentrum Weihenstephan (WZW), Technical University Munich, Freising, 85354, Germany;
- 7John Innes Centre, Norwich, NR4 7UH, United Kingdom;
- 8School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
Abstract
Wheat has been domesticated into a large number of agricultural environments and has the ability to adapt to diverse environments. To understand this process, we survey genotype, repeat content, and DNA methylation across a bread wheat landrace collection representing global genetic diversity. We identify independent variation in methylation, genotype, and transposon copy number. We show that these, so far unexploited, sources of variation have had a significant impact on the wheat genome and that ancestral methylation states become preferentially “hard coded” as single nucleotide polymorphisms (SNPs) via 5-methylcytosine deamination. These mechanisms also drive local adaption, impacting important traits such as heading date and salt tolerance. Methylation and transposon diversity could therefore be used alongside SNP-based markers for breeding.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.233551.117.
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Freely available online through the Genome Research Open Access option.
- Received December 12, 2017.
- Accepted July 16, 2018.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
