RT Journal
A1 Gardiner, Laura-Jayne
A1 Joynson, Ryan
A1 Omony, Jimmy
A1 Rusholme-Pilcher, Rachel
A1 Olohan, Lisa
A1 Lang, Daniel
A1 Bai, Caihong
A1 Hawkesford, Malcolm
A1 Salt, David
A1 Spannagl, Manuel
A1 Mayer, Klaus F.X.
A1 Kenny, John
A1 Bevan, Michael
A1 Hall, Neil
A1 Hall, Anthony
T1 Hidden variation in polyploid wheat drives local adaptation
JF Genome Research 
JO Genome Research 
YR 2018 
FD September 01 
VO 28 
IS 9 
SP 1319 
OP 1332 
DO 10.1101/gr.233551.117 
UL http://genome.cshlp.org/content/28/9/1319.abstract 
AB 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.