TY - JOUR
T1 - Hidden variation in polyploid wheat drives local adaptation
AU - Gardiner, Laura Jayne
AU - Joynson, Ryan
AU - Omony, Jimmy
AU - Rusholme-Pilcher, Rachel
AU - Olohan, Lisa
AU - Lang, Daniel
AU - Bai, Caihong
AU - Hawkesford, Malcolm
AU - Salt, David
AU - Spannagl, Manuel
AU - Mayer, Klaus F.X.
AU - Kenny, John
AU - Bevan, Michael
AU - Hall, Neil
AU - Hall, Anthony
N1 - Publisher Copyright:
© 2018 Gardiner et al.
PY - 2018/9
Y1 - 2018/9
N2 - 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.
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.
UR - http://www.scopus.com/inward/record.url?scp=85052747891&partnerID=8YFLogxK
U2 - 10.1101/gr.233551.117
DO - 10.1101/gr.233551.117
M3 - Article
C2 - 30093548
AN - SCOPUS:85052747891
SN - 1088-9051
VL - 28
SP - 1319
EP - 1332
JO - Genome Research
JF - Genome Research
IS - 9
ER -