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Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat.

Abstract：

BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION:We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.

journal_name

Genome Biol

journal_title

Genome biology

authors

Cheng H,Liu J,Wen J,Nie X,Xu L,Chen N,Li Z,Wang Q,Zheng Z,Li M,Cui L,Liu Z,Bian J,Wang Z,Xu S,Yang Q,Appels R,Han D,Song W,Sun Q,Jiang Y

doi

10.1186/s13059-019-1744-x

subject

Has Abstract

pub_date

2019-07-12 00:00:00

pages

136

issue

1

eissn

1474-7596

issn

1474-760X

pii

10.1186/s13059-019-1744-x

journal_volume

20

pub_type

杂志文章

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