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

Hong Cheng  Jing Liu  Jia Wen  Xiaojun Nie  Luohao Xu  Ningbo Chen  Zhongxing Li  Qilin Wang  Zhuqing Zheng  Ming Li  Licao Cui  Zihua Liu  Jianxin Bian  Zhonghua Wang  Shengbao Xu  Qin Yang  Rudi Appels  Dejun Han  Qixin Sun  Yu Jiang  Weining Song  
【摘要】:Bread wheat is one of the most important crops,with a long history of characterizing its domestication.However,complete comprehensions of the landscape of genomic variations and domestication history of bread wheat are still lacking up to now.In this study,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 reveal different patterns of genetic variations and diversity among bread wheat subgenomes.The B subgenome has more variations than A and D subgenomes,including SNPs and deletions.We propose that the asymmetric evolutionary changes among subgenomes have laid the genetic basis of wheat.Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant,with substantial introgressed genomic fragments from southern Levant,contributing to the large haplotypes more than 676 Mb in the AB subgenomes,enriched in pericentromeric regions where recombination rates are extremely low.The AB-subgenome specific introgressions at the early stage of wheat formation partially contributes to their larger genetic diversity in relative to the D subgenome.Furthermore,we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations,resulting in reintroduction of~709 Mb and~1,577 Mb sequences into bread wheat landraces and varieties,respectively.A large fraction of these intro-and inter-introgression fragments associated with QTLs of important traits and selection events are also identified.The discoveries in this study expand our knowledge of genetic diversity and evolutionary trajectories of present-day bread wheat Our findings reveal that the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat,which also provide important resources and new perspectives for future wheat breeding

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