Structural variation(SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons  

作　　者：Shangkun Jin Zegang Han Yan Hu Zhanfeng Si Fan Dai Lu He Yu Cheng Yiqjan Li Ting Zhao Lei Fang Tianzhen Zhang 

机构地区：[1]Zhejang Provincial Engineering Center for Crop Precision Breeding,Advanced Seed Institute,Plant Precision Breeding Academy,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,China [2]Hainan Institute of Zhejiang University,Sanya 572025,China

出　　处：《Molecular Plant》2023年第4期678-693,共16页分子植物（英文版）

基　　金：supported in part by the 2021 Research Program of Sanya Yazhou Bay Science and Technology City(SKJC-2021-02-001);the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2019R01002);the Fundamental Research Funds for the Central Universities(226-2022-00100 and 2022QZJH43).

摘　　要：Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.

关 键 词：genome assembly structural variations SV-based pan-genome GWAS INTROGRESSION QTL mapping 

分 类 号：Q94[生物学—植物学]