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Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

文献类型： 外文期刊

作者： Han, Zegang 1 ; Hu, Yan 2 ; Tian, Qin 3 ; Cao, Yiwen 2 ; Si, Aijun 3 ; Si, Zhanfeng 2 ; Zang, Yihao 1 ; Xu, Chenyu 1 ; Shen, 1 ;

作者机构： 1.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing, Peoples R China

2.Zhejiang Univ, Coll Agr & Biotechnol, Plant Precis Breeding Acad, Inst Crop Sci,Zhejiang Prov Key Lab Crop Genet Re, Hangzhou, Peoples R China

3.Xinjiang Acad Agr & Reclamat Sci, Cotton Res Inst, Minist Agr, Key Lab China Northwestern Inland Reg, Shihezi, Peoples R China

4.Esquel Grp, Wanchai, Hong Kong, Peoples R China

关键词： Gossypium hirsutum; Xinjiang cotton improvement; identity by descent; resequencing

期刊名称：PLANT BIOTECHNOLOGY JOURNAL （ 影响因子：9.803； 五年影响因子：9.555 ）

ISSN： 1467-7644

年卷期：

页码：

收录情况： SCI

摘要： Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep-sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108CYRILLIC CAPITAL LETTER EF, C1470, 611 and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re-sequenced sixty-nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high-quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108CYRILLIC CAPITAL LETTER EF, C1470, 611 and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity-by-descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis-antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108CYRILLIC CAPITAL LETTER EF and 611 was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next-generation precision breeding of cotton and other crops.

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