Association mapping and domestication analysis to dissect genetic improvement process of upland cotton yield-related traits in China

Guo C., Pan Z., You C., Zhou X., Huang C., Shen C., Zhao R., Yang Q., Zhu L., Shahzad R., Meng F., Lin Z., Nie X.

Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, Xinjiang 832003, China; Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang 832011, China; Cotton Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, Xinjiang 832000, China; National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Biotechnology, Faculty of Science and Technology, Universitas Muhammadiyah Bandung, Bandung, West Java 40614, Indonesia; Agricultural Science Research Institute of the 5th Division of Xinjiang Production and Construction Corps, Shuanghe, Xinjiang 833408, China


Background: Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield-related traits contributes to genetic improvement of cotton. Results: In this study, 503 upland cotton varieties covering the four breeding stages (BS1–BS4, 1911–2011) in China were used for association mapping and domestication analysis. One hundred and forty SSR markers significantly associated with ten fiber yield-related traits were identified, among which, 29 markers showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 markers showed decreased trend effect. Four favorable alleles of 9 major loci (R2 ≥ 3) were strongly selected during the breeding stages, and the candidate genes of the four strongly selected alleles were predicated according to the gene function annotation and tissue expression data. Conclusions: The study not only uncovers the genetic basis of 10 cotton yield-related traits but also provides genetic evidence for cotton improvement during the cotton breeding process in China. © 2021, The Author(s).

Favorable alleles; Genome wide association study; Upland cotton; Yield-related traits


Journal of Cotton Research

Publisher: BioMed Central Ltd

Volume 4, Issue 1, Art No 10, Page – , Page Count

Journal Link:

doi: 10.1186/s42397-021-00087-3

Issn: 20965044

Type: All Open Access, Gold, Green


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