Genomic insights into the genetic basis of cotton breeding in China

文献类型： 外文期刊

第一作者： Li, Yiqian

作者： Li, Yiqian;Si, Zhanfeng;Shi, Zhuolin;Chen, Jinwen;Qi, Guoan;Jin, Shangkun;Han, Zegang;Gao, Wenhao;Tian, Yue;Fang, Lei;Hu, Yan;Zhang, Tianzhen;Wang, Guoping;Tian, Yue;Mao, Yun;Zhu, Xiefei;Tian, Yue;Chen, Hong

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关键词： cotton; MAGIC population; GWAS; whole-genome sequencing; pleiotropic loci; breeding history

期刊名称：MOLECULAR PLANT （ 影响因子：27.5； 五年影响因子：22.6 ）

ISSN： 1674-2052

年卷期： 2023 年 16 卷 4 期

页码：

收录情况： SCI

摘要： The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to cotton production in China, the world's largest producer and consumer of cotton. However, the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear. In this study, we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality. Of them, 25 (46.30%) pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits, revealing complex trade-offs and linkage drags in Upland cotton agronomic traits. Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles. Interestingly, 85% of these elite alleles were selected and fixed from different American ancestors, consistent with cotton breeding practices in China. However, seven elite alleles of native origin that are responsible for Fusarium wilt resistance, early maturing, good-quality fiber, and other characteristics were not found in American ancestors but have greatly contributed to Chinese cotton breeding and wide cultivation. Taken together, these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

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