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High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement
Nature Genetics  (IF38.33),  Pub Date : 2021-08-09, DOI: 10.1038/s41588-021-00910-2
Ma, Zhiying, Zhang, Yan, Wu, Liqiang, Zhang, Guiyin, Sun, Zhengwen, Li, Zhikun, Jiang, Yafei, Ke, Huifeng, Chen, Bin, Liu, Zhengwen, Gu, Qishen, Wang, Zhicheng, Wang, Guoning, Yang, Jun, Wu, Jinhua, Yan, Yuanyuan, Meng, Chengsheng, Li, Lihua, Li, Xiuxin, Mo, Shaojing, Wu, Nan, Ma, Limei, Chen, Liting, Zhang, Man, Si, Aijun, Yang, Zhanwu, Wang, Nan, Wu, Lizhu, Zhang, Dongmei, Cui, Yanru, Cui, Jing, Lv, Xing, Li, Yang, Shi, Rongkang, Duan, Yihong, Tian, Shilin, Wang, Xingfen

Cotton produces natural fiber for the textile industry. The genetic effects of genomic structural variations underlying agronomic traits remain unclear. Here, we generate two high-quality genomes of Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90, and identify large-scale structural variations in the two species and 1,081 G. hirsutum accessions. The density of structural variations is higher in the D-subgenome than in the A-subgenome, indicating that the D-subgenome undergoes stronger selection during species formation and variety development. Many structural variations in genes and/or regulatory regions potentially influencing agronomic traits were discovered. Of 446 significantly associated structural variations, those for fiber quality and Verticillium wilt resistance are located mainly in the D-subgenome and those for yield mainly in the A-subgenome. Our research provides insight into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.