Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits.

Authors: Du, Xiongming and Huang, Gai and He, Shoupu and Yang, Zhaoen and Sun, Gaofei and Ma, Xiongfeng and Li, Nan and Zhang, Xueyan and Sun, Junling and Liu, Min and Jia, Yinhua and Pan, Zhaoe and Gong, Wenfang and Liu, Zhaohui and Zhu, Heqin and Ma, Lei and Liu, Fuyan and Yang, Daigang and Wang, Fan and Fan, Wei and Gong, Qian and Peng, Zhen and Wang, Liru and Wang, Xiaoyang and Xu, Shuangjiao and Shang, Haihong and Lu, Cairui and Zheng, Hongkun and Huang, Sanwen and Lin, Tao and Zhu, Yuxian and Li, Fuguang

The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243?G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduced to the Yangtze and Yellow River regions. Most accessions with domestication-related traits experienced geographic isolation. Genome-wide association study (GWAS) identified 98 significant peak associations for 11 agronomically important traits in G. arboreum. A nonsynonymous substitution (cysteine-to-arginine substitution) of GaKASIII seems to confer substantial fatty acid composition (C16:0 and C16:1) changes in cotton seeds. Resistance to fusarium wilt disease is associated with activation of GaGSTF9 expression. Our work represents a major step toward understanding the evolution of the A genome of cotton.

Journal: Nature genetics
DOI: 10.1038/s41588-018-0116-x
Year: 2018

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