April 21, 2020  |  

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars.

Authors: Yang, Zhaoen and Ge, Xiaoyang and Yang, Zuoren and Qin, Wenqiang and Sun, Gaofei and Wang, Zhi and Li, Zhi and Liu, Ji and Wu, Jie and Wang, Ye and Lu, Lili and Wang, Peng and Mo, Huijuan and Zhang, Xueyan and Li, Fuguang

Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.

Journal: Nature communications
DOI: 10.1038/s41467-019-10820-x
Year: 2019

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