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

Zhaoen Yang, Xiaoyang Ge, Zuoren Yang, Wenqiang Qin, Gaofei Sun, Zhi Wang, Zhi Li, Ji Liu, Jie Wu, Ye Wang, Lili Lu, Peng Wang, Huijuan Mo, Xueyan Zhang and Fuguang Li ()
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Zhaoen Yang: Zhengzhou University
Xiaoyang Ge: Zhengzhou University
Zuoren Yang: Zhengzhou University
Wenqiang Qin: Zhengzhou University
Gaofei Sun: Anyang Institute of Technology
Zhi Wang: Zhengzhou University
Zhi Li: Zhengzhou University
Ji Liu: Zhengzhou University
Jie Wu: Zhengzhou University
Ye Wang: Zhengzhou University
Lili Lu: Zhengzhou University
Peng Wang: Zhengzhou University
Huijuan Mo: Zhengzhou University
Xueyan Zhang: Zhengzhou University
Fuguang Li: Zhengzhou University

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract 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.

Date: 2019
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DOI: 10.1038/s41467-019-10820-x

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