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Nat Commun. 2019 Jul 5;10(1):2989. doi: 10.1038/s41467-019-10820-x.

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

Yang Z1,2, Ge X1,2, Yang Z1,2, Qin W1,2, Sun G3, Wang Z1,2, Li Z1,2, Liu J1,2, Wu J1,2, Wang Y1,2, Lu L1,2, Wang P1,2, Mo H1,2, Zhang X1,2, Li F4,5.

Author information

1
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
2
Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
3
Anyang Institute of Technology, Anyang, 455000, China.
4
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China. aylifug@163.com.
5
Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China. aylifug@163.com.

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.

PMID:
31278252
PMCID:
PMC6611876
DOI:
10.1038/s41467-019-10820-x
[Indexed for MEDLINE]
Free PMC Article

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