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.
Highlights
Given a majority of the cotton acreage in many countries is planted with transgenic cultivars, sequencing ZM24 genome and exploring the underlying reasons leading to different transformation ability from TM-1 can further promote the application of biotechnology in cotton production
high throughput chromosome conformation capture (Hi-C) libraries have been widely used to aid the assembly of contigs into chromosomes[8,23], and we here generated >324 million and 476 million valid Hi-C interacting unique pairs for the TM-1 and ZM24 genomes, respectively (Supplementary Table 2)
The core insight revealed by these assemblies is the presence of large-scale structural variations on the 8th chromosome of the At subgenome of this allotetraploid species which can, as a single pair of alleles, accurately differentiate two major haplotypes among worldwide upland cotton accessions
Summary
Multiple cotton genomes (diploid and tetraploid) have been assembled. genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Upland cotton (G. hirsutum) is the main source of renewable textile fiber and an excellent experimental system for studying polyploidization[1,2,3] This allotetraploid cotton species is derived from a single polyploidization event that united the Old World A genome (resembling G. arboreum) and the New World D-genome (resembling G. raimondii) around 1∼2 million years ago (MYA)[4,5]. The lower genetic diversity of cotton germplasm relative to many other crop species has made its genetic improvement challenging[14,15,16] One solution to this problem is to increase resolution of cotton breeding through identification of related genomic features. Genomic resources developed here can promote both basic plant biology research and applied cotton breeding
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