Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

Abstract

Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome-wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non-synonymous SNP (A-to-G) site in a gene encoding the cell wall-associated receptor-like kinase 3 (GhWAKL3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

“…Based on a group of SNPs, a number of improvement‐selective sweeps involving a string of causal genes and IBD segments inherited from foundation parents have been identified, laying a foundation for germplasm resource analysis and breeding by design in the future. In recent years, an abundance studies have been performed to trace IBD segments and exploit key trait regions during the breeding process following their well‐defined genetic paths (Chen et al , ; Fang et al , ; Lai et al , ; Lu et al , ; Ma et al , ; Wu et al , ). Based on more than 2 million SNPs, the Xinjiang cotton population could be divided into two groups (Figure ), preliminarily indicating that Upland cotton populations in Xinjiang were not only spawned from DPL15, STV2B and UGDM, which are the original germplasms used for modern Upland cotton breeding in Yangtze River and Yellow River cotton‐growing regions in China (Fang et al , ), but also have a close kinship with the former Soviet Union cotton landraces.…”

“…In addition, the nonsynonymous SNP in these two genes is significantly correlated with LP (Figure ). Similarly, a nonsynonymous SNP in GhWAKL 3 (Ma et al , ), two nonsynonymous SNPs in AIL6 (Fang et al , ) and two SNPs in Dof‐binding motif have all been associated with high lint yield (Wang et al , ).…”

“…These cultivars exhibit phenotypes commensurate with important traits (Shinada et al , ), as exemplified in the development of Kitaake, Kyowa and Huanghuazhan in rice (Shinada et al , ; Zhou et al , ), B73, Mo17, etc. in maize (Lai et al , ; Smith et al , ; Wu et al , ), and Ekangmian 9 and CRI12 in cotton (Lu et al , ; Ma et al , ). Moreover, identity‐by‐descent (IBD) regions have been demonstrated to be powerful in relatedness evaluation and mapping of genetic loci associated with phenotypic variations in many studies (Browning and Browning, ; Browning and Thompson, ; Stevens et al , ; Westerlind et al , ) .…”

An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton

“…In the last decades, abundant QTL for cotton yield-related traits had been detected via linkage mapping method, and the QTL mapping results were summarized in cotton [5]. Over the past 5 years, a lot of significant single-nucleotide polymorphisms (SNPs) associated with fiber yield component traits have been identified by using genome-wide association studies (GWAS) methods in upland cotton [1,4,[6][7][8][9]. These GWAS findings laid a good foundation for deciphering the genetic basis underlying cotton yieldrelated traits.…”

Construction of a High-Density Genetic Map via Genome Resequencing and QTL Detection for Key Fiber Traits in Asiatic Cotton

“…In recent years, SNP (single nucleotide polymorphism) molecular marker has become popular in high-density genetic map construction, QTL mapping and marker assisted selection (MAS) due to its abundance in plant genome and advancement in next generation sequencing (NGS) [13][14][15]. And many NGS-related approaches have been developed to identify SNPs in cotton, such as whole genome resequencing [16,17], restriction site-associated DNA sequencing (RAD-seq) [18,19], speci c locus ampli ed fragment sequencing (SLAF-seq) [20][21][22] and genotyping-by-sequencing (GBS) [23,24]. In addition, the release of genome sequences of cotton species including G. arboreum [16], G. raimondii [25], G. hirsutum [26] and G. barbadense [27] made it easy to construct genetic map and detect QTL via NGS technology.…”