Genomic divergence in cotton germplasm related to maturity and heterosis

Abstract

Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high‐quality single‐nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage‐specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity‐related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage‐specific regions and heterozygous loci, in the high‐yield hybrids, suggests a role for these regions in cotton heterosis.

Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton

“…The Second introduction of tetraploid cotton into China was at the beginning of the 20th century when upland cotton was systematically introduced into China. During these years, cotton was mainly distributed in the Yangtze River region and the Yellow River region in China [7].…”

“…During recent years, cotton production has been mainly shifted to Xinjiang province. Prior to the introduction and implementation of Seed Law (SL) and Plant Variety Protection Act (PVPA) in China [8], most of the southwest varieties (introduced in early 20th century from the United States of America in the Yangtze River region and Yellow River region in China [7]) were maintained by farmers over the years. From this diverse southern gene pool, which is not only from different ecosystems but also has lower human intervention, useful information can be excavated to study the diversity of cotton crop in China through the evaluation of current Chinese varieties and their genetic background with reference to southern varieties and landraces from Central America.…”

Genome Resequencing Reveals Genetic Variation between the Parents of An Elite Hybrid Upland Cotton

“…Heterosis is that a hybrid is superior to two parents in one or more traits, and it is a common genetic phenomenon in nature [11]. Compared with the parental lines, CCRI63 showed superior performances in terms of lint percentage and boll weight.…”

“…In tomato, the overdominance model was proven, and revealed that heterozygous mutations perform better than homozygous ones [10]. In cotton, the researchers investigated the distribution of heterozygous loci among 12 commercial cotton hybrids, and suggested that heterozygous loci-enrichment may be responsible for the hybrid high yield performance and cotton heterosis was driven, in part, by these heterozygous sites [11].…”

Introgression Leads to Genomic Divergence and Responsible for Important Traits in Upland Cotton

“…A recent study, based on SNP microarray, demonstrated the presence of extensive genomic divergence in the Upland cotton source germplasm and suggested that divergent genomic regions might be related to maturity and heterosis ( He et al, 2019 ). However, the origin of these regions is still unknown.…”