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

Abstract

Understanding the genetic diversity and population structure of germplasms is essential when selecting parents for crop breeding. The genomic changes that occurred during the domestication and improvement of Upland cotton ( Gossypium hirsutum ) remains poorly understood. Besides, the available genetic resources from cotton cultivars are limited. By applying restriction site-associated DNA marker sequencing (RAD-seq) technology to 582 tetraploid cotton accessions, we confirmed distinct genomic regions on chromosomes A06 and A08 in Upland cotton cultivar subgroups. Based on the pedigree, reported QTLs, introgression analyses, and genome-wide association study (GWAS), we suggest that these divergent regions might have resulted from the introgression of exotic lineages of G. hirsutum landraces and their wild relatives. These regions were the typical genomic signatures that might be responsible for maturity and fiber quality on chromosome A06 and chromosome A08, respectively. Moreover, these genomic regions are located in the putative pericentromeric regions, implying that their application will be challenging. In the study, based on high-density SNP markers, we reported two genomic signatures on chromosomes A06 and A08, which might originate from the introgression events in the Upland cotton population. Our study provides new insights for understanding the impact of historic introgressions on population divergence and important agronomic traits of modern Upland cotton cultivars.

Hybridization and introgression in sympatric and allopatric populations of four oak species

“…Nuclear DNA markers, such as microsatellites (SSRs) [12], randomly amplified polymorphic DNA markers [13], and chloroplast DNA [14] have been used to detect introgression across species. With advancements in genomic studies, our understanding of the ecological, genetic, and genomic factors underlying the diverse outcomes of interspecific introgression in hybrid zones is increasing [15][16][17].…”

Research progress in the population differentiation and geographical adaptation of cotton

“…Differentiation of upland cotton core collection had an obvious geographical distribution and phenotypic characteristics (Ma et al 2018;Dai et al 2020), which might be driven by three largescale inversions on chromosome A08 and A06 by directly comparing genome assembles and using population genetics approaches (Yang et al 2019;Dai et al 2020). This phenomenon was also found in other Upland cotton populations (He et al 2019(He et al , 2020. He et al (2021) published a study in Nature Genetics that provided insights into the genomic basis of population differentiation and geographical distribution in cultivated G. hirsutum.…”

Genome-wide association study for seedling biomass-related traits in Gossypium arboreum L.

“…To date, a still fewer study has been reported for genetic control of seedling biomass-related traits in cotton. Multigenic control and elusive environmental influences make it difficult to understand the genetic control and development of molecular markers for seedling biomass-related traits [ 17 ]. Owing to advances in omics, recent reports suggested the identification of molecular markers concerning seedling biomass-related traits in different species, viz., rice [ 18 ], Brassica [ 19 ], and wheat [ 20 – 22 ].…”

“…Recent advances in sequencing technology have led to extensive Genome-wide association studies (GWAS) in crop plants [ 17 , 18 , 23 – 26 ]. Based on population genetics and genome analysis of natural genetic populations, GWAS has proven to be an efficient tool for understanding the relationship between phenotype and associated genetic variation [ 27 – 29 ].…”