Genetic dissection of fiber quality traits in an interspecific Gossypium barbadense × Gossypium darwinii recombinant inbred lines population

Cotton ( Gossypium spp. ) is one of the most important fiber crops worldwide, providing natural fibers that support the textile industry and human livelihoods. Fiber quality traits are major determinants of cotton economic value because they directly influence spinning performance, yarn strength, and the quality of textile products. However, the genetic mechanisms underlying the complex inheritance of fiber quality traits remain incompletely understood, particularly in populations derived from wild and cultivated cotton relatives. In this study, a recombinant inbred line (RIL) population developed from an interspecific cross between Gossypium barbadense and Gossypium darwinii was used to dissect the genetic basis of fiber quality traits. A high-density genetic linkage map was constructed using single nucleotide polymorphism (SNP) markers, comprising 3 518 markers spanning a total genetic distance of 3 801.17 cM. Phenotypic evaluations of three yield-related traits and five fiber quality traits were conducted across three consecutive years. A total of 89 quantitative trait loci (QTLs) were identified, including 20 stable QTLs consistently detected across multiple environments. These QTLs were associated with boll weight (BW), fiber length (FL), fiber strength (FS), fiber elongation (FE), seed index (SI), micronaire (MIC), and lint percentage (LP). Major QTLs were distributed mainly on chromosomes chr-D07, chr-A12, chr-D01, chr-D06, chr-D04, and chr-D12. A QTL hotspot region on chr-D07 was identified, where co-localized loci controlling FL, FS, FE, and SI were detected. Within this hotspot, two candidate genes, ZINC FINGER PROTEIN and LOC107929956 , were identified as potential regulators of fiber development. Among them, ZINC FINGER PROTEIN showed significantly higher expression in developing fiber and ovule tissues at 10, 15, 20, and 25 days post-anthesis (DPA), indicating its potential role in fiber formation. This study provides new insights into the genetic architecture of cotton fiber yield and quality traits by identifying stable QTLs and promising candidate genes derived from G. barbadense and G. darwinii . The identified QTL hotspot and candidate genes represent valuable genetic resources for marker-assisted selection and molecular breeding strategies targeted at improving fiber quality while maintaining high yield potential in cotton.