Genome-wide QTL mapping and candidate gene analysis reveal elite yield-, fiber- and seed-associated alleles in Gossypium hirsutum race purpurascens

Traditional and effective crossbreeding techniques are widely used to introduce and create desired genetic variation, while integrating main characteristics of elite parents into the progeny. Improvement of cultivars using alleles from wild and semi-wild species has become a current focus in cotton genetic improvement and resources research. In this study, we created a backcrossed inbred lines (BIL) population from parents Gossypium hirsutum cultivar and G. hirsutum race purpurascens and identified Quantitative Trait Loci (QTL) for yield-, fiber- and seed-related traits. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to develop single nucleotide polymorphism (SNP) markers and construct a high-density genetic linkage map. QTL localization was performed by utilizing phenotype data for yield-, fiber- and seed-related traits under seven environments. A total of 633 QTL were identified, among which 318 favorable alleles derived from G. hirsutum race purpurascens . One hundred and fifty stable QTL were identified in more than two environments, and candidate genes for two QTL were further analyzed. These results highlight the great potential of utilizing G. hirsutum race purpurascens germplasm to improve yield-, fiber- and seed-related traits in G. hirsutum . • Gossypium hirsutum race purpurascens , a "forgotten landrace," demonstrates significant potential for improving yield, fiber quality, and seed traits in Gossypium hirsutum . • SLAF-seq-based QTL mapping revealed 633 loci (318 favorable alleles from G. hirsutum race purpurascens ) across 26 chromosomes in BIL population. • 150 stable QTL were identified, including key loci for qLP_D03.3 , qFL_A11.1 and qOC_D03.1 . • Purpurascens introgression boosted traits: 8.5 % LP increase and 5.4 % FM improvement, proving exotic germplasm value. • Co-localized QTL qOC_D03.1 / qPC_D03.1 pinpoint GH_D03G1283 ( HSD1 ) as key regulator for oil/protein biosynthesis via transcriptomics.