QTL Mapping of Fiber- and Seed-Related Traits in Chromosome Segment Substitution Lines Derived from Gossypium hirsutum × Gossypium darwinii

A narrow genetic basis limits further the improvement of modern <i>Gossypium hirsutum</i> cultivar. The abundant genetic diversity of wild species provides available resources to solve this dilemma. In the present study, a chromosome segment substitution line (CSSL) population including 553 individuals was established using <i>G. darwinii</i> accession 5-7 as the donor parent and <i>G. hirsutum</i> cultivar CCRI35 as the recipient parent. After constructing a high-density genetic map with the BC₁ population, the genotype and phenotype of the CSSL population were investigated. A total of 235 QTLs, including 104 QTLs for fiber-related traits and 132 QTLs for seed-related traits, were identified from four environments. Among these QTLs, twenty-seven QTLs were identified in two or more environments, and twenty-five QTL clusters consisted of 114 QTLs. Moreover, we identified three candidate genes for three stable QTLs, including <i>GH_A01G1096</i> (<i>ARF5</i>) and <i>GH_A10G0141</i> (<i>PDF2</i>) for lint percentage, and <i>GH_D01G0047</i> (<i>KCS4</i>) for seed index or oil content. These results pave way for understanding the molecular regulatory mechanism of fiber and seed development and would provide valuable information for marker-assisted genetic improvement in cotton.