QTL Analysis on Yield and Its Components in Recombinant Inbred Lines of Upland Cotton

To facilitate the application of simple sequence repeat (SSR) markers in molecular marker-assisted selection (MAS) of upland cotton (Gossypium hirsutum L.), a linkage map harboring 192 SSRs was constructed from the CRI-G6 population (Acala 1517 × Dezhou 047) using mixed-model-based composite interval mapping (MCIM) method. This map was used to detect quantitative trait loci (QTLs) associated with cotton yield traits in 3 environments. In the separate analysis, 24 main-effect QTLs were identified including each one stable QTL for seed yield, lint yield, lint percentage, seed index, and boll number per plant. In the joint analysis, 14 main-effect QTLs and 20 pairs of additive–additive epistatic QTLs were detected including 6 main-effect and 7 pairs of epistatic QTLs with environmental interactions. Eight main-effect QTLs were mapped in the same regions using both methods. Some main-effect QTLs with stability in different growing environments had phenotypic contributions larger than 10%, and these QTLs are candidate genes/loci in MAS of upland cotton.