Abstract
Cotton leaf curl disease (CLCuD) is a major threat to cotton production in Asia and Africa. Using marker-assisted breeding can be the best sustainable approach to tackle CLCuD. Identification of new QTLs in the indigenous cotton germplasm is necessary to combat CLCuD. The current study was designed to construct a genetic linkage map of bi-parental F2:F3 populations developed from highly tolerant MNH-886 and highly susceptible S-12 cotton cultivars. One hundred seven CLCuD-associated simple sequence repeat (SSR) marker alleles were identified as polymorphic and three new QTLs were found on chromosomes C11, C19 and C21. Two QTLs on chromosomes C11 and C19 were detected in both F2 and F3 populations in the region flanked by SSR markers CIR316 and BNL4094, and BNL285 and BNL3348, respectively. Whereas, one QTL on chromosome C21 was detected in the region flanked by SSR markers JESPR158 and JESPR135 in both F2 and F3 generations. The CLCuD-associated QTLs identified in this study can help fine-tune the molecular mapping of the QTLs on the cotton genome against CLCuD.