Mapping of quantitative trait loci (QTLs) controlling cotton leaf curl disease (CLCuD) resistance in Upland cotton

Abstract

Cotton leaf curl disease (CLCuD), caused by begomoviruses, is a major threat to cotton (Gossypium hirsutum L.) production, especially in Asia and Africa. The use of marker-assisted breeding to utilize host plant resistance can be the best sustainable approach to tackle CLCuD. Because most of the available cotton germplasm is susceptible to CLCuD, so it demands the identification of potentially new quantitative trait loci (QTLs) in the indigenous germplasm. The current study was designed to construct a broader genetic linkage map of bi-parental F2:F3 populations developed from a highly tolerant MNH 886 and a highly susceptible S-12 cotton cultivars. One hundred seven (107) CLCuD-associated simple sequence repeat (SSR) marker alleles were identified as polymorphic and eight new QTLs were found on chromosomes 11, 19 and 21. On homologous chromosomes 11 and 17, the QTLs qCL-11-120d2 and qCL-21-m2 were detected in both F2 and F3 populations. Another QTL on chromosome 11, qCL-11-m3, showed the highest phenotypic variance (PV%) of 16.66% and LOD score > 3. Other QTLs on chromosome 11 were qCL-11-m2, qCL-11-120d3. On chromosome 19, three QTLs (qCL-19-m2, qCL-19-90d2 and qCL-19-120d3) were detected with PV% >8 and LOD score > 3. The CLCuD-associated QTLs identified in this study can contribute to develop CLCuD-resistant cultivars using marker assisted selection and can help to fine-tune the molecular mapping of the QTLs on the cotton genome.