Dissection of a Verticillium wilt resistance QTL on chromosome At_chr9 in cotton (Gossypium hirsutum L.)

Verticillium wilt is one of the most destructive diseases affecting global cotton production. The development of Verticillium wilt resistant cultivars is one way to control the disease. Several studies have demonstrated that there existed Verticillium wilt resistant identify quantitative trait loci (QTL) on Dt_chr9 and its homologous chromosome At_chr9. In this study we combined the QTL detection power of genetic linkage mapping with the high resolution power of association mapping study to precisely dissect QTL controlling Verticillium wilt resistance on Dt_chr9 and At_chr9. 237 F2 lines from a cross between Zhongzhimian 2 (a cotton variety with superior resistance) and a sensitive variety, Jimian 11 were used to identify QTL for Verticillium wilt resistance with 72 SSRs randomly distributed on Dt_chr9 and At_chr9. At the same time, 120 lines from the China Elite Cotton germplasm collection were used to identify loci associated with Verticillium wilt resistance with more than 6000 SNPs distributed on Dt_chr9 and At_chr9, by using a regional association analysis-based fine-mapping strategy. We identified four Verticillium wilt resistance QTL on chromosome Dt_chr9 and At_chr9, among which one QTL, qVW- At_chr9-1 was validated by association mapping. Interestingly, this validated QTL explained 24.49% phenotype variation with a LOD value of 13.78, and located outside of the previously reported QTL regions on At_chr9 chromosome, implying a new major QTL detection. Linkage mapping defined the confidence interval of qVW- At_chr9-1 within 49539236 bp - 50898755 bp on At_chr9, while association mapping further narrowed down the confidence interval of qVW- At_chr9-1 within 49993040 bp - 50208544 bp on At_chr9, a region of 215.5 kb ( about 0.54cM). It is concluded that the application of Linkage mapping combined with association analysis enabled us to dramatically increase the resolution within the confidence interval of Verticillium wilt resistance QTL by-passing labor- and time-intensive fine mapping and accelerate the pace of QTL mapping projects.