Identification of candidate genes associated with major QTL controlling Vertcillium wilt resistance in cotton (Gossypium hirsutum L.).

Vertcillium wilt (VW), a soil-borne disease causing cotton yield loss and fiber quality reduction, is a major stumbling block in cotton production. It is a challenging job to detect key genes associated with major quantitative trait loci (QTL) that can be used to develop VW-resistant varieties. In this study, several genome regions associated with major QTL controlling VW resistance were fine mapped by constructing the high-density genetic map of major QTL regions using Kompetitive Allele-Specific PCR (KASP) markers. Candidate genes were subsequently identified by combining gene annotation, genome resequencing, transcriptome sequencing and qRT-PCR, and functions of several genes associated with major QTL were demonstrated based on gene VIGS silencing and overexpressing. The results showed that six QTL were identified, among which five were regarded as major QTL detected in at least two environments, and four QTL, qVW-D05-1, qVW-D05-2, qVW-D05-3 and qVW-A01-1, were fine mapped to 15.2-241.3 kb physical regions located on chromosome D05 and A01, respectively. Polymerizing of major QTL on different chromosomes showed that the more the resistant QTL were polymerized in a line, the stronger the VW resistance of the line became, and those lines polymerizing 4 resistant QTL showed much higher and more stable VW resistance in each environments, implying the potential of multi-locus QTL polymerization in improving VW resistance. Fifteen candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines were identified to be associated with VW resistance in cotton. Four candidate genes associated with qVW-D05-1 were cloned and conducted function analysis, it was showed that the sequence variation of functional genes, especially the variation resulting in amino acid differences of the domains, might be the molecular mechanisms of VW resistance in cotton.