The identification of QTLs and candidate genes associated with VW resistance of Gossypium hirsutum utilizing BSA-seq and QTL mapping

Abstract Background Verticillium wilt (VW), a soil-borne fungal disease caused by Verticillium dahliae, causes severe yield losses in cotton production in China. Due to the scarcity of highly resistant upland cotton germplasm, the genetic improvement of VW resistance has progressed slowly. Results In this study, we combined QTL mapping and bulked segregant analysis sequencing (BSA-seq) in an F₂ population derived from a cross between the resistant parent JM122 and the susceptible parent XLZ 4 and identified two stable VW-resistance QTLs. The QTL qVW-A05, located on chromosome A05, accounted for an average of 8. 5% of the phenotypic variation; qVW-D07, on chromosome D07, explained an average of 12. 3% of the phenotypic variation. Comparative analysis revealed that both QTLs overlapped with known VW-resistance hotspots. Association analysis in a natural population of 468 cotton accessions showed that genotypes carrying the same allele as the resistant parent JM122 at the linked markers exhibited significantly higher VW resistance. Based on expression profiles and sequence variation, 25 candidate genes from the two QTL regions were selected for functional validation using virus-induced gene silencing (VIGS). Silencing of GHA05G0294 (encoding TRX1), GHA05G0389 (encoding an Fd-like protein), GHD07G0616 (encoding MSR1) and GHD07G0638 (encoding a calcium-sensing receptor, CAS) significantly reduced VW resistance in the resistant parent JM122. Notably, silencing of GHD07G0638 (encoding a calcium-sensing receptor, CAS) in the susceptible parent XLZ 4 markedly enhanced its resistance, indicating that GhCAS may act as a critical susceptibility factor. Conclusion Two stable VW-resistance QTLs (qVW-A05 and qVW-D07) and their linked markers were identified, providing valuable tools for marker-assisted selection in cotton breeding. Furthermore, four candidate genes which played key roles in VW resistance were validated, among which GhCAS was revealed for the first time as a potential susceptibility factor. These findings offer new genetic resources and theoretical insights for elucidating the cotton– V. dahlia interaction and developing resistant cultivars.