Identification and validation of QTLs associated with resistance to tomato leaf curl Bangalore virus disease using QTL-seq analysis in tomato (Solanum spp.).

Tomato leaf curl Bangalore virus disease (ToLCBaVD) is a significant biotic constraint on tomato production in India and globally. Breeding for ToLCBaVD resistance poses challenges due to the complexity of whitefly transmission. Conventional phenotype-based breeding methods for ToLCBaVD resistance are often less effective, primarily due to high recombination rates and genotype × environment interactions. This underscores the need for marker-assisted selection (MAS) and the identification and validation of genomic regions associated with resistance to improve breeding efficiency. In this study, we employed a QTL sequencing (QTL-seq) approach combined with bulk segregant analysis (BSA) in an F2 population derived from a cross between ‘IIHR 2843’ (susceptible parent) and ‘IIHR 2611’ (resistant parent). QTL-seq analysis identified one QTL on chromosome 3 and six QTLs on chromosome 12 based on the ∆SNP-index. Among all the seven QTL regions identified, five QTLs were validated through expression analysis. The candidate genes selected for expression study includes Catalase 3 (tolcv3.1), CC-NBS-LRR (tolcv3.1), Serine/threonine-protein kinase (tolcv12.2), LRR family protein (tolcv12.3), Zinc finger transcription factor 77, and DdRP-α (tolcv12.6). Differential expression patterns of these genes in resistant and susceptible plants during infection suggest their roles in conferring resistance to ToLCBaVD. The identified QTLs and candidate genes provide valuable insights into the molecular mechanisms of ToLCBaVD resistance and hold potential for application in MAS and genetic engineering to improve tomato cultivars.