Identification of candidate regions associated with resistance to early blight in tomato (Solanum lycopersicum L.) using BSA-seq

Early blight, caused by Alternaria alternata, is a key factor that reduces tomato yield and tomato product quality. Owing to the quantitative nature of resistance and the limited number of characterized loci, identification of genomic regions associated with resistance remains an urgent task for breeding programs. Here, bulked segregant analysis with whole-genome resequencing (BSA-Seq) was used to identify candidate regions for resistance to early blight in the F₂ population obtained by crossing a resistant line (Gloria×BSS335) and a susceptible cultivar (Samaladay). A total of 14 overlapping candidate genomic regions were identified on chromosome 2 by intersecting SNP- and InDel-associated regions (totaling 0.26 Mb). Functional annotation of the 33 genes in this locus revealed the involvement of membrane proteins, components of signaling pathways, transcriptional regulators, and Rab GTPase family proteins, which are potentially involved in stress and immune responses. This is the first genome-wide study of early blight resistance in tomato in Kazakhstan. These results expand our understanding of the genetic architecture of early blight resistance and may serve as a basis for the functional validation of key candidate genes and their application in marker-assisted selection (MAS).