Detection and Utilisation of KASPar SNP Marker Assays for Early Blight Resistance in Tomato

Early blight is a major disease affecting tomato crops worldwide and poses a significant threat to tomato production. The development of novel marker systems through next-generation sequencing (NGS) technologies has created unprecedented opportunities for high-throughput functional genomics research. Among these, Kompetitive Allele Specific PCR (KASPar), developed by K Bioscience, has become one of the most widely used techniques for high-throughput single-nucleotide polymorphism (SNP) genotyping. In the present study, phenotypic screening for early blight resistance was conducted on 21 tomato germplasm lines and 163 recombinant inbred lines (RILs) of the F₈ generation. The results revealed that 'EC-520061', 'Swarna Naveen', and 'H-88-78-1' exhibited symptomless, highly resistant, and resistant responses, respectively. Among the 163 RILs, only 44.75% of the genotypes were found to be resistant to early blight. A total of 14 SNP assays were identified and mapped onto different chromosomes, as validated using germplasm lines. Of these, three assays (SAG_T_EB_4, SAG_T_ST11, and SAG_T_ST12) exhibited homozygosity and no polymorphism. These assays were further subsequently utilized for validation in both RILs and parental lines. Genetic diversity and correlation matrix analyses indicated that the highest number of polymorphic markers occurred between 'Swarna Naveen' and 'EC-520061', as well as between 'Punjab Chhuhara' and 'H-88-78-1'. The identified SNP KASPar marker assays proved to be robust and highly reliable for detecting resistance alleles and distinguishing heterozygous from homozygous genotypes. These validated assays can be effectively employed as a tools for high-throughput marker-assisted selection (MAS), aimed at improving of early blight resistance in tomato breeding programs.