Identification of Meloidogyne incognita resistance QTLs using high density GBS linkage map in bittergourd

The root knot nematode (RKN; Meloidogyne incognita) is a very serious biotic constraint that limits the yield potential of bittergourd. The resistance within the cultivated germplasm of bittergourd is limited, therefore, introgressing resistance from related species of bittergourd offers a sustainable breeding solution. In this study, a RKN-susceptible cultivated parent M. charantia cv. Punjab-14 was crossed with resistant wild species of M. balsamina cv. Punjab Jhaar Karela-1 to generate F_2:3 mapping population. A genetic linkage map was constructed via Genotyping-by Sequencing (GBS). Joint phenotyping and genotyping analysis identified a total of five quantitative trait loci (QTLs) governing RKN resistance. Under artificial screening, two QTLs namely QTLs qRKN_pau6.1 (chromosome 6) and qRKN_pau11.1 (chromosome 11) were detected, explaining 10.11% and 7.53% of phenotyping variance (PVE), respectively. Under field conditions, three QTLs namely, qRKN_pau3.1, qRKN_pau6.2 and qRKN_pau9.1 were mapped on chromosome 3, 6 and 9 accounting for 9.09%, 6.49% and 9.16% PVE respectively. The major artificial screening locus qRKN_pau6.1 was successfully validated using kompetitive Allele-Specific PCR (KASP) assays. One diagnostic KASP marker, BGST_19012274 and one linked marker BGST_29234979 located within the resistance-associated genomic region, narrowed the genetic interval to 4.23 cM and 19.05 cM, respectively. To our knowledge, this is the first report on pathogen resistance introgression from M. balsamina into M. charantia and provides the first SNP-validated blueprint for marker-assisted selection against M. incognita in bittergourd.