Genetic mapping of quantitative trait loci associated with nematode resistance in melon using genotyping-by-sequencing

Muskmelon, a widely cultivated cucurbit crop valued for its delicious fruit, is severely threatened by different biotic stresses, including root-knot nematodes (RKNs). RKN, a soilborne pathogen belonging to the genus Meloidogyne, adversely affects crop yield, causing up to 30% damage in highly susceptible crops such as muskmelon. Developing resistant cultivars through breeding can be an effective approach to combat this disease. In the present study, 110 plants from the F2:4 mapping population were generated by crossing snapmelon accession “SM2012-1” (resistant parent) with melon cultivar “Punjab Sunehri” (susceptible parent) and used to map RKN resistance genes using genotyping-by-sequencing (GBS). Phenotyping was carried out by artificial screening of F2:4 plants against nematodes in a net house, in the rainy season, and in the spring season in 2023. Quantitative trait loci (QTL) analysis was conducted using WinQTL Cartographer, by integrating the high-density genetic linkage map (with an average marker density of 5.48 markers/Mb) and corresponding phenotypic data, which identified a total of nine QTLs associated with RKN resistance located on chromosomes 2, 8, 9, and 12. The QTLs were designated as qRKN_Cm2.1, qRKN_Cm2.2, qRKN_Cm2.3, qRKN_Cm8.1, qRKN_Cm8.2, qRKN_Cm9.1, qRKN_Cm9.2, qRKN_Cm12.1, and qRKN_Cm12.2, respectively. Among these, three QTLs (qRKN_Cm8.1, qRKN_Cm12.1, and qRKN_Cm12.2) were identified in the net house exhibiting phenotypic variance explained (PVE) that ranged from 10.1% to 26.8%. Two QTLs (qRKN_Cm2.1 and qRKN_Cm9.1) were detected in the rainy season with a PVE of 8.2% to 8.3%, while four QTLs (qRKN_Cm2.2, qRKN_Cm2.3, qRKN_Cm8.3, and qRKN_Cm9.2) were identified in the spring season, with a PVE of 8.1% to 10.3%. The logarithm of odds (LOD) score for these QTLs ranged from 2.5 to 3.3. QTL mapping of RKN resistance carried out in the present study will provide linked molecular markers for marker-assisted selection (MAS), thereby providing a valuable resource for effective deployment of RKN resistance in melon breeding programs to developing elite resistant cultivars.