Quantitative trait loci mapping for Fusarium wilt using genotyping by sequencing based genetic map in melon (Cucumis melo L.)

• Muskmelon is highly susceptible to the most destructive disease, Fusarium wilt, caused by Fusarium oxysporum f. sp. melonis and resulting crop losses have restricted muskmelon production in India. • Fusarium wilt has complex nature because it carries four physiological races: FOM 0, 1, 2, 1.2 which is difficult to understand in different areas. • To study the genetics and map the FW resistance gene(s) in snapmelon by genotyping by sequencing (GBS) analysis. • Five QTLs associated with fusarium wilt resistance were successfully mapped, marking the first report of such mapping in muskmelon. Fusarium wilt (FW) is a highly damaging disease that impacts melon production globally. There is no practical solution to address this fungus; however, developing resistant varieties through breeding programs might be considered an efficient and cost-effective approach. During the screening of snapmelon germplasm for Fusarium wilt, the advance line "SM2012–1″ was identified as highly resistant. In order to identify the FW resistance-linked gene(s) in muskmelon, the resistant parent "SM2012–1″ was crossed with the susceptible parent "Punjab Sunehri" to generate an F 2:4 mapping population of 110 individuals. A high-density genetic linkage map was constructed using genotyping by sequencing (GBS) approach. The genetic map included 1962 single nucleotide polymorphism (SNP) markers, organized into 13 linkage groups, and covered a total distance of 5865.60 cM, with an average distance of 3.47 cM between markers. F 2:3 individuals were screened for FW resistance using artificial inoculation techniques. The QTL analysis identified five QTLs for FW resistance located on chromosomes 4, 6 and 7. These QTLs have been designated as qFW_pau4.1, qFW_pau6.1, qFW_pau7.1 and qFW_pau7.2, respectively. Among these, four major QTLs ( qFW_pau4.1, qFW_pau7.1, qFW_pau7.2 ), explained >10% phenotypic variance explained (PVE). This study identified QTLs linked to FW resistance in an F 2:4 muskmelon population, representing the first report using SNP-based markers. These QTLs facilitate marker-assisted and genomic selection, enhancing disease resistance and yield. Their integration can accelerate breeding programs and improve cultivar development with greater precision. These findings provide a foundation for fine-mapping and advanced selection strategies for FW resistance in muskmelon.