High-density genetic map and quantitative trait loci map of fruit-related traits in wax gourd ( Benincasa hispida )

Wax gourd ( Benincasa hispida [Thunb] Cogn.) is an important horticultural crop in the Cucurbitaceae family that has high nutritive and medicinal value. We analysed quantitative trait loci (QTLs) related to the fruit-related traits of wax gourd by constructing a high-density genetic map through whole-genome resequencing. We obtained an F 2 population of 195 individuals by crossing two inbred wax gourd lines: XDJQ-1 and SL-7. A high-density genetic map was constructed after generating a sequencing library and identifying and genotyping single-nucleotide polymorphisms (SNPs). Finally, we used QTL mapping to analyse the fruit-related traits of wax gourd. The high-density genetic map showed sufficient coverage to detect recombination breakpoints and contained 323,107 SNP markers, spanned 1243.87 cM, and had an average distance between adjacent markers of 0.33 cM. Furthermore, 3,720 bin markers (including SNP markers) were mapped to 12 linkage groups. Based on the high-density genetic map, one major QTL for fruit flesh colour ( fc5.1 ) was mapped on the 3.379 Mb region of chromosome 5, and two major QTLs for fruit length ( fl2.1 ) and fruit width ( fw2.1 ) were mapped on the (0.345 Mb) and (0.602 Mb) regions of chromosome 2 respectively. The QTLs for fc5.1 , fl2.1 , and fw2.1 accounted for 28.684%, 63.562%, and 59.979% of wax gourd phenotypic variation, respectively. To our knowledge, ours is the first high-density genetic map of wax gourd constructed using whole-genome resequencing and is the highest density genetic map available for wax gourd. Our results provide a foundation for future map-based cloning, candidate gene identification, and marker-assisted breeding.