High-throughput single nucleotide polymorphism (SNP) arrays have emerged as essential genotyping tools, significantly accelerating breeding programs and advancing basic research. In this study, a high-throughput 10K SNP genotyping array for wax gourd was developed using genotyping by target sequencing (GBTS), featuring 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with key economic traits. To demonstrate its utility, genetic distances among 19 elite inbred lines were calculated from SNP data and correlated with heterosis for single fruit weight. The results revealed that greater genetic distance was associated with higher middle parent heterosis (MPH) for single fruit weight. Furthermore, 56 commercial wax gourd cultivars collected from eight regions were selected and genotyped. Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively indicated that these cultivars fall into two major groups. Group I, comprising black or dark green skinned wax gourds, exhibited lower genetic diversity than Group II, which includes green or light green skinned varieties, reflecting shorter genetic distances within Group I. Finally, 60 polymorphic SNPs were used to construct DNA fingerprints for distinguishing the 56 cultivars. As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.

seedless grape  /  embryo rescue  /  parental genotype  /  plant hormones  /  abnormal plantlets