A new 10K liquid SNP genotyping array for wax gourd and its application in heterosis utilization and cultivars identification

1 Developed the first high-density 10 K SNP array for wax gourd, featuring 10,722 genome-wide SNPs that include 278 functional trait loci, using GBTS technology. 2 Demonstrated its utility for heterosis prediction, population structure analysis, and fingerprint establishment, proving its value in genetic studies and breeding programs. High-throughput single nucleotide polymorphism (SNP) arrays have emerged as a vital genotyping tool, to significantly accelerate breeding process and promoting basic research. In this study, a high-throughput 10 K SNP genotyping array for wax gourd was developed based on genotyping by target sequencing (GBTS), with 10,722 SNPs evenly distributed across all 12 chromosomes, including 278 functional loci associated with important economic traits. To demonstrate its applications, we calculated the genetic distances among 19 elite inbred lines using the SNP data and analyzed their relationship with heterosis for single fruit weight. The results indicated that greater genetic distance was associated with higher middle parent heterosis (MPH) of single fruit weight. Additionally, we selected and genotyped 56 commercial wax gourd cultivars collected from eight regions. Population structure analysis, phylogenetic analysis, and principal component analysis (PCA) collectively revealed that these cultivars could be divided into two major groups. Group I, consisting of black or dark green skinned wax gourds, exhibited lower genetic diversity than group II, which comprised green or light green skinned varieties, reflecting the shorter genetic distances within group I. Finally, 60 polymorphic SNPs were selected to construct fingerprints for distinguishing the 56 wax gourd cultivars. As the first high-throughput genotyping platform for wax gourd, this SNP array provides an effective and powerful tool for genetic analysis.