Hierarchical Core SNP Panels for Genetic Discrimination of Red- and White-Fleshed Selenicereus Accessions

This dataset contains seven Variant Call Format (VCF) files representing a tiered set of diagnostic single nucleotide polymorphism (SNP) panels developed for distinguishing red-fleshed and white-fleshed accessions of Selenicereus (pitaya/dragon fruit). The panels were derived from a genome-wide SNP dataset of 45 accessions using population genetic filters (FST, allele frequency divergence, and population specificity). The collection includes: key_snps_10025.vcf.gz: The full set of 10,025 highly differentiated SNPs. ultra_core_10.vcf.gz: Minimal 10-SNP panel with fixed differences between groups. ultra_core_20.vcf.gz: 20-SNP panel. core_50.vcf.gz: 50-SNP panel. core_100.vcf.gz: 100-SNP panel. extended_200.vcf.gz: 200-SNP panel. extended_500.vcf.gz: 500-SNP panel. All SNPs are sorted by a composite informativeness score. These panels enable cost-effective genotyping for germplasm authentication, hybrid verification, and breeding applications in Selenicereus. The ultra-core 10-SNP panel has been experimentally validated via Sanger sequencing and shows perfect co-segregation with fruit flesh color. Associated scripts for panel construction are available in the manuscript’s supplementary materials or upon request.