Development of a 775 SNP array for peach based on whole-genome resequencing data, and assessment of the potential of its application

•The choice of SNPs to construct a minimal SNP array for variety identification involved a strict filtering parameter: minor allele frequency, missing rate, sequencing depth, quality score, π and allele number.•The array was successfully used for genetic diversity, association anaylsis for qualitative traits.•A genome region with high SNP density was screened to identify varieties in a single PCR reaction.