Design and Selection of SNP Markers for Grape Integrated Chip Arrays

Grape (Vitis vinifera spp.) accessions exhibit rich diversity, and understanding their genetic variation and evolutionary relationships is crucial for cultivar selection and utilization. A highly representative SNP marker set was developed in this study based on re-sequencing data analysis, to clarify the phylogenetic relationships among 96 grape accessions and to evaluate the genetic resolution of core markers. Using PN40024 as the reference genome, high-quality SNP loci were screened from resequencing data of the 96 accessions. A phylogenetic tree was constructed, and genetic diversity was analyzed using PCA and population structure analysis. The results showed that the 96 accessions were mainly divided into four groups: European (‘Merlot’, ‘Chardonnay’), American (‘Beta’, ‘Concord’), Euro-American hybrids (‘Vidal’, ‘Miguang’), and wild populations along with their hybrid progeny (‘Zuoyouhong’, ‘Huajia 8’). PCA and ADMIXTURE validated population differentiation, revealing clear separation between wild and cultivated accessions. Through screening of core SNP markers, 384,304 candidate SNPs suitable for probe design were identified. Further refinement yielded 2000 and 10,000 SNP markers. Detailed analysis of core marker characteristics showed that their minor allele frequency (MAF) was predominantly between 0.1 and 0.3, with the majority distributed in CDS (38.65%), intronic (30.2%), and intergenic regions. The most common mutation types were [A/G] (35%) and [C/T] (34%) transitions. The 2000 core SNPs were associated with 1220 functional genes and were significantly enriched in pathways such as protein binding, RNA transport, and plant–pathogen interaction. These findings provide an efficient tool for grape genetic diversity analysis, cultivar identification, and molecular breeding, laying the groundwork for the precise utilization of grape germplasm resources.