An Axiom SNP genotyping array for potato: development, evaluation and applications

Abstract

Potato is a versatile food crop and a major component of human nutrition worldwide. Genomic-assisted breeding methods have the potential to increase the gain of selection. We report the development and validation of a high-density Axiom-based SNP array for potato (Solanum tuberosum L.). Whole-genome 10X Genomics based sequencing of 108 diverse clones representing landraces, improved cultivars, and wild relatives identified around 23.8 million sequence variants, from which 929,127 variants, alongside with 18,718 markers from a previously developed Illumina Infinium 21K array (GGP3), were tiled on the array. The array demonstrated high reproducibility, with replicate samples showing an average concordance of 99.88% in genotype calls for PotatoTools specific variants, compared to 99.93% for the Illumina Infinium 21K array variants. A panel of 1,247 diploid and tetraploid clones was genotyped with the developed array. Genotype calling, considering allele dosage, was realized using fitpoly and yielded 852,793 calls. The array informativeness was optimized by applying Euclidean distance, heterozygous strength offset metrics, call rate, minor allele frequency filtering, and diploid-based allele correction, yielding a final set of 206,616 robust and informative markers. The filtered marker set enables precise characterization of genetic variation across diverse germplasm, thereby supporting robust analyses of population structure, genome-wide association studies (GWAS), and genomic prediction in potato. Population structure analysis genotyped clones revealed clear subpopulation differentiation consistent with known ploidy groups. In addition, our discriminant analysis of principal components revealed a weak but structured diversity among clones of different market segments. GWAS analysis of 998 potato clones identified sequence variants significantly associated with polyphenol oxidase (PPO) activity, confirming the platforms efficacy for trait mapping. For the same trait, genomic prediction accuracies of 0.72-0.86 have been observed. The developed potato SNP array provides a robust platform for high-throughput genotyping, supporting genetic diversity studies, association mapping, and genomic-assisted breeding in this important crop.