The Contribution of the genome-wide SNPs to Potato Breeding and Genetics

Historically, potato breeding and germplasm development efforts have relied upon phenotypic evaluations to select and advance germplasm. The goal of the USDA-funded Solanaceae Coordinated Agricultural Project (SolCAP) was to translate genomic resources into tools that can be used by breeders and geneticists. A major outcome of this project was the development of a genome-wide single nucleotide polymorphism (SNP) array that can be used to evaluate elite potato breeding germplasm. This array was utilized to genotype numerous biparental tetraploid and diploid populations, a diversity panel, and a core collection of Solanum species. The SNP array provides a marker density sufficient to generate genetic maps to identify numerous quantitative trait loci (QTL) for agronomic, quality, and disease resistance traits. Many new diploid and tetraploid genetic maps have been constructed and are being used to identify numerous QTL for economically important traits. We used SNP markers to assess relationships among germplasm, fingerprint varieties, and identify candidate genes. The Infinium 8303 Potato SNP Array provides a common set of SNP markers that can reliably be used for mapping, germplasm assessment, and fingerprinting. This array has also been a useful tool to advance our understanding of the potato genome. Recently a second generation of the SNP array has been expanded to 12,000 SNP. The SNP array can complement alternate genotyping platforms. Continued mapping of QTL across populations that will expand our understanding of economically important traits and lead to marker-assisted selection and breeding in potato.