What the Infinium 8303 Potato SNP Array Tells Us about 100 Years of Potato Breeding

In order to characterize the phenotypic and genotypic diversity, and changes that have occurred within cultivated potato, a germplasm panel was created, which is composed of important and historical cultivars, advanced breeding lines, and wild species previously used in breeding to characterize changes that have occurred within cultivated potato species.  A retrospective look into the genomic changes that occurred through a century of breeding was conducted. In addition, populations were generated to map traits important to the North American breeding community.  This material was genotyped using the SolCAP Infinium potato SNP array which provides a set of genome-wide markers.  We have used two diploid potato populations to assess concordance between map location of SNPs and the potato genome sequence location; generated a SNP-based tetraploid genetic map; conducted QTL analysis of a tetraploid population; and examined the genome wide level of SNP heterozygosity. Population structure analysis demonstrated four subpopulations within the diversity panel with chip processing clones, wild species, and genetic stocks grouping separately from the other cultivated potato market classes. Additionally, pair-wise kinship estimates revealed clear separation of the market classes as well as two distinct subgroups within the chip processing germplasm. Diversification between market classes was observed for traits under selective pressure within market classes (i.e., tuber sucrose in chip processing clones). In contrast, market class diversification was not observed for traits of universal importance such as yield. Across the panel little change was observed for most traits over the century of breeding, however, within market classes improvement over time was evident (i.e., SFA chip color in chip processing clones). While diversification and improvement has been made within the cultivated accessions through phenotypic selection, understanding the genetic basis of traits will allow for more rapid improvement to occur over the next century of breeding.