Novel Diagnostic SNP Markers for Potato Starch and Tuber Yield Identified By Association Mapping

Starch of potato (Solanum tuberosum) tubers is a renewable resource and an important component of multiple food and non-food products. Optimized starch yield, the product of tuber starch content and tuber yield, is therefore the central selection criterion in breeding programs for starch potatoes. Our study aimed at the detection of diagnostic single nucleotide polymorphism (SNP) markers for starch yield optimization by marker-assisted selection. A novel association mapping population of 282 potato genotypes was assembled and phenotyped in replicated field trials in Northern Spain for tuber starch content, tuber yield and tuber number, traits that determine starch yield. The population was genotyped for known diagnostic PCR markers and novel SNPs in candidate genes, which were reported in the literature to have a function in starch or yield accumulation in potato or other organisms. In addition, three case-control subpopulations were selected based on the highest and lowest trait values for tuber yield, starch content and starch yield. Ninety varieties and breeding clones in total were genome wide genotyped for 8303 SNPs using the SolCAP Potato SNP array. SNPs with highly significantly different allele frequency between pooled cases and controls for each trait were selected and genotyped in the entire population. Using a mixed linear model including population structure and kinship for association analysis, we identified novel marker-trait associations. These associations resulted from the targeted candidate gene approach as well as from the genome wide case-control study.