Genomic Regions and Markers Associated with Micronutrient Accumulation in Diploid Potatoes

Breeding for micronutrient content is complicated by soil composition, and genotype x environment (GxE) interaction. Phenotypic data from assessment of iron, zinc, and vitamin C tuber concentrations in 2x potato landraces were used to identify genomic regions controlling these traits and determine the GxE interaction effect using two environments of the Peruvian highlands. A sample of 150 diploid landraces of the S. tuberosum L groups Phureja and Stenotomum was genotyped by genotyping by sequencing (GBS) and a genome wide association study (GWAS) performed to identify single nucleotide polymorphism markers (SNP) significantly correlated with quantitative variation for these traits. Significant GxE interaction was reflected in the lack of common trait-associated SNP markers across environments. Significant trait-SNP marker associations accounted for up to 37% of phenotypic variation for vitamin C, 35% for iron, and 33% for zinc. A total of 23 SNPs were found associated.

Iron and zinc tuber content were found positively correlated with one another (r=0.5, p<1.00E-04) in the location with higher soil zinc level. The most significant marker-trait associations (p< 1.00E-06) found were two SNP markers associated with both iron and zinc content located at 35 Mbp on chromosome 8 within a region to which an annotated gene that encodes a metal transporter i.e., ZIP family metal transporter has been mapped. Genotypes carrying the minor frequency allele of these two SNP showed increasing iron and zinc levels, and were found in the highest frequency in the Goniocalyx group (62%). Further studies will be conducted for SNP validation.