| Cultivated potato (Solanum tuberosum L.) ranks among maize, rice and wheat as one of the most important global food crops, but lags behind in the application of molecular tools towards varietal improvement due to its autotetraploid genome and high heterozygosity. Recent efforts in genome sequencing and statistical genetics have developed new tools including an 8303 single nucleotide polymorphism (SNP) genotyping array and algorithms to perform genetic mapping despite these difficulties. In this project, these tools were applied to develop linkage maps and identify quantitative trait loci (QTL) for chip color and tuber size.;Potato chip color is greatly dependent on storage temperature and duration. In the first study, a diverse set of breeding materials was evaluated for chip color across storage environments to quantify genotype x storage interaction. In the second study, three bi-parental families were evaluated for yield, tuber traits, and chip color across three years, two growing environments, and three storage regimes. SNP genotyping and pedigree analysis revealed effects of inbreeding depression and heterosis to be contributing to yield and chip color performance across families. Chip color was found to be highly heritable and an ideal trait for QTL analysis.;A linkage map was assembled using 2095 SNP markers and QTL which associate with potato chip fry color and tuber size were identified. QTL by storage interactions were observed with different loci contributing to chip performance in short (3 month), mid (6 month) and long (9 month) duration cold storage (5.5°C). QTL for chip color in short duration storage were identified on chromosome 3, which co-localized with potato vacuolar invertase ( VInv/Pain-1) and vacuolar invertase inhibitor (INH2), and chromosome 9 which co-localizes with apoplastic invertase (Inv-ap(b) ). Under longer durations, QTL associations with invertase genes were not detected, but a QTL on chromosome 2 was identified which is associated with a conserved gene of unknown function (PGSC0003DMT400032972). Tuber size and weight QTL were identified on chromosome 5 which co-localized with a well-documented maturity QTL. The QTL was also detected through a tetraploid dosage GWA model. A single SNP, Solcap_snp_c2_23049 was highly associated with tuber size and has potential for use as a screening marker. |
