Genetic mapping of red skin color as a quantitative trait in a partial diallel population of tetraploid potato

Tuesday, July 27, 2021
3:15 PM - 3:35 PM

The intensity of red coloration in the skin of fresh market potato varieties influences their marketability and thus is an important trait for breeding. Previous research has established that two genes are responsible for the presence/absence of red skin color. The dihydroflavonol 4-reductase (dfr) gene encodes an enzyme needed to produce the red anthocyanin pigment, and the an2 gene encodes a transcription factor that regulates the expression of dfr in tuber periderm. However, since our understanding of red skin color as a quantitative trait is limited, our objective was to conduct QTL mapping of this trait in tetraploid breeding populations. A partial diallel population of 530 F1 progeny derived from five founders was evaluated in field trials in 2018 and 2019, and skin color was quantified using image-based phenotyping methods. Using genetic marker data from the potato SNP array, founder genotype probabilities were computed using the software PolyOrigin. Regression analysis with the software diaQTL revealed that an2, dfr, and CDF1 (the potato maturity gene) all influenced skin lightness. The relative importance of additive and dominance effects at each locus was estimated, and the dosage of functional alleles at an2 and dfr in the founders was predicted based on the haplotype effects. Genome-wide association analysis with a simplex dominance model identified an additional QTL on chromosome 12, near a gene annotated to play a role in anthocyanin metabolism. Future studies are planned to connect the estimated haplotype effects with sequence data to further elucidate the biology of red skin color.
Breeding and Genetics