Rate of double reduction and genetic variability in yield, quality, and senescence related traits in tetraploid potato (Solanum tuberosum L.)

Muhammad Farhan Yousaf ^1* Vipin Tomar ¹ Hélène Romé ¹ Merethe Bagge ² Mathias Timmermann ² Thinh Tuan Chu ¹ Just Jensen ^1*

• ¹ Center for Quantitative Genetics and Genome Research, Faculty of Technical Sciences, Aarhus University, Tjele, Denmark
• ² DANESPO A/S, Dyrskuevej 15, 7323, Give, Denmark

Our study investigates the impact of genetic variability and double reduction on genetic gain and future diversity in polyploid species. We analyzed a dataset of 13,131 potato breeding lines and phenotypic data from Scandinavian environments spanning 17 years using variance components analysis. Pedigree information was incorporated into quantitative genetic models to estimate additive genetic variance and the relative importance of additive and non-additive genetic variance. We used two models: a baseline model (M1) without specific combining ability (SCA) effects and a model including SCA (M2). Two cross-validation schemes, 5-Fold and leave-one-breeding-cycle-out (LBCO), were used to evaluate the prediction accuracy of each model.We estimated the rate of the double reduction phenomenon (DRP) using a marginal likelihood approach, finding that a DRP rate of 0.05 best fit the data. Our results showed considerable variation in traits, with a high proportion of additive genetic variance in dry matter content (DMC), while relative yield (RY), germination (GR), and withering (WNG) showed intermediate levels of additive variance. Non-additive genetic variance was modest across all traits. Genotype x environment (G x E) interaction played a significant role in trait variability, though it was smaller than additive genetic variance.Heritability estimates indicated a strong genetic basis for DMC, with moderate heritability for other traits, reflecting both additive and interaction contributions. Model comparison via 5-Fold CV and LBCO, along with the log-likelihood ratio test (LRT), highlighted the importance of incorporating SCA in genetic models. In 5-Fold CV, prediction accuracy (PA) ranged from 0.296 to 0.812 in M1 and 0.300 to 0.813 in M2. Under LBCO CV, PA ranged from 0.180 to 0.726 in M1 and 0.180 to 0.728 in M2. The inclusion of SCA effects in M2 improved prediction accuracy.Our analysis emphasizes the need for models that account for both additive and SCA effects and the importance of considering G x E interactions to maximize the accuracy of predicted breeding values in tetraploid potato clones. The rate of double reductions was small and insignificant.