Muders, K. | bioRxiv Science

bioRxiv2024

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: II. Effect of selection strategy and cross-selection method on long-term genetic gain

Different cross-selection (CS) methods incorporating genomic selection (GS) have been used in diploid species to improve long-term genetic gain and preserve diversity. However, their application to heterozygous and autotetraploid crops such as potato is lacking so far. The objectives of our study were to (i) assess how different CS methods incorporating GS with or without consideration of genetic variability affect both short- and long-term genetic gains compared to strategies using phenotypic selection (PS); (ii) evaluate the changes in genetic variability and the efficiency of converting diversity into genetic gain across different CS methods; and (iii) investigate the interaction effects between different genetic architectures and CS methods on long-term genetic gain. In our simulation results, implementing GS with optimal selection intensities had a higher short- and long-term genetic gain compared to any PS strategy. The CS method considering additive and dominance effects to predict progeny mean based on simulated progenies (MEGV-O) reached the highest long-term genetic gain among the assessed mean-based CS methods. Compared to MEGV-O and usefulness criteria (UC), the linear combination of UC and genome-wide diversity (called EUCD) kept the same level of genetic gain but resulted in a higher diversity and a lower number of fixed QTL. Moreover, EUCD had a relatively high efficiency in converting diversity into genetic gain. However, choosing the most appropriate weight to account for diversity in EUCD depends on the genetic architecture of the target trait and the breeders objectives. Our results provide breeders with concrete methods to improve their potato breeding programs. Key messageCross-selection method considering progeny mean performance and genetic variability can improve long-term genetic gain and keep genetic diversity in clone breeding.

genetics↗

bioRxiv2022

Optimal implementation of genomic selection in clone breeding programs - exemplified in potato: I. Effect of selection strategy, implementation stage, and selection intensity on short-term genetic gain

Genomic selection (GS) is used in many animal and plant breeding programs to enhance genetic gain for complex traits. However, its optimal integration in clone breeding programs that up to now relied on phenotypic selection (PS) requires further research. The objectives of this study were to (i) investigate under a fixed budget how the weight of GS relative to PS, the stage of implementing GS, the correlation between an auxiliary trait assessed in early generations and the target trait, the variance components, and the prediction accuracy affect the genetic gain of the target trait of GS compared to PS, (ii) determine the optimal allocation of resources maximizing the genetic gain of the target trait in each selection strategy and for varying cost scenarios, and (iii) make recommendations to breeders how to implement GS in clone and especially potato breeding programs. In our simulation results, any selection strategy involving GS had a higher short-term genetic gain for the target trait than Standard-PS. In addition, we show that implementing GS in consecutive selection stages can largely enhance short-term genetic gain and recommend the breeders to implement GS at single hills and A clone stages. Furthermore, we observed for selection strategies involving GS that the optimal allocation of resources maximizing the genetic gain of the target trait differed considerably from those typically used in potato breeding programs. Therefore, our study provides new insight for breeders regarding how to optimally implement GS in a commercial potato breeding program to improve the short-term genetic gain for their target trait.

genetics↗