Integrating genomic selection into potato breeding: A comparison of genotyping platforms and cross‐environmental predictions

Abstract

Abstract Genomic selection (GS) is a powerful tool for accelerating genetic gain in potato (Solanum tuberosum L.) breeding, particularly for complex traits. In this study, three practical aspects of GS implementation in a potato breeding program were examined. First, the predictive ability of GS models was evaluated for three key traits (total yield, marketable yield, and specific gravity) using two elite potato populations with shared ancestry, tested across seven location‐year environments. Two cross‐validation strategies were used to reflect practical breeding scenarios: predicting unphenotyped lines in known environments and predicting clonal performance in unknown environments. Four models were evaluated, two of which included genotype‐by‐environment interactions. Tuber specific gravity showed higher and more consistent prediction accuracy across environments, supporting the evidence that it is a more stable trait. Second, the impact of genotyping platforms and marker density on GS performance were examined, as the two populations were genotyped using two different targeted sequencing platforms: Flex‐seq (22K loci) and DArTag (4K loci), sharing ∼4K common loci, that allowed direct comparison. Prediction accuracies were comparable across platforms, indicating that both are suitable for GS implementation, with the choice depending on breeding goals, cost, and throughput considerations. Finally, the long‐term impact of GS on genetic gain was assessed through stochastic simulation of a 30‐year breeding pipeline, comparing conventional phenotypic selection with GS‐assisted selection scenarios. GS scenarios achieved higher long‐term genetic gains, though practical deployment should consider both cost and breeding objectives. Our findings for the three aspects of this study support the integration of GS into potato breeding programs, while highlighting key considerations for its effective implementation.