Journal Article

Evaluation of genomic and phenomic prediction for application in apple breeding

Knauf, Andrea, Kupper, Daniela, Jung, Michaela, Bühlmann-Schütz, Simone, Hodel, Marius, Broggini, Giovanni AL, Patocchi, Andrea, Neuditschko, Markus, Studer, Bruno

2025

Overview

Background Apple breeding schemes can be improved by using genomic prediction models to forecast the performance of breeding material. The predictive ability of these models depends on factors like trait genetic architecture, training set size, relatedness of the selected material to the training set, and the validation method used. Alternative genotyping methods such as RADseq and complementary data from near-infrared spectroscopy could help improve the cost-effectiveness of genomic prediction. However, the impact of these factors and alternative approaches on predictive ability beyond experimental populations still need to be investigated. In this study, we evaluated 137 prediction scenarios varying the described factors and alternative approaches, offering recommendations for implementing genomic selection in apple breeding. Results Our results show that extending the training set with germplasm related to the predicted breeding material can improve average predictive ability across eleven studied traits by up to 0.08. The study emphasizes the usefulness of leave-one-family-out cross-validation, reflecting the application of genomic prediction to a new family, although it reduced average predictive ability across traits by up to 0.24 compared to 10-fold cross-validation. Similar average predictive abilities across traits indicate that imputed RADseq data could be a suitable genotyping alternative to SNP array datasets. The best-performing scenario using near-infrared spectroscopy data for phenomic prediction showed a 0.35 decrease in average predictive ability across traits compared to conventional genomic prediction, suggesting that the tested phenomic prediction approach is impractical. Conclusions Extending the training set using germplasm related with the target breeding material is crucial to improve the predictive ability of genomic prediction in apple. RADseq is a viable alternative to SNP array genotyping, while phenomic prediction is impractical. These findings offer valuable guidance for applying genomic selection in apple breeding, ultimately leading to the development of breeding material with improved quality.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agricultural research / Agriculture / Apple breeding / Apple REFPOP / Apples / Arrays / Biomedical and Life Sciences / Breeding / Cost effectiveness / data collection / Data mining / Fruits / Genome, Plant / Genomic selection / Genomics / Genomics - methods / Genotype / Genotyping / Germplasm / Infrared spectra / Infrared spectroscopy / Life Sciences / Malus - genetics / Malus × domestica / marker-assisted selection / Methods / Missing data / Near infrared radiation / near-infrared spectroscopy / new family / Performance evaluation / Phenomic selection / Phenomics - methods / Phenotype / Plant breeding / Plant Breeding - methods / Plant Sciences / Polymorphism, Single Nucleotide / Population studies / prediction / Prediction models / Predictions / Quantitative traits / single nucleotide polymorphism arrays / Single-nucleotide polymorphism / Tree Biology