ArticleFrontiers in plant science2021
Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato.
Article in Frontiers in plant science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Integrating genomic selection into potato breeding: A comparison of genotyping platforms and cross-environmental predictions.The plant genome · 2026Article
- Article
- PotatoMASH is a cost-effective marker system for genomic prediction in potato based on short-read haplotypes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- The transmission ability in a population of elite tetraploid potatoes.The plant genome · 2025Article
- Transferability of genomic prediction models across market segments in potato and the effect of selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass.Plant physiology · 2025Article
- Multienvironment genomic prediction in tetraploid potato.G3 (Bethesda, Md.) · 2024Article
- To be or not to be tetraploid-the impact of marker ploidy on genomic prediction and GWAS of potato.Frontiers in plant science · 2024Article
- Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family.Frontiers in plant science · 2024Review
- The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato.Frontiers in plant science · 2024Article
- Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.Genome biology · 2023Article
- Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content.Scientific reports · 2023Article
- Efficient Genomic Prediction of Yield and Dry Matter in Hybrid Potato.Plants (Basel, Switzerland) · 2023Article
- 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.The plant genome · 2023Article
- Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity.The Plant cell · 2023Review
- Evaluating the impact of modeling the family effect for clonal selection in potato-breeding programs.Frontiers in plant science · 2023Article
- Genome-wide association study and genomic prediction for yield and grain quality traits of hybrid rice.Molecular breeding : new strategies in plant improvement · 2022Article
- Genome-Based Genotype × Environment Prediction Enhances Potato (Frontiers in plant science · 2022Article
- Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes.Frontiers in plant science · 2022Article
- Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Cells · 2021Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Use of genomic prediction (GP) in tetraploid is becoming more common. Therefore, we think it is the right time for a comparison of GP models for tetraploid potato. GP models were compared that contrasted shrinkage with variable selection, parametric vs. non-parametric models and different ways of accounting for non-additive genetic effects. As a complement to GP, association studies were carried out in an attempt to understand the differences in prediction accuracy. We compared our GP models on a data set consisting of 147 cultivars, representing worldwide diversity, with over 39 k GBS markers and measurements on four tuber traits collected in six trials at three locations during 2 years. GP accuracies ranged from 0.32 for tuber count to 0.77 for dry matter content. For all traits, differences between GP models that utilised shrinkage penalties and those that performed variable selection were negligible. This was surprising for dry matter, as only a few additive markers explained over 50% of phenotypic variation. Accuracy for tuber count increased from 0.35 to 0.41, when dominance was included in the model. This result is supported by Genome Wide Association Study (GWAS) that found additive and dominance effects accounted for 37% of phenotypic variation, while significant additive effects alone accounted for 14%. For tuber weight, the Reproducing Kernel Hilbert Space (RKHS) model gave a larger improvement in prediction accuracy than explicitly modelling epistatic effects. This is an indication that capturing the between locus epistatic effects of tuber weight can be done more effectively using the semi-parametric RKHS model. Our results show good opportunities for GP in 4x potato.
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