ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2022
Genomic prediction with allele dosage information in highly polyploid species.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Balancing gain and diversity: Optimal contribution selection for sustainable genetic improvement in sugarcane.The plant genome · 2026Review
- From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Leveraging AI and integrated genomic-enviromic prediction for intelligent sugarcane breeding.Plant communications · 2026Review
- Towards a sweetpotato genomic-enabled breeding: optimizing two-stage analysis of multi-environment augmented trials.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Multiomic insights into sucrose accumulation in sugarcane.Plant molecular biology · 2025Article
- Tests for segregation distortion in higher ploidy F1 populations.G3 (Bethesda, Md.) · 2025Article
- Genome analyses and breeding of polyploid crops.Nature plants · 2025Review
- Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass.Plant physiology · 2025Article
- Optimization of Microsatellite Multiplex PCRs for Triploidy Verification and Genetic Diversity Assessment in the Pacific Oyster, Crassostrea gigas.Marine biotechnology (New York, N.Y.) · 2025Article
- Tests for segregation distortion in tetraploid F1 populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Refining polyploid breeding in sweet potato through allele dosage enhancement.Nature plants · 2025Article
- Machine learning for genomic and pedigree prediction in sugarcane.The plant genome · 2024Article
- Article
- Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Sugarcane breeding: a fantastic past and promising future driven by technology and methods.Frontiers in plant science · 2024Article
- Article
- Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane.Frontiers in plant science · 2023Article
- Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species.Frontiers in plant science · 2022Review
- Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Cells · 2021Review
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Authors and funding
4 authors.
Funding
Abstract
key messageIncluding allele, dosage can improve genomic selection in highly polyploid species under higher frequency of different heterozygous genotypic classes and high dominance degree levels. Several studies have shown how to leverage allele dosage information to improve the accuracy of genomic selection models in autotetraploid. In this study, we expanded the methodology used for genomic selection in autotetraploid to higher (and mixed) ploidy levels. We adapted the models to build covariance matrices of both additive and digenic dominance effects that are subsequently used in genomic selection models. We applied these models using estimates of ploidy and allele dosage to sugarcane and sweet potato datasets and validated our results by also applying the models in simulated data. For the simulated datasets, including allele dosage information led up to 140% higher mean predictive abilities in comparison to using diploidized markers. Including dominance effects were highly advantageous when using diploidized markers, leading to mean predictive abilities which were up to 115% higher in comparison to only including additive effects. When the frequency of heterozygous genotypes in the population was low, such as in the sugarcane and sweet potato datasets, there was little advantage in including allele dosage information in the models. Overall, we show that including allele dosage can improve genomic selection in highly polyploid species under higher frequency of different heterozygous genotypic classes and high dominance degree levels.
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