ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2023
Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed, 27 citations in OpenAlex.
- Integrating genomic selection into potato breeding: A comparison of genotyping platforms and cross-environmental predictions.The plant genome · 2026Article
- Unveiling the interactions between design optimization, modeling strategies, and spatial analysis in genomic selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Revisiting additive and dominance effects.G3 (Bethesda, Md.) · 2026Article
- Genotype-by-sequencing-enabled genome-wide association studies reveal genetic architecture of biomass and nitrogen modulation in tepary bean (Phaseolus acutifolius).G3 (Bethesda, Md.) · 2026Article
- Optimising realised genetic gain with low forward predictive ability across cycles for cooking time and correlated traits in common bean based on multivariate genomic selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Multi-traits and stability-based selection of high-yielding mungbean (Vigna radiata L.) genotypes in Benin.Scientific reports · 2026Article
- Feed-forward neural networks for genomic selection: insights into varying levels of dominance heritability.BMC genomics · 2026Article
- MateR: a novel genomic mating framework.Genetics · 2026Article
- 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
- Genome-wide association studies and genomics-informed breeding for tuber dormancy in tetraploid potatoes.The plant genome · 2026Article
- BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.).The plant genome · 2025Article
- Leveraging unmanned aerial vehicle derived multispectral data for improved genomic prediction in potato (Solanum tuberosum).The plant genome · 2025Article
- Combining ability of banana triploid hybrid progenitors and genomic prediction of cross performance for agro-morphological traits.Genetics · 2025Article
- Optimizing fully-efficient two-stage models for genomic selection using open-source software.Plant methods · 2025Article
- Article
- Identification of novel candidate genes for regulating oil composition in soybean seeds under environmental stresses.Frontiers in plant science · 2025Article
- Genomic prediction for potato (Solanum tuberosum) quality traits improved through image analysis.The plant genome · 2024Article
- Don't BLUP Twice.G3 (Bethesda, Md.) · 2024Article
- A Dominance Hypothesis Argument for Historical Genetic Gains and the Fixation of Heterosis in Octoploid Strawberry.Genetics · 2024Article
- Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
key messageR/StageWise enables fully efficient, two-stage analysis of multi-environment, multi-trait datasets for genomic selection, including support for dominance heterosis and polyploidy. Plant breeders interested in genomic selection often face challenges to fully utilizing multi-trait, multi-environment datasets. R package StageWise was developed to go beyond the capabilities of most specialized software for genomic prediction, without requiring the programming skills needed for more general-purpose software for mixed models. As the name suggests, one of the core features is a fully efficient, two-stage analysis for multiple environments, in which the full variance-covariance matrix of the Stage 1 genotype means is used in Stage 2. Another feature is directional dominance, including for polyploids, to account for inbreeding depression in outbred crops. StageWise enables selection with multi-trait indices, including restricted indices with one or more traits constrained to have zero response. For a potato dataset with 943 genotypes evaluated over 6 years, including the Stage 1 errors in Stage 2 reduced the Akaike Information Criterion (AIC) by 29, 67, and 104 for maturity, yield, and fry color, respectively. The proportion of variation explained by heterosis was largest for yield but still only 0.03, likely because of limited variation for the genomic inbreeding coefficient. Due to the large additive genetic correlation (0.57) between yield and maturity, naïve selection on an index combining yield and fry color led to an undesirable response for later maturity. The restricted index coefficients to maximize genetic merit without delaying maturity were identified. The software and three vignettes are available at https://github.com/jendelman/StageWise .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.