ArticleBMC bioinformatics2019
Optimum contribution selection for animal breeding and conservation: the R package optiSel.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it, 132 citations in OpenAlex.
- Genomic loci involved in sensing environmental cues and metabolism affect seasonal coat shedding in Bos taurus and Bos indicus cattle.G3 (Bethesda, Md.) · 2024Pooled it
- Balancing gain and diversity: Optimal contribution selection for sustainable genetic improvement in sugarcane.The plant genome · 2026Review
- Uncertainty-aware breeding decisions: MCMC-based optimum contribution selection increases breeding decision robustness.Genetics · 2026Article
- OptOrch: a modular optimization toolkit for forest tree seed orchard deployment.G3 (Bethesda, Md.) · 2026Article
- Unravelling the Genetic Structure of Local and Mainstream Red-Pied Cattle Breeds Using Genomics and Extended Pedigree Analysis.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- Heat-load-dependent inbreeding depression for production traits in Italian Holstein cattle.Genetics, selection, evolution : GSE · 2026Article
- Targeted allele frequency tuning in breeding populations via alternative optimum contribution selection.Genetics · 2026Article
- An analysis of the genomic architecture of the worldwide Irish Wolfhound dogs.Scientific reports · 2026Article
- Restructuring breeding programs 2: Assortative mating for improved commercial genetic gain when using optimum contribution selection and diversity introduction.Genetics, selection, evolution : GSE · 2026Article
- Restructuring breeding programs 1: Integration of diversity.Genetics, selection, evolution : GSE · 2026Article
- Strategies to improve on selection based on estimated breeding values.Genetics, selection, evolution : GSE · 2026Article
- Probabilities of two alleles being identity by state at unobserved loci predicted by observed loci in cattle populations.Scientific reports · 2026Article
- Runs of homozygosity in Italian Holstein bulls: a permutation approach and time-based mapping of the genomic regions potentially under selection.BMC genomics · 2026Article
- Application of optimal contribution selection, trait distribution management, and group selection in layer chickens.Genetics, selection, evolution : GSE · 2026Article
- A random regression model for total litter weight in mice.Journal of animal science · 2026Article
- Optimising the Use of Cryopreserved Genetic Resources for the Selection and Conservation of Animal Populations.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2026Article
- visPedigree: a comprehensive R package for tidying, analyzing, and visualizing breeding pedigrees.Bioinformatics advances · 2026Article
- Optimization of family sizes in sets of crosses with a greedy allocation strategy based on automatic differentiation.Frontiers in plant science · 2026Article
- Applying Genomic Offsets to Breeding Programmes: Bridging Evolutionary Insights With Practical Applications.Evolutionary applications · 2025Article
- Exploring the Genetic Link Between Coat Colour and Morphological Traits: The Case of Peruano de Paso Horse.Animals : an open access journal from MDPI · 2025Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
backgroundSelecting animals for breeding in the optimum way plays an essential role for the management of genetic resources and in selective breeding of livestock species. It requires to compute the optimum genetic contribution of each selection candidate to the next generation. Current software packages for optimum contribution selection (OCS) are not able to handle the main conflicting objectives of animal breeding programs simultaneously, which includes to increase genetic gain, to increase or to maintain genetic diversity, to recover the original genetic background of endangered breeds with historic introgression, and to maintain or increase genetic diversity at native alleles.
resultsThe free R package optiSel offers functions for estimating the above mentioned parameters from pedigree and marker data, and for solving OCS problems. One parameter can be optimized, whereas the remaining ones can be constrained. The results reveal the optimum numbers of offspring of all selection candidates, and can subsequently be used for mate allocation. Different solvers can be used. Solver slsqp was superior when the genetic diversity at native alleles was to be maximized, whereas solvers cccp and cccp2 were superior for all other OCS problems.
conclusionOptimum contribution selection applied to local breeds requires special attention due to the conflicting objectives of their breeding programs. The free R package optiSel is an easy-to-use software taking these conflicting objectives into account.
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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.