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Optimum contribution selection for animal breeding and conservation: the R package optiSel.
1Institute of Animal Science, University of Hohenheim, Garbenstraße, Stuttgart, Germany. r.wellmann@uni-hohenheim.de.
BMC Bioinformatics
|January 16, 2019
Summary
The R package optiSel enables optimum contribution selection (OCS) for livestock breeding programs, balancing conflicting objectives like genetic gain and diversity. This tool helps manage genetic resources effectively for endangered breeds.
Area of Science:
- Animal Breeding and Genetics
- Quantitative Genetics
- Bioinformatics
Background:
- Optimum contribution selection (OCS) is crucial for genetic resource management and livestock breeding.
- Existing OCS software struggles to simultaneously address conflicting breeding objectives.
- These objectives include maximizing genetic gain, preserving genetic diversity, and managing native alleles in local breeds.
Purpose of the Study:
- To introduce the free R package optiSel for solving complex optimum contribution selection problems.
- To provide a user-friendly tool for estimating parameters and solving OCS issues in animal breeding.
- To address the challenge of conflicting objectives in breeding programs, particularly for local and endangered breeds.
Main Methods:
- The optiSel R package utilizes pedigree and marker data for parameter estimation.
- It employs various optimization solvers (e.g., slsqp, cccp, cccp2) to address OCS problems.
- The software allows for one primary objective to be optimized while others are constrained.
Main Results:
- optiSel can estimate key parameters and solve OCS problems, providing optimal offspring numbers for selection candidates.
- The package facilitates mate allocation based on calculated optimum contributions.
- Solver performance varied, with slsqp excelling in maximizing genetic diversity at native alleles, while cccp and cccp2 were better for other OCS tasks.
Conclusions:
- Optimum contribution selection in local breeds presents unique challenges due to conflicting breeding goals.
- The R package optiSel offers a practical and accessible solution for incorporating these complex objectives.
- This tool supports the effective management of genetic resources and the sustainability of local livestock breeds.
Keywords:
Animal breedingConservationNative contributionNative kinshipOptimum contribution selectionRuns of homozygositySegment-based kinshipoptiSelMore Related Videos
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