optiSel

optiSel computes optimal genetic contributions for livestock breeding programs as an R package implementing optimum contribution selection and mate allocation to balance genetic gain and genetic diversity.

Key Features:

• Optimum Genetic Contribution Calculation: Computes ideal genetic contributions for each selection candidate to balance multiple conflicting objectives in breeding programs.
• Handling Conflicting Objectives: Manages simultaneous goals such as increasing genetic gain, maintaining or enhancing genetic diversity, recovering original genetic backgrounds of endangered breeds with historic introgression, and preserving native allele diversity.
• Parameter Optimization and Constraints: Allows optimization of one parameter while constraining others to tailor breeding strategies to specific objectives.
• Pedigree and Marker Data Utilization: Integrates pedigree and marker data to estimate parameters required for optimum contribution selection problems.
• Solver Flexibility: Implements multiple solvers (slsqp, cccp, and cccp2), with slsqp preferred for maximizing diversity at native alleles and cccp/cccp2 suited to other OCS scenarios.
• Special Considerations for Local Breeds: Supports objectives specific to local breeds, including recovery and preservation of breed-specific genetic backgrounds.

Scientific Applications:

• Genetic Resource Management: Optimizes contributions to preserve and enhance the genetic diversity of livestock populations.
• Selective Breeding Programs: Facilitates design of breeding strategies that maximize genetic gain while maintaining or increasing genetic diversity.
• Conservation Efforts: Aids recovery and preservation of genetic backgrounds of endangered breeds, including those with historic introgression.

Methodology:

Solves optimum contribution selection (OCS) problems by estimating parameters from pedigree and marker data and applying solvers slsqp, cccp, and cccp2 to find constrained optimal solutions.