AlloMate — Genetic Mate Allocation and Breeding Optimization App

AlloMate is a Shiny web application developed by the Breeding Insight team to support genetic mate allocation and breeding optimization. The app integrates pedigree-based kinship, estimated breeding values (EBVs), and Optimum Contribution Selection (OCS) to help breeding programs balance genetic gain while controlling inbreeding.

This repository reflects the current main branch and follows a golem-based application structure.

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Overview

Modern breeding programs must optimize selection decisions while managing inbreeding and long-term genetic diversity. AlloMate provides an interactive and reproducible framework for:

• Evaluating genetic relatedness among breeding candidates
• Combining multiple EBV traits using user-defined weights
• Optimizing individual contributions via Optimum Contribution Selection
• Producing feasible mating plans under kinship constraints

The application is designed to be species-agnostic and adaptable to a wide range of breeding program designs.

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Key Features

Breeding and Optimization

• Pedigree-based kinship matrix calculation
• Support for multiple EBV traits with configurable weights (weights must sum to 1)
• Optimum Contribution Selection (OCS) to balance gain and inbreeding
• Kinship threshold filtering to exclude unfavorable crosses
• Automated generation of mating plans

Technical Highlights

• Implemented in R and Shiny
• Uses the optiSel package when available
• Includes a pure-R OCS fallback implementation for environments where optiSel cannot be installed
• Designed for modularity and extensibility
• Exportable results for downstream analysis and reporting

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Installation and Running the App

AlloMate uses a golem application structure, allowing it to be installed like a standard R package.

Install from GitHub

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

remotes::install_github("Breeding-Insight/AlloMate")

Run AlloMate

AlloMate::run_app()

Dependencies

Key R packages used by AlloMate include:

• shiny
• dplyr
• tidyr
• kinship2
• quadprog
• DT
• openxlsx

Optional:

• optiSel (used when available for Optimum Contribution Selection)

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Usage Summary

1. Upload required input files:

   • Candidate list (IDs and sex)
   • Pedigree file (individual, sire, dam)
   • EBV files for one or more traits

2. Configure analysis parameters:

   • Trait weights (must sum to 1)
   • Kinship thresholds
   • OCS constraints

3. Review outputs:

   • Kinship matrices and summaries
   • Combined EBV scores
   • Optimal contributions and mating plans

4. Export results:

   • Download Excel reports containing all outputs and diagnostics

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Citation

If you use AlloMate in research or breeding analyses, please cite it as:

Chinchilla-Vargas, J., Ackerman, A. J., & Taniguti, C. H.
AlloMate: Genetic Mate Allocation and Breeding Optimization App.
RRID: SCR_027115

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Contributing

Contributions are welcome. Please:

• Follow existing coding and naming conventions
• Clearly document new functions and modules
• Test changes before submitting pull requests

Submit issues and pull requests via GitHub.

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License

AlloMate is released under the Apache License, Version 2.0.
See the LICENSE file or https://www.apache.org/licenses/LICENSE-2.0 for details.

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Acknowledgments

AlloMate is developed as part of the Breeding Insight initiative to provide open-source, data-driven tools for modern breeding programs.