AlphaPart

AlphaPart partitions breeding values and genetic trends to quantify contributions to genetic gain within breeding programs.

Key Features:

• Partitioning Functionality: The core function AlphaPart decomposes breeding values and genetic trends along analyst-defined paths.
• Quantification of Sources: Outputs quantify contributions from selection accuracy, selection intensity, and gene flow.
• Multi-population Support: Supports analysis across population segments such as nucleus and multiplier populations.
• Auxiliary Data Functions: Includes auxiliary functions for data handling and result management.
• Implementation: Implemented in R.

Scientific Applications:

• Quantify Genetic Gain Sources: Partition breeding values to quantify contributions of selection accuracy, selection intensity, and gene flow between population segments.
• Analyze Multi-trait Breeding Programs: Dissect genetic trends when multiple traits are measured and selected across different segments or populations (e.g., nucleus and multiplier).
• Inform Strategy Optimization: Provide quantitative insights to guide adjustments to selection practices and management of gene flow to maximize genetic gain.
• Simulation-Based Evaluation: Applied to simulated pig breeding data to evaluate how selection and gene flow influence differences between nucleus and multiplier populations.

Methodology:

The main partitioning function AlphaPart decomposes breeding values and genetic trends along analyst-defined paths, and auxiliary functions perform data handling and result management; the package is implemented in R.