Abstract
BackgroundIn this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from estimated breeding values averaged by year of birth. While sources of the overall genetic gain are generally known, their realised contributions are hard to quantify in complex breeding programmes. The aim of this paper is to present the AlphaPart R package and demonstrate it with a simulated stylized multi-tier breeding programme mimicking a pig or poultry breeding programme.ResultsThe package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by pre-defined selection paths, and a set of functions for handling data and results. The package is freely available from the CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by partitioning the nucleus and multiplier genetic gain of the stylized breeding programme by tier-gender paths. For traits measured and selected in the multiplier, the multiplier selection generated additional genetic gain. By using AlphaPart, we show that the additional genetic gain depends on accuracy and intensity of selection in the multiplier and the extent of gene flow from the nucleus. We have proven that AlphaPart is a valuable tool for understanding the sources of genetic gain in the nucleus and especially the multiplier, and the relationship between the sources and parameters that affect them.ConclusionsAlphaPart implements the method for partitioning breeding values and genetic trends and provides a useful tool for quantifying the sources of genetic gain in breeding programmes. The use of AlphaPart will help breeders to improve genetic gain through a better understanding of the key selection points that are driving gains in each trait.
Highlights
In this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain
We can write a vector of breeding values as a linear combination of Mendelian sampling terms of individuals and their ancestors: a = Tw, where T is a triangular matrix of expected gene flow between ancestors and individuals [4, 5] and w is a vector of Mendelian sampling terms
The aim of this paper is to present the AlphaPart R package that implements a method for partitioning breeding values and genetic trends
Summary
We present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. The method of García-Cortés et al [3] uses a path variable to partition the gene flow matrix T = T1 + T2 + · · · + Tp and with this partitions breeding values by selection paths a = (T1 + T2 + · · · + Tp)w = a1 + a2 + · · · + ap), where Ti describes the gene flow for a selection path i Aggregating these partitions by other variables (such as year of birth, countries, gender, etc.) is a powerful way to analyse sources of genetic gain
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