AlphaPart - R implementation of the method for partitioning genetic trends

Jana Obšteter, Justin Holl, John Hickey, Gregor Gorjanc

Research output: Contribution to journalArticlepeer-review

Abstract

Background: 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. 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.
Results: The 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.
Conclusions: AlphaPart 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.
Original languageEnglish
JournalGenetics Selection Evolution
Volume53
Issue number1
Early online date18 Mar 2021
DOIs
Publication statusE-pub ahead of print - 18 Mar 2021

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