Apr 25, 2020

AlphaPart - R implementation of the method for partitioning genetic trends

BioRxiv : the Preprint Server for Biology
Jana ObsteterG. Gorjanc


In this paper we present the AlphaPart R package, an open-source software that implements a method for partitioning breeding values and genetic trends to identify sources of genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from averaged year of birth estimated breeding values of selection candidates. 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 pig breeding example. The package includes the main partitioning function AlphaPart, that partitions the breeding values and genetic trends by analyst defined paths, and a set of functions for handling data and results. The package is freely available from CRAN repository at http://CRAN.R-project.org/package=AlphaPart. We demonstrate the use of the package by examining the genetic gain in a pig breeding example, in which the multiplier achieved higher breeding values than the nucleus for traits measured and selected in the multiplier. The partitioning analysis revealed that these higher values depended on the accurac...Continue Reading

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