Abstract
Abstract
Background
Genetic connectedness is a critical component of genetic evaluation as it assesses the comparability of predicted genetic values across units. Genetic connectedness also plays an essential role in quantifying the linkage between reference and validation sets in whole-genome prediction. Despite its importance, there is no user-friendly software tool available to calculate connectedness statistics.
Results
We developed the GCA R package to perform genetic connectedness analysis for pedigree and genomic data. The software implements a large collection of various connectedness statistics as a function of prediction error variance or variance of unit effect estimates. The GCA R package is available at GitHub and the source code is provided as open source.
Conclusions
The GCA R package allows users to easily assess the connectedness of their data. It is also useful to determine the potential risk of comparing predicted genetic values of individuals across units or measure the connectedness level between training and testing sets in genomic prediction.
Funder
College of Agriculture and Life Sciences, Virginia Polytechnic Institute and State University
Publisher
Springer Science and Business Media LLC
Reference22 articles.
1. Foulley J, Schaeffer L, Song H, Wilton J. Progeny group size in an organized progeny test program of ai beef bulls using reference sires. Can J Anim Sci. 1983; 63(1):17–26.
2. Foulley JL, Bouix J, Goffinet B, Elsen MJ. Connectedness in genetic evaluation In: Gianola D, Hammond K, editors. Advances in statistical methods for genetic improvement of livestock. Heidelberg: Springer Verlag: 1990. p. 277–308.
3. Kuehn L, Notter D, Nieuwhof G, Lewis R. Changes in connectedness over time in alternative sheep sire referencing schemes. J Anim Sci. 2008; 86(3):536–44.
4. Yu H, Spangler ML, Lewis RM, Morota G. Genomic relatedness strengthens genetic connectedness across management units. G3 Genes Genomes Genet. 2017; 7(10):3543–56.
5. Pszczola M, Strabel T, Van Arendonk J, Calus M. The impact of genotyping different groups of animals on accuracy when moving from traditional to genomic selection. J Dairy Sci. 2012; 95(9):5412–21.
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