A simulation study using AlphaSimR to simulate both nuclear and mitochondrial genomes in the context of a dairy cattle breeding programme. The study looks at how accountning for nuclear and mitochondrial genome variation in estmation of breeding values and selection impacts the accuracy of estimation and the magnitude of response to selection.
This study was initiated as an intership of Gabriela Mafra Fortuna during her MSc in Animal Breeding and Genetics, which then became her MSc thesis, and finally the following manuscript.
@article{MafraFortuna2023Accounting,
title = {Accounting for nuclear and mito genome in dairy cattle breeding-a simulation study},
author = {Mafra Fortuna, Gabriela and Zumbach, Birgit Jutta and Johnsson, Martin and Pocrnic, Ivan and Gorjanc, Gregor},
year = {2023},
journal = {bioRxiv},
doi = {10.1101/2023.11.20.567907}
}
To run the simulation, run the replicates_run.R script. The script states the required R packages.