This repository contains the code used to produce results in "Genomic selection strategies to increase genetic gain in tea breeding programs" (Lubanga et al., 2023). The code was run using R 4.0.0 and AlphaSimR 1.0.4.

Note that this manuscript is currently under revision, so changes are expected.

If you find any issues or errors, please do not hesitate to contact [email protected] and [email protected].

Lubanga, N., Massawe, F., Mayes, S., Gorjanc, G., & Bančič, J. (2023). Genomic selection strategies to increase genetic gain in tea breeding programs. The Plant Genome, 16, e20282. https://doi.org/10.1002/tpg2.20282

The repository contains two folders with scripts for 25% and 100% parent replacement. Within each folder, scripts labelled 01-06 contain the code for the burnin and the five breeding program scenarios presented in the paper. In addition, there is also a script for pedigree analysis used by script 03, as well as other scripts for post-analysis (e.g., plotting, ratio calculation, and statistical testing).