Plant breeding simulations with AlphaSimR

Introduction

This repository contains R scripts that demonstrate simulations of plant breeding programs and techniques using AlphaSimR https://cran.r-project.org/package=AlphaSimR. These scripts and the process of simulating plant breeding programs are described in:

Bancic et al. (2023) bioRxiv https://www.biorxiv.org/content/10.1101/2023.12.30.573724v1

@article{BancicEtAl2023,
  title = {Plant breeding simulations with AlphaSimR},
  author = {Bančič, Jon and Greenspoon, Philip and Gaynor, R Chris and Gorjanc, Gregor},
  journal = {bioRxiv},
  year = {2023},
  doi = {10.1101/2023.12.30.573724}
}

If you use this material, please cite the above publication and the original AlphaSimR publication:

@article{Gaynor2021AlphaSimR,
  author = {Gaynor, R. Chris and Gorjanc, Gregor and Hickey, John M.},
  title = {{AlphaSimR}: An {R}-package for Breeding Program Simulations},
  volume = {11},
  year = {2021},
  doi = {10.1093/g3journal/jkaa017},
  journal = {G3: Genes|Genomes|Genetics}
}

If you have no prior experience with AlphaSimR, we suggest you complete the free online course "Breeding Programme Modelling with AlphaSimR" at https://www.edx.org/course/breeding-programme-modelling-with-alphasimr. The course is continually open, so you can enroll when it's convenient for you.

If you are interested in animal breeding simulations, see https://github.com/HighlanderLab/gmafrafortuna_alphasimr_animals (work in progress) ...

Repository contents

• README.md is this file.

• LineBreeding.Rmd (and its output LineBreeding.html) - Introductory vignette describing the logic of provided R scripts.

• jbancic_alphasimr_plants.Rproj is the RStudio/Posit project file (to set the working directory etc.).

• 01_LineBreeding folder contains scripts for simulating a line breeding program - showing a wheat example that can be adapted to other selfing species. The scripts show several phenotypic selection strategies (mass selection, single seed descent, pedigree selection, and doubled haploids) and genomic selection strategies (conventional and two-part).

• 02_ClonalBreeding folder contains scripts for simulating a clonal breeding program - showing a tea example that can be adapted to other clonal species. The scripts show phenotypic, pedigree, or genomic selection strategies.

• 03_HybridBreeding folder contains scripts for simulating a hybrid breeding program - showing a maize example that can be adapted to other outcrossing species. The scripts show a phenotypic selection strategy and two genomic selection strategies (conventional and two-part).

• 04_Features folder contains scripts for simulating plant breeding programs using various breeding and genetic techniques. The scripts show:

  • Mating plans (matingPlans.R)

  • Genome-wide association study (simulateGWAS.R)

  • Setting heritability (setHeritability.R)

  • Multi-trait selection with selection index (multipleTraits.R)

  • Miscellaneous slot to store user-defined information (miscellaneousSlot.R)

  • Simulate genotype by environment interaction (simulateGxE.R)

  • Genomic prediction & selection models (genomicModels.R)

  • Trait introgression (traitIntrogression.R)

  • Genome editing (genomeEditing.R)

  • Speed breeding (speedBreeding.R)

  • Import external haplotypes (importExternalHaplo.R)

  • Specifying demography for simulating founder genomes (specifyDemography.R)

  • Extra functions used across scripts (functions.R)

How to work with the provided R scripts

1. Read the manuscript and browse the introductory vignette LineBreeding.Rmd (and its output LineBreeding.html).

2. Download this whole repository

3. In RStudio/Posit, open project file jbancic_alphasimr_plants.Rproj

4. For each of the three types of plant breeding programs, select a folder and work through the 00RUNME.R file to run simulations and then work through the ANALYZERESULTS.R file to analyze the simulations' results.