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A framework for simulating genotype by environment interaction using multiplicative models

Introduction

This repository contains supplementary R scripts that demonstrate the simulation of genotype by environment interaction using the R package FieldSimR as a part of a manuscript "A framework for simulating genotype by environment interaction using multiplicative models". This manuscript is currently under revision in Applied and Theoretical Genetics, so changes are expected.

Citation:

@article{Bancic2024,
    title = {A framework for simulating genotype by environment interaction using multiplicative models},
    author = {Bančič, Jon and Gorjanc, Gregor and Tolhurst, Daniel},
    journal = {Research Square},
    year = {2024},
    note = {Preprint version 1, 28 January 2024},
    doi = {10.21203/rs.3.rs-3855188/v1},
    url = {https://doi.org/10.21203/rs.3.rs-3855188/v1}
}

Repository contents

  • README.md is this file.

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

  • S0_WorkingExample demonstrates how to simulate a small example TPE with 100 environments from which a MET dataset is sampled with 10 environments using base R functions. This script is equivalent to Appendix C in the manuscript.

  • S1_SimulateGe demonstrates how to simulate a reduced rank between-environment genetic variance matrix, Ge, that captures genotype by environment interaction.

  • S2_SampleMET demonstrates how to simulate a MET dataset that captures genotype by environment interaction and spatial variation within environments.

  • S3_ModelComparison demonstrates model comparison using ASReml-R with a simulated MET dataset generated in S2_SampleMET.

  • S4_BreedingProgrammeComparison demonstrates how to simulate a phenotypic line breeding program in the presence of genotype by environment interaction.