Temporal & genomic additive-variance analysis
Jun 1, 2021
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1 min read
This workflow reproduces Lara et al. (2021, Heredity) “Temporal and genomic analysis of additive genetic variance in breeding programmes.” It simulates a multi-stage wheat breeding programme, partitions additive variance over time, and generates the figures/tables published in the paper.
Repository layout
10simulations/: optimised scripts for running ten repetitions of the analysis.Result_paper/: simulation + analysis scripts used in the manuscript, including plotting and table outputs (requires AlphaSimR v0.11.0).Sensitivity_Genetic_Architecture/: evaluates the framework under different genetic architectures (varying QTL counts, genotype-by-year interactions; uses AlphaSimR v1.0.1).
Highlights
- Tracks additive variance across pipeline stages and through time, leveraging AlphaSimR outputs and custom partitioning scripts.
- Provides ready-to-run scenarios for assessing breeding programme design choices.
- Documents software requirements (AlphaSimR versions, R dependencies) for reproducibility.
Clone the repo, follow the README instructions for AlphaSimR setup, and execute the scripts in each folder to replicate the analyses from Lara et al. (2021).
