Multi-Environment Trials
This tutorial covers GWAS analysis with repeated measurements across multiple environments.
Overview
Multi-environment trials (MET) are common in plant breeding where the same genotypes are evaluated across multiple locations, years, or treatments. Binx handles these designs through:
- Repeated sample IDs in phenotype files
- Environment as a covariate
- Appropriate mixed model handling
Data Structure
Your phenotype file can include repeated measurements:
sample_id,yield,environment,replicate
Sample001,45.2,field_A,1
Sample001,47.8,field_A,2
Sample001,44.1,field_B,1
Sample002,52.1,field_A,1
Sample002,50.3,field_A,2
Running MET GWAS
binx gwas \
--geno genotypes.tsv \
--pheno phenotypes.csv \
--trait yield \
--covariates environment \
--ploidy 4 \
--out results.csv
Analyzing G×E Interactions
Coming soon: Detailed tutorial on G×E analysis