GxE and changes to the genetic architecture of flowering time in an overwintering environment

In Arabidopsis thaliana, flowering time shows extensive genotype-by-environment effects between an overwintering common garden and growth chamber conditions, with the top 1% SNP effects only moderately correlated.

• Why it matters: Genetic architecture can shift across environments, affecting how we infer adaptation and plasticity; standard chamber results may not reflect ecologically realistic selection.
• What they did: The study grew 479 Arabidopsis thaliana accessions in an overwintering common garden and compared them to prior 1001 Genomes Project chamber phenotypes using multivariate GWAS and analyses of polygenic architecture.
• The result: Large-effect loci were not shared across conditions, while allelic differential sensitivity, conditional neutrality, and antagonistic pleiotropy were linked to GxE; this implies flowering-time regulatory pathways are revealed more in the overwintering environment.

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