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

Investigating how genetic variation influences the expression of flowering time in Arabidopsis thaliana across different environments is crucial for understanding evolution in complex settings, phenotypic plasticity, and the genetic basis of adaptation. Researchers compared the phenotypic distribution, large-effect genes, and polygenic architecture of flowering time in 479 Arabidopsis thaliana accessions grown in an overwintering common garden with those grown in standard chamber conditions.

The results indicate extensive genotype-by-environment (GxE) interaction for flowering time between the two environments. No large-effect loci were shared between growth conditions when using a multivariate Genome Wide Association Study (GWAS). Evidence suggests allelic differential sensitivity, conditional neutrality, and antagonistic pleiotropy contribute to GxE for flowering time between different environments.

The study also reveals that the effects of genetic variation across multiple flowering time regulatory pathways become apparent when grown in an environment more representative of natural conditions. The effects of the most significant percent of SNPs are moderately correlated between outdoor and growth chamber conditions, suggesting a partially shared genetic basis.

Overall, the findings emphasize the importance of conducting experiments in ecologically realistic environments to accurately infer the genetic basis and evolution of complex traits.