Coherent synthesis of genomic associations with phenotypes and home environments

Abstract

Local adaptation is often studied via 1) multiple common garden experiments comparing performance of genotypes in different environments and 2) sequencing genotypes from multiple locations and characterizing geographic patterns in allele frequency. Both approaches aim to characterize the same pattern (local adaptation), yet the complementary information from each has not yet been coherently integrated. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (GxE), i.e. reaction norms. We present an approach to impute relative fitness, allowing us to coherently synthesize evidence from common garden and genome-environment associations. Our approach identifies loci exhibiting environmental clines where alleles are associated with higher fitness in home environments. Simulations show our approach can increase power to detect loci causing local adaptation. In a case study on Arabidopsis thaliana, most identified SNPs exhibited home allele advantage and fitness tradeoffs along climate gradients, suggesting selective gradients can maintain allelic clines. SNPs exhibiting GxE associations with fitness were enriched in genic regions, putative partial selective sweeps, and associations with an adaptive phenotype (flowering time plasticity). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point toward the loci underlying GxE and local adaptation; coherent models of diverse data provide a principled basis for synthesis.