Uncovering the genomic basis of local adaptation by coherent synthesis of associations with phenotypes and home environments

20 Running title: Genomic basis of G×E and local adaptation. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. Abstract A substantial portion of intraspecific diversity is associated with local adaptation to environment, which is driven by genotype-by-environment interactions (G×E) for fitness. 25 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 identify the same pattern (local adaptation), yet the complementary information from each approach has not been coherently integrated into a modeling 30 framework. Here, we develop a genome-wide association model of genotype interactions with continuous environmental gradients (G×E). We employ an imputation approach to synthesize evidence from common garden and genome-environment associations, allowing us to identify loci exhibiting climatic clines where alleles are associated with higher fitness in home environments. We apply this model to published data on natural 35 Arabidopsis thaliana accessions. Our approach reveals candidate genes for local adaptation based on known involvement in environmental stress response. Most outlier SNPs exhibit home allele advantage and fitness tradeoffs along climate gradients, suggesting selective gradients may maintain allelic clines. SNPs exhibiting G×E associations with fitness are enriched in genic regions, putative partial selective sweeps, 40 and G×E associations with an important adaptive phenotype (flowering time). We discuss extensions for situations where only adaptive phenotypes other than fitness are available. Many types of data may point toward the loci underlying G×E and local adaptation; coherent models of these diverse data provide a principled basis for synthesis. 45. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not .