Apr 29, 2016

Coherent synthesis of genomic associations with phenotypes and home environments

BioRxiv : the Preprint Server for Biology
Jesse R LaskyMatthew Reimherr


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 associ...Continue Reading

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Mentioned in this Paper

Genome-Wide Association Study
Genome Assembly Sequence
Nucleic Acid Sequencing
Home Environment

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