Data from: The complex genetics of symbiotic extended phenotypes across environments in a model mutualism

A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here we use naturally-occurring genetic variation in 191 strains of the model microbial symbiont Ensifer meliloti in four mapping experiments to study the genomic architecture of a key symbiotic extended phenotype — partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, 1) loci whose identities depend on the environment, 2) those that depend on the host genotype with which rhizobia interact, and 3) universal loci that are likely important in all or most environments.