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.All raw data and code to reproduce analyses will be made available on GitHub upon publication. While we focus the main text on shoot biomass, we additionally have data on leaf chlorophyl A content, plant height, and leaf number, which will be accessible via GitHub. Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: IOS-1645875Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: NPGI-1401864Funding provided by: Joint Genome InstituteCrossref Funder Registry ID: http://dx.doi.org/10.13039/100015911Award Number: CSP-1223795Funding provided by: Carl R. Woese Institute for Genomic BiologyCrossref Funder Registry ID: http://dx.doi.org/10.13039/100017185Award Number:Detailed methods are included in the PDF associated with this dataset. We performed four greenhouse experiments to estimate partner quality phenotypes in Ensifer meliloti. In each experiment, plants from one of two host lines (either A17 or DZA) were grown in single inoculation with each of 191 E. meliloti strains, with three to four replicates per strain per experiment (six to eight total replicates for each plant line x strain combination, N = 2,825 plants total). We measured multiple proxies of partner quality, namely leaf chlorophyll A content, plant height, number of leaves, and above-ground dried shoot biomass. Simutaneously, we sequenced the entire genomes of all 191 E. meliloti strains, called single nucleotide polymorphisms (SNPs, henceforth referred to as variants), and performed genome-wide association tests that accounted for rhizobium population structure and included only unlinked variants. We determined which loci were significantly associated with partner quality using a permutation method, and binned these loci into three categories based on the context-dependency of their phenotypic effects, and thus, their contribution to the layers of the G→P map for each of our symbiotic extended phenotypes, as described in the abstract