Abstract：
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 Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine 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, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
摘要：
现代生物学的目标是开发基因型-表型（G→P）图，对基因组信息如何产生性状变异的预测性理解，这些性状变异构成了自然和管理社区的基础。随着微生物组研究的进展，然而,很明显，这些特征中的许多都是共生扩展的表型，不仅受宿主自身基因组编码的遗传变异控制，还有无数神秘共生体的基因组。因此，建立可靠的G→P图谱需要考虑许多相互作用的基因，甚至涉及共生的基因组。这里,我们在四个全基因组关联研究（GWAS）中使用了191个模型微生物共生体中华根瘤菌与两种基因型宿主苜蓿配对的自然发生的遗传变异，以确定关键共生扩展表型伴侣质量的基因组结构。或特定共生体基因型赋予宿主的健身益处，在环境背景和宿主基因型之内和之间。我们在根瘤菌基因组中定义了三个新的基因座类别，如果我们想建立可靠的伙伴质量G→P图，则必须考虑这些基因座；即，（i）其身份取决于环境的基因座，（ii）那些依赖于与根瘤菌相互作用的宿主基因型的，和（iii）在所有或大多数环境中可能很重要的通用基因座。重要性鉴于有关如何利用微生物组来改善宿主健康的研究迅速兴起，了解微生物遗传变异对宿主表型变异的贡献是当务之急，并且将使我们能够更好地预测影响宿主健康的共生扩展表型的进化（并更精确地选择）。我们在控制宿主生长的共生体基因座的身份和功能中发现了广泛的上下文依赖性，这使得预测在不同条件下确定共生结果的重要基因和途径更具挑战性。尽管存在这种上下文依赖性，我们还解析了在所有或大多数环境中可能很重要的一组核心通用基因座，因此，作为基因工程和未来共生共同进化研究的极好目标。
