Abstract
Genes have been thought to affect community ecology and evolution, but their identification at the whole-genome level is challenging. Here, we develop a conceptual framework for the genome-wide mapping of quantitative trait loci (QTLs) that govern interspecific competition and cooperation. This framework integrates the community ecology theory into systems mapping, a statistical model for mapping complex traits as a dynamic system. It can characterize not only how QTLs of one species affect its own phenotype directly, but also how QTLs from this species affect the phenotype of its interacting species indirectly and how QTLs from different species interact epistatically to shape community behavior. We validated the utility of the new mapping framework experimentally by culturing and comparing two bacterial species, Escherichia coli and Staphylococcus aureus, in socialized and socially isolated environments, identifying several QTLs from each species that may act as key drivers of microbial community structure and function.
Highlights
QTLs from different species interact epistatically to shape community behavior
Functional mapping has been upgraded to the level of systems mapping by regarding a complex trait as a system composed of interactive components[15,16]
A similar antagonistic relationship was observed for the other three genotypic combinations C/T, T/C, and T/T, but the pattern of antagonistic relationship varies among the four genotypic combinations. All these results suggest that E4614704 and S188004 are antagonistic QTLs that participate in determining and shaping the antagonistic relationship between E. coli and S. aureus when they are co-cultured in the same medium
Summary
QTLs from different species interact epistatically to shape community behavior. We validated the utility of the new mapping framework experimentally by culturing and comparing two bacterial species, Escherichia coli and Staphylococcus aureus, in socialized and socially isolated environments, identifying several QTLs from each species that may act as key drivers of microbial community structure and function. The Pennsylvania State University, Hershey, PA 17033, USA. These authors contributed : Libo Jiang, Xiaoqing He, Yi Jin, Meixia Ye. Given its capacity to genome-wide search for quantitative trait loci (QTLs) that control complex phenotypes, genetic or association mapping has been widely used as an approach for studying complex genetic questions[11,12]. Functional mapping has been upgraded to the level of systems mapping by regarding a complex trait as a system composed of interactive components[15,16]. By dissolving the phenotype into its underlying components based on morphogenetic, physiological, and anatomic principles[15], systems mapping can map and identify specific. QTLs that govern the interconnections of different components, gleaning new insight into the mechanistic basis of trait formation and progression
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