Abstract:[Background] The interaction between species is an important driving force for the evolution of species. But it is challenging to determine the single nucleotide polymorphism (SNPs) that play an important role in the process of interaction between species and establish an accurate genotype-phenotype map. [Objective] To obtain the significant SNPs that play an important role in the interaction between Escherichia coli and Staphylococcus aureus and to detect how do these SNPs relate to each other over time. [Methods] Real-time quantitative PCR (qPCR) was used to determine the abundance of all strains. We reared E. coli and S. aureus in monoculture and compared to the difference of growth between the same strain in monoculture and co-culture. The phenotypes and genotypes of all strains were analyzed by systems mapping and the significant SNPs were found out. [Results] We obtained a three-dimensional Manhattan plot that identifies 54 significant combinations of SNPs derived from 41 SNPs in E. coli and 12 SNPs in S. aureus. Among them, 6 genes we obtained by annotation can directly or indirectly affect the growth of microorganisms, nhaR (E19056) was involved in the formation of biofilm, rhlE (E832164) is related to ribosome assembly, the expression of csiD (E2789300) can make cells face stress environment, alkB (E2309274) can participate in DNA damage repair, sucA (E759230) and yjjW (E4614704) are involved in the metabolic process of cells. [Conclusion] Systems mapping can detect the significant SNPs. The genetic effects of different SNPs are variable in the process of species interaction. Bacterial interaction was found to exert direct genetic effects, indirect genetic effects and interspecific epistatic effects.
