Rong Mengdi, Zheng Xuyang, Ye Meixia, Bai Jun, Xie Xiangming, Jin Yi, He Xiaoqing
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.
Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Front Microbiol. 2019 Apr 16;10:809. doi: 10.3389/fmicb.2019.00809. eCollection 2019.
Phenotypic plasticity enables individuals to develop different phenotypes in a changing environment and promotes adaptive evolution. Genome-wide association study (GWAS) facilitates the study of the genetic basis of bacterial phenotypes, and provides a new opportunity for bacterial phenotypic plasticity research. To investigate the relationship between growth plasticity and genotype in bacteria, 41 strains, including 29 vancomycin-intermediate (VISA) strains, were inoculated in the absence or presence of vancomycin for 48 h. Growth curves and maximum growth rates revealed that strains with the same minimum inhibitory concentration (MIC) showed different levels of plasticity in response to vancomycin. A bivariate GWAS was performed to map single-nucleotide polymorphisms (SNPs) associated with growth plasticity. In total, 227 SNPs were identified from 14 time points, while 15 high-frequency SNPs were mapped to different annotated genes. The -values and growth variations between the two cultures suggest that non-coding region (SNP 738836), (SNP 1394043), drug transporter (SNP 264897), and (SNP 1775112) play important roles in the growth plasticity of . Our study provides an alternative strategy for dissecting the adaptive growth of in vancomycin and highlights the feasibility of bivariate GWAS in bacterial phenotypic plasticity research.
表型可塑性使个体能够在不断变化的环境中发育出不同的表型，并促进适应性进化。全基因组关联研究（GWAS）有助于研究细菌表型的遗传基础，为细菌表型可塑性研究提供了新的契机。为了研究细菌生长可塑性与基因型之间的关系，将包括29株万古霉素中介（VISA）菌株在内的41株菌株分别接种在有无万古霉素的条件下培养48小时。生长曲线和最大生长速率表明，具有相同最低抑菌浓度（MIC）的菌株对万古霉素的可塑性水平不同。进行了双变量GWAS以定位与生长可塑性相关的单核苷酸多态性（SNP）。总共从14个时间点鉴定出227个SNP，同时将15个高频SNP定位到不同的注释基因。两种培养物之间的P值和生长变化表明，非编码区（SNP 738836）、（SNP 1394043）、药物转运蛋白（SNP 264897）和（SNP 1775112）在[细菌名称未给出]的生长可塑性中起重要作用。我们的研究为剖析[细菌名称未给出]在万古霉素中的适应性生长提供了一种替代策略，并突出了双变量GWAS在细菌表型可塑性研究中的可行性。
