Explore The Gene-phenotype Association Of Arabidopsis Thaliana Through Systems Biology Approach

Analysis of phenotype-gene association mediated by mutations is one of the most efficient methods to discover gene function and biological mechanism in plant. In parallel, phenotypic information of mutant resources in Arabidopsis thaliana was partially curated in literatures and released in many seed resource databases. After retrieving data directly from these mutant resources through a data interface and manually from published literatures, we finally hold a large size of mutant collection with 5,665 mutant lines, involving 3,874 genes. We then classified the existing phenotype in accordance with Plant Ontology (PO), and obtained 8,119 phenotype-gene relationships involving 176 PO terms.Next, we explored the functional linkages between genes, the results suggested that genes associated with same phenotype were more likely to participate in the same molecular complex, functional module, or have the high correlated expression profile. At the same time, we constructed the phenotype-gene network, phenotype-phenotype network and gene-gene network, which offered platforms to explore the mechanism of gene and phenotype relationships at the molecular level.We then identified novel associations between genes and phenotypes with Naive Bayes approach, and further verified our predicted results by mapping with other Arabidopsis phenotype datasets and calculating pathway enrichment, which infering high confident.In all, our project of mutants research at the phenotypic level provides a systematic method to predict new gene function and explore the relationship between gene and phenotype, the result provides new insight into a variety of important biological questions and enhances the utility of Arabidopsis as a reference plant in studying crop breeding.