title: A computational systems biology study for understanding salt tolerance mechanism in rice.
abstract: Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving grain yield. In this study, a gene regulatory network of rice salt tolerance is constructed using a systems biology approach with a number of novel computational methods. We developed an improved volcano plot method in conjunction with a new machine-learning method for gene selection based on gene expression data and applied the method to choose genes related to salt tolerance in rice. The results were then assessed by quantitative trait loci (QTL), co-expression and regulatory binding motif analysis. The selected genes were constructed into a number of network modules based on predicted protein interactions including modules of phosphorylation activity, ubiquity activity, and several proteinase activities such as peroxidase, aspartic proteinase, glucosyltransferase, and flavonol synthase. All of these discovered modules are related to the salt tolerance mechanism of signal transduction, ion pump, abscisic acid mediation, reactive oxygen species scavenging and ion sequestration. We also predicted the three-dimensional structures of some crucial proteins related to the salt tolerance QTL for understanding the roles of these proteins in the network. Our computational study sheds some new light on the mechanism of salt tolerance and provides a systems biology pipeline for studying plant traits in general.
authors.affiliation: College of Computer Science and Technology, Jilin University, Changchun, China.
authors.forename: Juexin
authors.initials: J
authors.lastname: Wang
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Jingfen
authors.initials: J
authors.lastname: Zhang
authors.forename: Yanchun
authors.initials: Y
authors.lastname: Liang
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics / Q000502:physiology*; D010940:Plant Proteins / Q000378:metabolism; D060066:Protein Interaction Maps; D040641:Quantitative Trait Loci / Q000235:genetics; D055049:Salt Tolerance / Q000235:genetics / Q000502:physiology*
chemical_list: D010940:Plant Proteins