title: Identification of altered metabolic pathways of γ-irradiated rice mutant via network-based transcriptome analysis.
abstract: In order to develop rice mutants for crop improvement, we applied γ-irradiation mutagenesis and selected a rice seed color mutant (MT) in the M14 targeting-induced local lesions in genome lines. This mutant exhibited differences in germination rate, plant height, and root length in seedlings compared to the wild-type plants. We found 1645 different expressed probes of MT by microarray hybridization. To identify the modified metabolic pathways, we conducted integrated genomic analysis such as weighted correlation network analysis with a module detection method of differentially expressed genes (DEGs) in MT on the basis of large-scale microarray transcriptional profiling. These modules are largely divided into three subnetworks and mainly exhibit overrepresented gene ontology functions such as oxidation-related function, ion-binding, and kinase activity (phosphorylation), and the expressional coherences of module genes mainly exhibited in vegetative and maturation stages. Through a metabolic pathway analysis, we detected the significant DEGs involved in the major carbohydrate metabolism (starch degradation), protein degradation (aspartate protease), and signaling in sugars and nutrients. Furthermore, the accumulation of amino acids (asparagine and glutamic acid), sucrose, and starch in MT were affected by gamma rays. Our results provide an effective approach for identification of metabolic pathways associated with useful agronomic traits in mutation breeding.
authors.affiliation: Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea.
authors.forename: Sun-Goo
authors.initials: SG
authors.lastname: Hwang
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, South Korea.
authors.forename: Dong Sub
authors.initials: DS
authors.lastname: Kim
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk, 580-185, South Korea.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Hwang
authors.affiliation: Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea.
authors.forename: Hyeon Mi
authors.initials: HM
authors.lastname: Park
authors.affiliation: Plant Genomics Lab, Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-713, South Korea. csjang@kangwon.ac.kr.
authors.forename: Cheol Seong
authors.initials: CS
authors.lastname: Jang
mesh_terms: D003116:Color; D005720:Gamma Rays; D020869:Gene Expression Profiling; D053858:Metabolic Networks and Pathways / Q000502:physiology* / Q000528:radiation effects*; D016296:Mutagenesis; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000502:physiology* / Q000528:radiation effects*
keywords: Gamma ray mutagenesis; Microarray; Rice; Weighted correlation network analysis (WGCNA)