Differential gene expression analysis of stress-responsive rice PPBG3. Differential gene expression analysis of stress-responsive rice (Oryza sativa L.) LMS mutant using RNA-Seq- based approach
2018
Undan, J.R. | Maron, L. | Arbelaez, J.D. | Terauchi, R. | McCouch, S.
The lesion mimic senescence (LMS) mutant in rice (O.sativa) used in this study was identified from population of an elite japonica rice cultivar Hitomebore generated by ethly-methanesulfonate (EMS) treatment. Genetic linkage analysis identified a mutation in Os02g0639000 gene transcript and was named OsLMS. The cDNA libraries was prepared and was sequenced using HiSeq 2,500 (100-bp reads) for RNA-sequencing. Differential gene expression analysis in lms mutant revealed a total of 863 differentially expressed genes in relation to wild type. There are 126 genes exclusively showed transcript abundance and 737 genes were found to have transcript reduction. From the 126 genes that were up-regulated, 123 genes were annotated and are involved in monooxygenase, iron-ion binding, ADP binding, heme-binding activity, protein kinase, serine type endopeptidase, terpene synthase activity and protein phosphorylation. On the other hand, from 737 genes that were down-regulated, 698 were annotated and mostly involved in gene expression, intracellular organelle part, cellular macromolecule biosynthetic process, RNA metabolic process, ribosome, nucleic acid binding and peptide biosynthetic process. Elucidation of the mechanism of each useful group of genes that found up/down regulated in this study would help us further in the understanding of the molecular aspect of stress response of rice and of plants in general.
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