title: Genome-wide transcriptome analysis of expression in rice seedling roots in response to supplemental nitrogen.
abstract: Nitrogen (N) is the most important macronutrient for plant growth and grain yields. For rice crops, nitrate and ammonium are the major N sources. To explore the genomic responses to ammonium supplements in rice roots, we used 17-day-old seedlings grown in the absence of external N that were then exposed to 0.5mM (NH4)2SO4 for 3h. Transcriptomic profiles were examined by microarray experiments. In all, 634 genes were up-regulated at least two-fold by the N-supplement when compared with expression in roots from untreated control plants. Gene Ontology (GO) enrichment analysis revealed that those upregulated genes are associated with 23 GO terms. Among them, metabolic processes for diverse amino acids (i.e., aspartate, threonine, tryptophan, glutamine, l-phenylalanine, and thiamin) as well as nitrogen compounds are highly over-represented, demonstrating that our selected genes are suitable for studying the N-response in roots. This enrichment analysis also indicated that nitrogen is closely linked to diverse transporter activities by primary metabolites, including proteins (amino acids), lipids, and carbohydrates, and is associated with carbohydrate catabolism and cell wall organization. Integration of results from omics analysis of metabolic pathways and transcriptome data using the MapMan tool suggested that the TCA cycle and pathway for mitochondrial electron transport are co-regulated when rice roots are exposed to ammonium. We also investigated the expression of N-responsive marker genes by performing a comparative analysis with root samples from plants grown under different NH4(+) treatments. The diverse responses to such treatment provide useful insight into the global changes related to the shift from an N-deficiency to an enhanced N-supply in rice, a model crop plant.
authors.affiliation: Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
authors.forename: Anil Kumar Nalini
authors.initials: AK
authors.lastname: Chandran
authors.affiliation: Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea.
authors.forename: Ryza A
authors.initials: RA
authors.lastname: Priatama
authors.affiliation: Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea.
authors.forename: Vikranth
authors.initials: V
authors.lastname: Kumar
authors.affiliation: College of Plant Protection, Shengyang Agricultural University, Dongling Road 120, Shengyang 110866, China.
authors.forename: Yuanhu
authors.initials: Y
authors.lastname: Xuan
authors.affiliation: Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea.
authors.forename: Byoung Il
authors.initials: BI
authors.lastname: Je
authors.affiliation: Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea.
authors.forename: Chul Min
authors.initials: CM
authors.lastname: Kim
authors.affiliation: Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea. Electronic address: khjung2010@khu.ac.kr.
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.affiliation: Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology & Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea. Electronic address: cdhan@gsnu.ac.kr.
authors.forename: Chang-Deok
authors.initials: CD
authors.lastname: Han
mesh_terms: D064751:Ammonium Compounds / Q000494:pharmacology; D018556:Crops, Agricultural / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D063990:Gene Ontology; D017343:Genes, Plant; D056726:Genetic Association Studies; D018745:Genome, Plant; D009584:Nitrogen / Q000494:pharmacology*; D012275:Oryza / Q000187:drug effects / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D036226:Seedlings / Q000187:drug effects / Q000235:genetics*
chemical_list: D064751:Ammonium Compounds; D010940:Plant Proteins; D018749:RNA, Plant; D009584:Nitrogen
keywords: Gene ontology; MapMan; Nitrogen supplementation; Rice; Transcriptome