title: RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies.
abstract: Ammonium is the main inorganic nitrogen source in paddy soil. Rice (Oryza sativa), an ammonium-preferring and -tolerant grain crop, is a valuable resource for researching ammonium-uptake mechanism and understanding the molecular networks that the plant copes with ammonium variation. To generate a broad survey of early responses affected by varied ammonium supplies in rice, RNA samples were prepared from the roots and shoots of rice plants subjected to nitrogen-free (0mM ammonium), 1mM ammonium and high ammonium (10mM ammonium) for a short period of 4h (1mM ammonium treatment as the control), respectively, and the transcripts were sequenced using the Illumina/HiSeq™ 2000 RNA sequencing (RNA-Seq) platform. By comparative analysis, 394 differentially expressed genes (DEGs) were identified in roots, among which, 143 and 251 DEGs were up- and down-regulated under nitrogen-free condition, respectively. In shoots, 468 (119 up-regulated/349 down-regulated) DEGs were found under such condition. However, with high ammonium treatment, only 63 genes (6 up-regulated/57 down-regulated) in roots and 115 genes in shoots (93 up-regulated/22 down-regulated) were differentially expressed. According to KEGG analysis, when exposed to nitrogen-free condition, DEGs participating in the carbohydrate and amino acid metabolisms were down-regulated (with 1 exception) in roots as well as in shoots, implying reduced carbohydrate and nitrogen metabolisms. Under high ammonium supply, all DEGs associated with carbohydrate and amino acid metabolisms were down-regulated in roots and to the contrary, up-regulated in shoots. Aldehyde dehydrogenase (ALDH, NAD(+)) [EC: 1.2.1.3] seemed to have played an important role in rice shoots under high ammonium condition, analysis results implicated a coordinative regulation of carbohydrate with amino acid metabolisms under nitrogen deficiency as well as the high ammonium conditions during a short period of several hours in rice. Moreover, transcripts with abundance variation might be precious gene resources in responding to different ammonium supplies in rice.
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Shun-ying
authors.initials: SY
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Dong-li
authors.initials: DL
authors.lastname: Hao
authors.affiliation: Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing 210008, China.
authors.forename: Zhi-zhong
authors.initials: ZZ
authors.lastname: Song
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
authors.forename: Guang-zhe
authors.initials: GZ
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Li
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China. Electronic address: yhsu@issas.ac.cn.
authors.forename: Yan-hua
authors.initials: YH
authors.lastname: Su
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000641:Ammonia / Q000737:chemistry; D050260:Carbohydrate Metabolism; D018076:DNA, Complementary / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D009584:Nitrogen / Q000737:chemistry*; D012275:Oryza / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D018520:Plant Shoots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D000596:Amino Acids; D018076:DNA, Complementary; D010940:Plant Proteins; D018749:RNA, Plant; D000641:Ammonia; D009584:Nitrogen
keywords: Ammonium; Differentially expressed genes; RNA-Seq; Rice