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RNA-Seq analysis of differentially expressed genes in rice under varied nitrogen supplies

文献类型： 外文期刊

作者： Yang, Shun-ying 1 ; Hao, Dong-li 1 ; Song, Zhi-zhong 3 ; Yang, Guang-zhe 1 ; Wang, Li 1 ; Su, Yan-hua 1 ;

作者机构： 1.Chinese Acad Sci, Inst Soil Sci, State Key Lab Soil & Sustainable Agr, Nanjing 210008, Peoples R China

2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China

3.Jiangsu Acad Agr Sci, Inst Hort, Nanjing 210008, Peoples R China

关键词： Rice;Ammonium;RNA-Seq;Differentially expressed genes

期刊名称：GENE （ 影响因子：3.688； 五年影响因子：3.329 ）

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收录情况： SCI

摘要： 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 (0 mM ammonium), 1 mM ammonium and high ammonium (10 mM ammonium) for a short period of 4 h (1 mM ammonium treatment as the control), respectively, and the transcripts were sequenced using the Illumina/HiSeq (TM) 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: 1.2.13] 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. (C) 2014 Elsevier B.V. All rights reserved.

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