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

文献类型： 外文期刊

第一作者： Yang, Shun-ying

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

作者机构：

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 ）

ISSN：

年卷期：

页码：

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.

分类号： R394

  • 相关文献

[1]GADD45 beta, an anti-tumor gene, inhibits avian leukosis virus subgroup J replication in chickens. Zhang, Xinheng,Yan, Zhuanqiang,Li, Xinjian,Lin, Wencheng,Dai, Zhenkai,Yan, Yiming,Lu, Piaopiao,Chen, Weiguo,Chen, Feng,Ma, Jingyun,Xie, Qingmei,Zhang, Xinheng,Yan, Zhuanqiang,Li, Xinjian,Lin, Wencheng,Dai, Zhenkai,Yan, Yiming,Lu, Piaopiao,Chen, Weiguo,Chen, Feng,Ma, Jingyun,Xie, Qingmei,Zhang, Xinheng,Yan, Zhuanqiang,Li, Xinjian,Lin, Wencheng,Dai, Zhenkai,Yan, Yiming,Lu, Piaopiao,Chen, Weiguo,Chen, Feng,Ma, Jingyun,Xie, Qingmei,Zhang, Xinheng,Li, Xinjian,Lin, Wencheng,Dai, Zhenkai,Yan, Yiming,Lu, Piaopiao,Chen, Weiguo,Chen, Feng,Ma, Jingyun,Xie, Qingmei,Lin, Wencheng,Chen, Weiguo,Chen, Feng,Xie, Qingmei,Zhang, Huanmin. 2016

[2]RNA-Seq analysis of immune-relevant genes in Lateolabrax japonicus during Vibrio anguillarum infection. Zhao, Chao,Fu, Mingjun,Wang, Chengyang,Qiu, Lihua,Wang, Chengyang,Zhao, Chao,Fu, Mingjun,Wang, Chengyang,Qiu, Lihua,Qiu, Lihua,Jiao, Zongyao.

[3]Effect of salt-stress on gene expression in citrus roots revealed by RNA-seq. Xie, Rangjin,Pan, Xiaoting,Zhang, Jing,Ma, Yanyan,He, Shaolan,Zheng, Yongqiang,Ma, Yingtao. 2018

[4]Transcriptional sequencing and analysis of major genes involved in the adventitious root formation of mango cotyledon segments. Li, Yun-He,Zhang, Hong-Na,Wu, Qing-Song,Li, Yun-He,Li, Yun-He,Muday, Gloria K..

[5]Effect of nitrogen form and root-zone pH on growth and nitrogen uptake of tea (Camellia sinensis) plants. Ruan, Jianyun,Gerendas, Joska,Hardter, Rolf,Sattelmacher, Burkhard.

[6]Aluminium tolerance in rice is antagonistic with nitrate preference and synergistic with ammonium preference. Zhao, Xue Qiang,Shen, Ren Fang,Guo, Shi Wei,Shinmachi, Fumie,Sunairi, Michio,Noguchi, Akira,Hasegawa, Isao.

[7]Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism. Wu, Ya,Yu, Meiling,Wang, Jianbo,Mao, Bigang,Zhao, Bingran.

[8]The effect of soil moisture on mineral nitrogen, soil electrical conductivity, and pH. Zhang, R,Wienhold, BJ. 2002

[9]Effect of pH on the uptake and metabolism of glycine in pak choi (Brassica chinensis L.). Ma, Qingxu,Xie, Yinan,Gu, Yan,Feng, Ying,Mi, Wenhai,Yang, Xin,Wu, Lianghuan,Ma, Qingxu,Xie, Yinan,Gu, Yan,Feng, Ying,Mi, Wenhai,Yang, Xin,Wu, Lianghuan,Cao, Xiaochuang.

[10]Localized application of sewage sludge improved plant nitrogen and phosphorus uptake by rhizobox-grown spring wheat. Wang, Yaosheng,Wang, Yaosheng,Jensen, Lars Stoumann,Magid, Jakob.

[11]Effect of nitrogen forms on reduction of manganese oxides in an Oxisol by plant root exudates. Liu, Yuan,Li, Zhong-yi,Deng, Kai-ying,Zhou, Qin,Xu, Ren-kou,Liu, Yuan,Li, Zhong-yi,Zhou, Qin,Liu, Yuan.

[12]Effects of cadmium stress on pakchoi (Brassica chinensis L.) growth and uptake of inorganic and organic nitrogenous compounds. Ma, Qingxu,Tan, Xiaoli,Si, Linlin,Wu, Lianghuan,Ma, Qingxu,Tan, Xiaoli,Si, Linlin,Wu, Lianghuan,Cao, Xiaochuang.

[13]Excessive ammonia inhibited transcription of MsU2 gene and furthermore affected accumulation distribution of allantoin and amino acids in alfalfa Medicago sativa. Wang Li,Jiang Lin-lin,Cheng Xian-guo,Mika, Nomura,Shigeyuki, Tajima. 2015

[14]Effects of ammonium application rate on uptake of soil adsorbed amino acids by rice. Cao, Xiao-chuang,Zhu, Lian-feng,Jin, Qian-yu,Ma, Qing-xu,Wu, Liang-huan. 2016

[15]Biochars derived from giant reed (Arundo donax L.) with different treatment: characterization and ammonium adsorption potential. Zhao, Yaqi,Huang, Lei,Chen, Yucheng,Zhao, Yaqi,Huang, Lei,Chen, Yucheng. 2017

[16]Effect of root zone pH and form and concentration of nitrogen on accumulation of quality-related components in green teat. Ruan, Jianyun,Gerendas, Joska,Haerdter, Rolf,Sattelmacher, Burkhard. 2007

[17]Effect of nitrogen form and phosphorus source on the growth, nutrient uptake and rhizosphere soil property of Camellia sinensis L.. Ruan, JY,Zhang, FS,Wong, MH. 2000

[18]Hexavalent chromium stress enhances the uptake of nitrate but reduces the uptake of ammonium and glycine in pak choi (Brassica chinensis L.). Ma, Qingxu,Tan, Xiaoli,Xie, Yinan,Xiao, Han,Wu, Lianghuan,Ma, Qingxu,Tan, Xiaoli,Xie, Yinan,Xiao, Han,Wu, Lianghuan,Cao, Xiaochuang,Ma, Jinzhao. 2017

[19]Effect of Nitrogen Form on Gene Expression in Leaf Tissue of Greenhouse Grown Potatoes During Three Stages of Growth. Tai, Helen,De Koeyer, David,Li, Xiu-Qing,Luo, Sainan,Millard, Pete,Xiong, Xingyao. 2012

[20]The relationship between anammox and denitrification in the sediment of an inland river. Zhou, Sheng,Zhou, Sheng,Borjigin, Sodbilig,Riya, Shohei,Terada, Akihiko,Hosomi, Masaaki.

作者其他论文 更多>>

微信小程序