title: Identification of microRNAs in rice root in response to nitrate and ammonium.
abstract: Nitrate and ammonium are two major nitrogen (N) sources for higher plants, but they differ in utilization and signaling. MicroRNAs (miRNAs) play an essential role in N signal transduction; however, knowledge remains limited about the regulatory role of miRNAs responsive to different N sources, especially in crop plants. To get global overview on miRNAs involved in N response in rice, we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments. The results demonstrated that only 16 and 11 miRNAs were significantly induced by nitrate and ammonium under short-term treatment, respectively. However, 60 differentially expressed miRNAs were found between nitrate and ammonium under long-term cultivation. These results suggested that miRNA response greatly differentiates between nitrate and ammonium treatments. Furthermore, 44 miRNAs were found to be differentially expressed between high- and low-N conditions. Our study reveals comprehensive expression profiling of miRNAs responsive to different N sources and different N treatments, which advances our understanding on the regulation of different N signaling and homeostasis mediated by miRNAs.
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Liang
authors.affiliation: School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China.
authors.forename: Xiaokai
authors.initials: X
authors.lastname: Gao
authors.affiliation: School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: School of Agriculture, Henan University of Science and Technology, Luoyang 471023, China.
authors.forename: Lianhe
authors.initials: L
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: ccchu@genetics.ac.cn.
authors.forename: Chengcai
authors.initials: C
authors.lastname: Chu
mesh_terms: D064751:Ammonium Compounds / Q000494:pharmacology*; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D035683:MicroRNAs / Q000235:genetics*; D009566:Nitrates / Q000494:pharmacology*; D012275:Oryza / Q000187:drug effects* / Q000235:genetics*; D010641:Phenotype; D018517:Plant Roots / Q000187:drug effects* / Q000235:genetics*; D036226:Seedlings / Q000187:drug effects / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D064751:Ammonium Compounds; D035683:MicroRNAs; D009566:Nitrates
keywords: Ammonium; MicroRNA; Nitrate; Nitrogen; Rice