title: Transcriptome analysis of nitrogen-starvation-responsive genes in rice.
abstract: BACKGROUND
  Nitrogen (N), a critical macronutrient for plant growth and development, is a major limiting factor in most agricultural systems. Microarray analyses have been conducted to investigate genome-wide gene expression in response to changes in N concentrations. Although RNA-Seq analysis can provide a more precise determination of transcript levels, it has not previously been employed to investigate the expression of N-starvation-induced genes.
  
  
  RESULTS
  We constructed cDNA libraries from leaf sheaths and roots of rice plants grown under N-deficient or -sufficient conditions for 12 h. Sequencing the libraries resulted in identification of 33,782 annotated genes. A comparison of abundances revealed 1,650 transcripts that were differentially expressed (fold-change ≥ 2) due to an N-deficiency. Among them, 1,158 were differentially expressed in the leaf sheaths (548 up-regulated and 610 down-regulated) and 492 in the roots (276 up, 216 down). Among the 36 deficiency-induced genes first identified via RNA-Seq analyses, 34 were subsequently confirmed by qRT-PCR. Our RNA-Seq data identified 8,509 multi-exonic genes with 19,628 alternative splicing events. However, we saw no significant difference in alternative splicing between N-sufficient and -deficient conditions. We found 2,986 novel transcripts, of which 192 were regulated under the N-deficiency.
  
  
  CONCLUSIONS
  We identified 1,650 genes that were differentially expressed after 12 h of N-starvation. Responses by those genes to a limited supply of N were confirmed by RT-PCR and GUS assays. Our results provide valuable information about N-starvation-responsive genes and will be useful when investigating the signal transduction pathway of N-utilization.
authors: Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea. wenzhuyang@khu.ac.kr.|Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. wenzhuyang@khu.ac.kr.|National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. wenzhuyang@khu.ac.kr.
authors: Wenzhu
authors: W
authors: Yang
authors: Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea. jmjh0120@postech.ac.kr.
authors: Jinmi
authors: J
authors: Yoon
authors: Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea. backy28@postech.ac.kr.
authors: Heebak
authors: H
authors: Choi
authors: Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. fanyunliu@caas.cn.|National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. fanyunliu@caas.cn.
authors: Yunliu
authors: Y
authors: Fan
authors: Department of Crop Genomics and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. chenrumei@caas.cn.|National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. chenrumei@caas.cn.
authors: Rumei
authors: R
authors: Chen
authors: Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea. genean@khu.ac.kr.
authors: Gynheung
authors: G
authors: An
mesh_terms: D017398:Alternative Splicing; D018076:DNA, Complementary; D017343:Genes, Plant; D009584:Nitrogen / Q000378:metabolism*; D012275:Oryza / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D009584:Nitrogen
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