Transcriptome analysis of nitrogen-starvation-responsive genes in rice. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Yang, Wenzhu; Yoon, Jinmi; Choi, Heebak; Fan, Yunliu; Chen, Rumei; An, Gynheung
• Is Part Of: BMC plant biology. Volume 15:Issue 1(2015)
• Page Start: 1
• Page End: 12
• Publication Date: 2015-12
• Subjects: N-starvation -- Oryza sativa -- Transcription factors -- Transcriptome sequencing; Plant molecular biology -- Periodicals; Botany -- Periodicals; 580.5
• DOI: 10.1186/s12870-015-0425-5
• Languages: English
• ISSNs: 1471-2229

Abstract

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. Conclusion 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.