Transcriptome analysis of nitrogen-starvation-responsive genes in rice.
Transcriptome analysis of nitrogen-starvation-responsive genes in rice.
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DOI：
10.1186/s12870-015-0425-5
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发表时间：
2015-02-03
影响因子：
5.3
通讯作者：
An G
中科院分区：
文献类型：
--
作者：
Yang W;Yoon J;Choi H;Fan Y;Chen R;An G
氮素是植物生长发育的重要营养元素，是大多数农业系统中的主要限制因子。微阵列分析已经进行了调查全基因组的基因表达响应N浓度的变化。虽然RNA-Seq分析可以提供更精确的转录水平测定，但它以前没有被用于研究N-饥饿诱导的基因的表达。我们从生长在缺氮或氮充足条件下12小时的水稻植株的叶鞘和根中构建了cDNA文库。对文库进行测序，鉴定了33，782个注释基因。丰度比较显示，1，650个转录本因N缺乏而差异表达（倍数变化≥ 2）。其中，1,158个在叶鞘中差异表达（548个上调，610个下调），492个在根中差异表达（276个上调，216个下调）。在通过RNA-Seq分析首次鉴定的36个缺陷诱导基因中，34个随后通过qRT-PCR确认。我们的RNA-Seq数据确定了8，509个多外显子基因，其中有19，628个选择性剪接事件。然而，我们没有看到显着的差异，选择性剪接之间的N-充足和缺乏的条件。我们发现了2，986个新的转录本，其中192个在N缺乏下受到调控。我们确定了1,650个基因，差异表达后12小时的N-饥饿。通过RT-PCR和GUS检测证实了这些基因对有限供氮的反应。我们的研究结果提供了有价值的信息，N饥饿响应基因，将有助于研究N利用的信号转导途径。本文的在线版本（doi：10.1186/s12870-015-0425-5）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12870-015-0425-5) contains supplementary material, which is available to authorized users.