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浙江大学学报（农业与生命科学版）
Journal of Zhejiang University (Agriculture and Life Sciences)  2016, Vol. 42 Issue (6): 643-653    DOI: 10.3785/j.issn.1008-9209.2016.01.142
Biological sciences & biotechnology     
RNA-seq approach to discriminate gene expression profiles in RIXI overexpressing transgenic rice
PENG Yaoyao1, HOU Chunxiao2, ZHAN Yihua1, HUANG Yingying3, SUN Xiangyu1, WENG Xiaoyan1*
(1. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; 2. Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; 3. School of Medicine, Zhejiang University, Hangzhou 310058, China)
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Abstract  To investigate whether RIXI overexpressing transgenic plants influence the expression of other genes, we analyzed transcriptomic changes between R7 (RIXI overexpression transgenic line 7) plants and WT (wild-type) plants using deep RNA sequencing combined with digital gene expression profile analysis. The differentially expressed genes between the WT and R7 libraries were identified by DEG-Seq (differentially expressed genes from RNA-seq) software. The profiling analysis revealed that the overexpression of RIXI in rice resulted in numerous changes in gene expressions, including upregulation of 391 genes and downregulation of 905 genes. These differentially expressed genes were categorized into 30 groups with broad functions using gene ontology (GO) assignments. Among the 30 groups, five groups (singleorganism metabolic process, biological regulation, anion binding, small molecule binding and nucleotide binding） had more differentially expressed genes. Biological pathways affected by RIXI overexpression were mapped using the detected genes to reference canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes were assigned to 98 KEGG pathways, and four enriched pathways were identified: metabolic, biosynthesis of secondary metabolites, plantpathogen interaction and plant hormone signal transduction. The measurement of agronomic traits of R7 showed that the overexpression of RIXI did not influence the growth and development of rice. Thus, we conclude that the xylanase inhibitor gene RIXI may play a role in activation of a complex signal transduction network in response to various biotic and abiotic stresses, but does not have a negative influence on growth and development of rice plants.

Published: 19 November 2016
CLC:  Q 945.78  
Fund:  the National Natural Science Foundation of China (Nos. 30971702 and 31271632), and Science and Technology Department of Zhejiang Province, China (Nos. 2013C32018 and 2016C32086).
Corresponding Authors: WENG Xiaoyan (http://orcid.org/0000-0001-6559-3386), E-mail: xyweng@zju.edu.cn   
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ZHAN Yihua
HUANG Yingying
SUN Xiangyu
HOU Chunxiao
PENG Yaoyao
WENG Xiaoyan
Cite this article:

PENG Yaoyao, HOU Chunxiao, ZHAN Yihua, HUANG Yingying, SUN Xiangyu, WENG Xiaoyan. RNA-seq approach to discriminate gene expression profiles in RIXI overexpressing transgenic rice. Journal of Zhejiang University (Agriculture and Life Sciences), 2016, 42(6): 643-653.

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http://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2016.01.142     OR     http://www.zjujournals.com/agr/Y2016/V42/I6/643


RIXI过量表达转基因水稻的全基因组表达谱分析(英文)

为研究水稻植株中木聚糖酶抑制剂基因RIXI过量表达是否会引起其他基因的差异表达，利用转录组测序（RNA-Seq）技术结合数字基因表达谱分析对RIXI过量表达单拷贝纯合株系R7进行基因差异表达分析。水稻全基因表达谱显示RIXI过表达引起水稻中大量基因的表达差异，包括391个上调基因，905个下调基因。GO分析将差异基因分成30个功能聚类，其中的5组聚类中含有较多的差异基因，分别为单个有机体代谢过程、生物调控、阴离子结合、小分子结合和核苷酸结合。利用KEGG数据库，通过Pathway显著性富集确定差异表达基因参与主要生化代谢途径和信号转导途径。与整个水稻基因组背景WT相比，R7的差异表达基因包含在98个KEGG通路中，包含差异基因数量最多的4个KEGG通路分别为代谢通路、次级代谢的生物合成、植物与病原菌互作和激素信号传导。农艺性状测量显示RIXI过表达对水稻生长发育几乎没有影响。以上结果说明，木聚糖酶抑制剂基因RIXI可能在各种生物和非生物胁迫中激活复杂的信号传导，但对水稻的生长和发育没有负面影响。
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