Genome-wide characterization of Rice Black Streaked Dwarf Virus-responsive genes in rice

IF 2.6 3区农林科学 Q2 FOOD SCIENCE & TECHNOLOGY

Journal of Food Science and Technology-mysore Pub Date : 2020-04-18 DOI:10.25177/JFST.5.2.RA.615

Wei Liu, Zhen Li, Qingguo Wang, J. Pan, Pengfei Wang, Gui-quan Zhang, L. Yang, F. Yao, Sift Desk Journals Open Access Journals

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引用次数: 1

Abstract

Background: Rice black streaked dwarf virus (RBSDV) is an important pathogen disease in rice and gramineous planting regions all over the world. The major phenotypes of RBSDV infected rice were dwarf with dark green leaves, which generally resulted in seriously loss of yield. The RBSDV known so far is preoperatively transmitted to rice in a persistent manner by small brown planthopper (SBPH), instead of transmitting to offspring through ovary. Results: To identify RBSDV responsive genes and to explore and clarify the molecular mechanisms involved in plantvirus interaction, digital gene expression profile (DGE) analysis was performed by high-throughput sequencing using wildtype (WT) and RBSDV infected rice leaves (IRL) as materials. A total of 165,975 and 165,940 unique tags were obtained in IRL and WT libraries, respectively. In comparison with the control, 896 differentially expressed genes (DEGs) were obtained, of which 500 DEGs were up regulated and 396 DEGs were down regulated. Functional analysis showed that DEGs mainly classified into10 groups, including metabolism, stress pathogen and defense, signal transduction, Transporter, transcription and post-transcription, cell structure and division etc. To further validate reliability and authenticity of the data, 10 DEGs were randomly picked and Real-time RT-PCR was carried out, and the expression trends of 7 genes were in line with the RNA-seq results. By searching the RBSDV related miRNA database of rice, 10 targeted genes of 6 significantly changed miRNAs were also identified in these DEGs. Conclusions: The data derived from RNA-seq were valid and credible. Through this research, a series of candidate RBSDV-responsive genes were obtained, and special signal transduction and metabolism pathways were built and pulled out in rice. This study provided further insight into the molecular mechanisms during compatible and incompatible interactions between viruses and their host plants. Copy rights: © This is an Open access article distributed under the terms of International License. Genome-wide characterization of Rice Black Streaked Dwarf Virus-responsive genes in rice Journal of Food Science & Technology (ISSN: 2472-6419) DOI: 10.25177/JFST.5.2.RA.615 Research

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水稻黑条矮缩病毒应答基因的全基因组鉴定

背景:水稻黑条矮缩病毒(Rice black stripes dwarf virus, RBSDV)是发生在世界各地水稻和禾草种植区的重要病原菌。侵染RBSDV的水稻主要表型为矮化，叶片深绿色，普遍造成严重的产量损失。目前已知的RBSDV是术前通过小褐飞虱(SBPH)持续传播到水稻，而不是通过卵巢传播给后代。结果:以野生型(WT)和RBSDV侵染水稻叶片(IRL)为材料，采用高通量测序技术进行了数字基因表达谱(DGE)分析，以鉴定RBSDV应答基因，探索和阐明植物与病毒相互作用的分子机制。在IRL和WT库中分别获得了165,975和165,940个唯一标签。与对照相比，共获得896个差异表达基因，其中上调500个，下调396个。功能分析表明，DEGs主要分为代谢、应激病原与防御、信号转导、转运体、转录与后转录、细胞结构与分裂等10个类群。为了进一步验证数据的可靠性和真实性，随机选取10个deg进行Real-time RT-PCR，其中7个基因的表达趋势与RNA-seq结果一致。通过检索水稻RBSDV相关miRNA数据库，在这些DEGs中还鉴定出6个显著变化的miRNA中的10个靶基因。结论:RNA-seq数据有效、可信。通过本研究，获得了一系列rbsdv候选响应基因，并在水稻中构建和提取了特殊的信号转导和代谢途径。该研究进一步揭示了病毒与寄主植物亲和和不亲和相互作用的分子机制。版权:©这是一篇根据国际许可条款发布的开放获取文章。水稻黑条矮缩病毒应答基因的全基因组鉴定。食品科学与技术杂志(ISSN: 2472-6419) DOI: 10.25177/JFST.5.2.RA.615研究

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来源期刊

Journal of Food Science and Technology-mysore 工程技术-食品科技

CiteScore

7.70

自引率

0.00%

发文量

274

审稿时长

11 months

期刊介绍： The Journal of Food Science and Technology (JFST) is the official publication of the Association of Food Scientists and Technologists of India (AFSTI). This monthly publishes peer-reviewed research papers and reviews in all branches of science, technology, packaging and engineering of foods and food products. Special emphasis is given to fundamental and applied research findings that have potential for enhancing product quality, extend shelf life of fresh and processed food products and improve process efficiency. Critical reviews on new perspectives in food handling and processing, innovative and emerging technologies and trends and future research in food products and food industry byproducts are also welcome. The journal also publishes book reviews relevant to all aspects of food science, technology and engineering.