Transcriptome analysis of rice root heterosis by RNA-Seq

文献类型： 外文期刊

第一作者： Feng, Yue

作者： Feng, Yue;Zhan, Xiaodeng;Shen, Xihong;Wu, Weiming;Zhang, Yingxin;Chen, Daibo;Cao, Liyong;Cheng, Shihua;Wang, Huimin;Dai, Gaoxing;Yang, Zhanlie

作者机构：

关键词： Heterosis;Root;Transcriptome;RNA-Seq;Hybrid rice

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2013 年 14 卷

页码：

收录情况： SCI

摘要： Background: Heterosis is a phenomenon in which hybrids exhibit superior performance relative to parental phenotypes. In addition to the heterosis of above-ground agronomic traits on which most existing studies have focused, root heterosis is also an indispensable component of heterosis in the entire plant and of major importance to plant breeding. Consequently, systematic investigations of root heterosis, particularly in reproductive-stage rice, are needed. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis studies. Results: Using the Illumina HiSeq 2000 platform, the root transcriptomes of the super-hybrid rice variety Xieyou 9308 and its parents were analyzed at tillering and heading stages. Approximately 391 million high-quality paired-end reads (100-bp in size) were generated and aligned against the Nipponbare reference genome. We found that 38,872 of 42,081 (92.4%) annotated transcripts were represented by at least one sequence read. A total of 829 and 4186 transcripts that were differentially expressed between the hybrid and its parents (DG(HP)) were identified at tillering and heading stages, respectively. Out of the DG(HP), 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DG(HP) were significantly enriched in pathways related to processes such as carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that are involved in the two pathways being up-regulated in the hybrid. Several significant DG(HP) that could be mapped to quantitative trait loci (QTLs) for yield and root traits are also involved in carbohydrate metabolism and plant hormone signal transduction pathways. Conclusions: An extensive transcriptome dataset was obtained by RNA-Seq, giving a comprehensive overview of the root transcriptomes at tillering and heading stages in a heterotic rice cross and providing a useful resource for the rice research community. Using comparative transcriptome analysis, we detected DG(HP) and identified a group of potential candidate transcripts. The changes in the expression of the candidate transcripts may lay a foundation for future studies on molecular mechanisms underlying root heterosis.

分类号：

  • 相关文献

[1]Heterosis Expression of Hybrid Rice in Natural-and Short-Day Length Conditions. Zhao Bing-ran,Lv Qi-ming,Fu Xi-qin,Xin Ye-yun,Yuan Long-ping. 2015

[2]Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase. Lv, Qiming,Zhou, Ming,Wu, Qi,Song, Xianwei,Liang, Chengzhi,Cao, Xiaofeng,Zhu, Lihuang,Huang, Zhiyuan,Xin, Yeyun,Lv, Qiming,Fu, Xiqin,Zhao, Bingran,Yuan, Longping,Zhu, Lihuang,Song, Shuhui,Tian, Dongmei,Chen, Tingting,Mao, Donghai,Tang, Mingfeng,Chen, Caiyan,Liu, Xue,Hu, Songnian,Li, Aihong,Liu, Guozhen,Li, Shigui.

[3]De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. Zhou, Yijun,Gao, Fei,Liu, Ran,Feng, Jinchao,Gao, Fei,Li, Hongjie. 2012

[4]Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress. Liu, Chunqing,Zhang, Ka,An, Hong,Hu, Kaining,Wen, Jing,Shen, Jinxiong,Ma, Chaozhi,Yi, Bin,Tu, Jinxing,Fu, Tingdong,Zhang, Xuekun. 2015

[5]Transcriptomic analysis of maize mature embryos from an elite maize hybrid Zhengdan958 and its parental lines. Li, Huiyong,Cao, Yanyong,Wang, Lifeng,Zhang, Yan,Li, Jingjing,Wang, Hao,Tang, Baojun,Liu, Tingsong.

[6]Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. Shen, Yifei,Sun, Shuo,Shen, Enhui,Ye, Chu-Yu,Fan, Longjiang,Shen, Yifei,Sun, Shuo,Shen, Enhui,Ye, Chu-Yu,Fan, Longjiang,Hua, Shuijin,Cai, Daguang,Timko, Michael P.,Zhu, Qian-Hao.

[7]De novo assembly of pen shell (Atrina pectinata) transcriptome and screening of its genic microsatellites. Sun, Xiujun,Li, Dongming,Liu, Zhihong,Zhou, Liqing,Wu, Biao,Yang, Aiguo,Sun, Xiujun,Li, Dongming,Liu, Zhihong,Zhou, Liqing,Wu, Biao,Yang, Aiguo. 2017

[8]De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissue. Wu, Shuanghua,Lei, Jianjun,Chen, Guoju,Cao, Bihao,Chen, Changming,Chen, Hancai. 2017

[9]De Novo Transcriptome Sequencing and the Hypothetical Cold Response Mode of Saussurea involucrata in Extreme Cold Environments. Li, Jin,Liu, Hailiang,Xia, Wenwen,Mu, Jianqiang,Feng, Yujie,Liu, Ruina,Wang, Aiying,Lin, Zhongping,Zhu, Jianbo,Chen, Xianfeng,Liu, Hailiang,Yan, Panyao,Chen, Xianfeng,Lin, Zhongping,Guo, Yong. 2017

[10]Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). Lin, Jing. 2015

[11]De Novo Assembly and Characterization of Pericarp Transcriptome and Identification of Candidate Genes Mediating Fruit Cracking in Litchi chinensis Sonn.. Li, Wei-Cai,Zhang, Hong-Na,Shi, Sheng-You,Liu, Li-Qin,Shu, Bo,Liang, Qing-Zhi,Xie, Jiang-Hui,Wei, Yong-Zan,Wu, Jian-Yang. 2014

[12]Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. Tong, Chaobo,Yu, Jingyin,Huang, Junyan,Dong, Caihua,Hua, Wei,Liu, Shengyi,Wang, Xiaowu,Wu, Jian,Li, Wanshun. 2013

[13]Transcriptome analysis of Cucumis sativus infected by Cucurbit chlorotic yellows virus. Sun, Xinyan,Wang, Zhenyue,Li, Honglian,Han, Weili,Shi, Yan,Gu, Qinsheng. 2017

[14]DE NOVO TRANSCRIPTOME ANALYSIS OF MULBERRY (MORUS L.) UNDER DROUGHT STRESS USING RNA-SEQ TECHNOLOGY. Wang, Heng,Tong, Wei,Feng, Li,Jiao, Qian,Long, Li,Fang, Rongjun,Zhao, Weiguo,Long, Li,Zhao, Weiguo,Fang, Rongjun,Zhao, Weiguo.

[15]Comparative transcriptome analysis of latex from rubber tree clone CATAS8-79 and PR107 reveals new cues for the regulation of latex regeneration and duration of latex flow. Chao, Jinquan,Chen, Yueyi,Wu, Shaohua,Tian, Wei-Min. 2015

[16]RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose. Yuan, Tiezheng,Meng, Kun,Yang, Peilong,Shi, Pengjun,Yao, Bin,Ren, Yan,Feng, Yun,Wang, Shaojing,Wang, Lei,Ren, Yan,Feng, Yun,Wang, Shaojing,Wang, Lei,Xie, Daoxin.

[17]Transcriptome analysis of Brassica napus pod using RNA-Seq and identification of lipid-related candidate genes. Xu, Hai-Ming,Kong, Xiang-Dong,Chen, Fei,Huang, Ji-Xiang,Zhao, Jian-Yi,Lou, Xiang-Yang. 2015

[18]Transcriptomic analysis of mouse liver reveals a potential hepato-enteric pathogenic mechanism in acute Toxoplasma gondii infection. He, Jun-Jun,Ma, Jun,Song, Hui-Qun,Huang, Si-Yang,Zhu, Xing-Quan,Elsheikha, Hany M.,Ma, Jun,Huang, Si-Yang,Zhu, Xing-Quan. 2016

[19]Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp chinensis). Wang, Aihua,Huang, Xingxue,Li, Xia,Zhou, Guolin,Hu, Jihong,Hu, Jihong,Yan, Zhixiang. 2016

[20]Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa. Zhang, Yu,Peng, Lifang,Wu, Ya,Shen, Yanyue,Wang, Jianbo,Wu, Xiaoming.

作者其他论文 更多>>

微信小程序