Transcriptome analysis of rice root heterosis by RNA-Seq

BMC Genomics

Research Article

Huimin Wang¹  Gaoxing Dai²  Zhanlie Yang³  Xihong Shen⁴  Yingxin Zhang⁴  Yue Feng⁴  Xiaodeng Zhan⁴  Liyong Cao⁴  Weiming Wu⁴  Daibo Chen⁴  Shihua Cheng⁴  Rongrong Zhai⁴ 

[1] College of Agronomy, Shenyang Agricultural University, 110161, Shenyang, China;Rice Research Institute, Guangxi Academy of Agricultural Sciences, 530007, Nanning, China;Rice Research Institute, Guizhou Academy of Agricultural Sciences, 550006, Guiyang, China;State Key Laboratory of Rice Biology, China National Rice Research Institute, 310006, Hangzhou, China;

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

DOI  :  10.1186/1471-2164-14-19

 received in 2012-06-29, accepted in 2013-01-03,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundHeterosis 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.ResultsUsing 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 (DGHP) were identified at tillering and heading stages, respectively. Out of the DGHP, 66.59% were down-regulated at the tillering stage and 64.41% were up-regulated at the heading stage. At the heading stage, the DGHP 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 DGHP 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.ConclusionsAn 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 DGHP 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.

【 授权许可】

Unknown   
© Zhai et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.