Next Article in Journal
Peptide Array on Cellulose Support—A Screening Tool to Identify Peptides with Dipeptidyl-Peptidase IV Inhibitory Activity within the Sequence of α-Lactalbumin
Previous Article in Journal
Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review
Article Menu
Issue 11 (November) cover image

Export Article

Open AccessArticle
Int. J. Mol. Sci. 2014, 15(11), 20833-20845; doi:10.3390/ijms151120833

Genome-Wide Transcriptome Profiles of Rice Hybrids and Their Parents

1
China National Rice Research Institute, Hangzhou 310006, China
2
ReaderBio Company, Ltd., Beijing 100193, China
3
Nantong Agricultural College, Nantong 226007, China
*
Author to whom correspondence should be addressed.
Received: 7 July 2014 / Revised: 11 October 2014 / Accepted: 3 November 2014 / Published: 13 November 2014
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
View Full-Text   |   Download PDF [585 KB, uploaded 13 November 2014]   |  

Abstract

Heterosis is a widely studied phenomenon in several plant species. However, its genetic basis still remains to be elucidated. In this study, we used RNA-seq data from two rice genotypes and their reciprocal hybrids, and used a combination of transcriptome profiling and allele-specific expression analysis to identify genes that are differentially expressed in the hybrids and their parents or expressed in an allele-specific manner. The differentially expressed genes (DEGs) were identified by a pairwise comparison of the four genotypes. Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes. A total of 1033 (10.24%) of 10,195 genes with informative single nucleotide polymorphism (SNPs) were identified as ASE genes. These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages. Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families. These ASE transcription factors may act in trans to regulate gene expression in filial 1 (F1) hybrids. Our analyses provide a comprehensive transcriptome profile of rice hybrids and their parents, and would be a useful resource for the rice research community. View Full-Text
Keywords: transcriptome profile; hybrid rice; allele-specific expressed genes; differentially-expressed genes transcriptome profile; hybrid rice; allele-specific expressed genes; differentially-expressed genes
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

E, Z.; Huang, S.; Zhang, Y.; Ge, L.; Wang, L. Genome-Wide Transcriptome Profiles of Rice Hybrids and Their Parents. Int. J. Mol. Sci. 2014, 15, 20833-20845.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top