Genome-Wide Transcriptome Profiles of Rice Hybrids and Their Parents

被引:9
作者
Zhiguo, E. [1 ]
Huang, Shanshan [2 ]
Zhang, Yuping [1 ]
Ge, Lei [3 ]
Wang, Lei [1 ]
机构
[1] China Natl Rice Res Inst, Hangzhou 310006, Zhejiang, Peoples R China
[2] ReaderBio Co Ltd, Beijing 100193, Peoples R China
[3] Nantong Agr Coll, Nantong 226007, Peoples R China
来源
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES | 2014年 / 15卷 / 11期
关键词
transcriptome profile; hybrid rice; allele-specific expressed genes; differentially-expressed genes; GENE-EXPRESSION; RNA-SEQ; HETEROSIS; FEATURES; REVEALS; PATTERNS; VIGOR; TOOL;
D O I
10.3390/ijms151120833
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 (F-1) 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.
引用
收藏
页码:20833 / 20845
页数:13
相关论文
共 28 条
  • [1] Anders S., 2010, GENOME BIOL, V11, pR106, DOI [10.1186/gb-2010-11-10-r106, DOI 10.1186/gb-2010-11-10-r106]
  • [2] Molecular mechanisms of polyploidy and hybrid vigor
    Chen, Z. Jeffrey
    [J]. TRENDS IN PLANT SCIENCE, 2010, 15 (02) : 57 - 71
  • [3] Transcriptome and methylome interactions in rice hybrids
    Chodavarapu, Ramakrishna K.
    Feng, Suhua
    Ding, Bo
    Simon, Stacey A.
    Lopez, David
    Jia, Yulin
    Wang, Guo-Liang
    Meyers, Blake C.
    Jacobsen, Steven E.
    Pellegrini, Matteo
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (30) : 12040 - 12045
  • [4] Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution
    Davidson, Rebecca M.
    Gowda, Malali
    Moghe, Gaurav
    Lin, Haining
    Vaillancourt, Brieanne
    Shiu, Shin-Han
    Jiang, Ning
    Buell, C. Robin
    [J]. PLANT JOURNAL, 2012, 71 (03) : 492 - 502
  • [5] Profile hidden Markov models
    Eddy, SR
    [J]. BIOINFORMATICS, 1998, 14 (09) : 755 - 763
  • [6] Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm
    Guo, M
    Rupe, MA
    Danilevskaya, ON
    Yang, XF
    Hut, ZH
    [J]. PLANT JOURNAL, 2003, 36 (01) : 30 - 44
  • [7] Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
    He, Guangming
    Zhu, Xiaopeng
    Elling, Axel A.
    Chen, Liangbi
    Wang, Xiangfeng
    Guo, Lan
    Liang, Manzhong
    He, Hang
    Zhang, Huiyong
    Chen, Fangfang
    Qi, Yijun
    Chen, Runsheng
    Deng, Xing-Wang
    [J]. PLANT CELL, 2010, 22 (01) : 17 - 33
  • [8] WGCNA: an R package for weighted correlation network analysis
    Langfelder, Peter
    Horvath, Steve
    [J]. BMC BIOINFORMATICS, 2008, 9 (1)
  • [9] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Langmead, Ben
    Trapnell, Cole
    Pop, Mihai
    Salzberg, Steven L.
    [J]. GENOME BIOLOGY, 2009, 10 (03):
  • [10] A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm
    Luo, Ming
    Taylor, Jennifer M.
    Spriggs, Andrew
    Zhang, Hongyu
    Wu, Xianjun
    Russell, Scott
    Singh, Mohan
    Koltunow, Anna
    [J]. PLOS GENETICS, 2011, 7 (06):