J Integr Plant Biol. ›› 2016, Vol. 58 ›› Issue (2): 150-164.DOI: 10.1111/jipb.12357

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing

Ying Wu1, Yue Sun1, Xutong Wang1, Xiuyun Lin2, Shuai Sun1, Kun Shen1, Jie Wang1, Tingting Jiang1, Silin Zhong3, Chunming Xu1* and Bao Liu1*   

  1. 1Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
    2Jilin Academy of Agricultural Sciences, Changchun, China
    3State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China


Interspecific hybridization is a driving force in evolution and speciation of higher plants. Interspecific hybridization often induces immediate and saltational changes in gene expression, a phenomenon collectively termed “transcriptome shock”. Although transcriptome shock has been reported in various plant and animal taxa, the extent and pattern of shock-induced expression changes are often highly idiosyncratic, and hence entails additional investigations. Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2n = 2x = 24, genome AA) and the tetraploid form of O. punctata (2n = 4x  = 48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico “hybrids” (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.


Wu Y, Sun Y, Wang X, Lin X, Sun S, Shen K, Wang J, Jiang T, Zhong S, Xu C, Liu B (2016) Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing. J Integr Plant Biol 58: 150–164 doi: 10.1111/jipb.12357

Key words: Cis- and trans-regulation, homeolog expression rewiring, interspecific hybrid, Oryza, promoter divergence, transcriptome shock

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