title: Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing.
abstract: 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.
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Xutong
authors.initials: X
authors.lastname: Wang
authors.affiliation: Jilin Academy of Agricultural Sciences, Changchun, 130032, China.
authors.forename: Xiuyun
authors.initials: X
authors.lastname: Lin
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Sun
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Shen
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Silin
authors.initials: S
authors.lastname: Zhong
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Chunming
authors.initials: C
authors.lastname: Xu
authors.affiliation: Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
authors.forename: Bao
authors.initials: B
authors.lastname: Liu
mesh_terms: D005075:Biological Evolution; D003198:Computer Simulation; D003433:Crosses, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*; D057885:Triploidy
chemical_list: D012333:RNA, Messenger
keywords: Cis- and trans-regulation; Oryza; homeolog expression rewiring; interspecific hybrid; promoter divergence; transcriptome shock