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Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

文献类型： 外文期刊

作者： Xu, Chunming 1 ; Bai, Yan 1 ; Lin, Xiuyun 3 ; Zhao, Na 1 ; Hu, Lanjuan 1 ; Gong, Zhiyun 5 ; Wendel, Jonathan F. 2 ; Liu, 1 ;

作者机构： 1.NE Normal Univ, Minist Educ MOE, Key Lab Mol Epigenet, Changchun, Peoples R China

2.Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Woodville, SA 5011, Australia

3.Jilin Acad Agr Sci, Changchun, Peoples R China

4.Jilin Agr Univ, Fac Agron, Changchun, Peoples R China

5.Yangzhou Univ, Coll Agr, Yangzhou, Peoples R China

关键词： hybridization;polyploidization;homoeologous expression;evolution of gene regulation;Oryza sativa L

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：16.24； 五年影响因子：18.67 ）

ISSN： 0737-4038

年卷期： 2014 年 31 卷 5 期

页码：

收录情况： SCI

摘要： Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed "transcriptomic shock." To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice (Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis-factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of "whole genome doubling" has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.

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[1]Endosperm-specific hypomethylation, and meiotic inheritance and variation of DNA methylation level and pattern in sorghum (Sorghum bicolor L.) inter-strain hybrids. Zhang, M. S.,Yan, H. Y.,Zhao, N.,Lin, X. Y.,Pang, J. S.,Xu, K. Z.,Liu, L. X.,Liu, B..

[2]Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice. Wang, Ningning,Zhang, Di,Wang, Zhenhui,Xun, Hongwei,Wang, Hui,Huang, Wei,Liu, Ying,Li, Ning,Ou, Xiufang,Zhang, Chunyu,Liu, Bao,Wang, Ningning,Ma, Jian,Lin, Xiuyun,Zhang, Chunyu,Wang, Ningning,Wang, Ming-Bo. 2014

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