ArticleMolecular biology and evolution2014
Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Homoeologous exchange-associated ABA catabolism rewiring contributes to salinity tolerance in a synthetic tetraploid rice.Plant cell reports · 2026Article
- The evolution of gene expression in allopolyploid cotton relative to parental diploids and induced haploids.aBIOTECH · 2026Article
- Haplotype-based multi-locus genome-wide association study reveals genomic regions associated with reproductive stage high temperature stress tolerance in rice.Plant molecular biology · 2026Article
- Dismantling Chromosomal Stasis Across the Eukaryotic Tree of Life.bioRxiv : the preprint server for biology · 2026Article
- Hybridization and Polyploidy Shaped the Evolutionary History of a Complex of Cryptic Species in European Woodrushes (Luzula sect. Luzula).Systematic biology · 2026Article
- Recent allopolyploidization and transcriptomic asymmetry in the mangrove shrub Acanthus tetraploideus.BMC genomics · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Rapid formation of stable autotetraploid rice from genome-doubled F1 hybrids of japonica-indica subspecies.Nature plants · 2025Article
- Transcriptomics and Metabolomics Reveal Biosynthetic Pathways and Regulatory Mechanisms of Phenylpropanes in Different Ploidy ofPlants (Basel, Switzerland) · 2024Article
- Evolutionary divergence of subgenomes in common carp provides insights into speciation and allopolyploid success.Fundamental research · 2024Article
- Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes.Nature communications · 2023Article
- Patterns of Chromosomal Variation, Homoeologous Exchange, and Their Relationship with Genomic Features in Early Generations of a Synthetic Rice Segmental Allotetraploid.International journal of molecular sciences · 2023Article
- Synthetic apomixis enables stable transgenerational transmission of heterotic phenotypes in hybrid rice.Plant communications · 2023Article
- Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis.Plant reproduction · 2023Review
- Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow (Salix spp.).G3 (Bethesda, Md.) · 2022Article
- Genomic and Meiotic Changes Accompanying Polyploidization.Plants (Basel, Switzerland) · 2022Review
- The Transcriptional and Splicing Changes Caused by Hybridization Can Be Globally Recovered by Genome Doubling during Allopolyploidization.Molecular biology and evolution · 2021Article
- Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids.National science review · 2021Article
- Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice.Rice (New York, N.Y.) · 2021Article
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8 authors.
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Abstract
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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