ArticleGenome biology and evolution2013
RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed, 168 citations in OpenAlex.
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- RNA-sequencing Analysis of Hybrid Females Reveals a Dominance of Expression of Alleles From Outcrossing Species Over Those From Selfing Species.Genome biology and evolution · 2025Article
- Intraspecific gene regulation in cis- and trans.Evolution; international journal of organic evolution · 2025Review
- Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids.Nature communications · 2024Article
- High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.Plant physiology · 2024Article
- Non-Additive and Asymmetric Allelic Expression ofAnimals : an open access journal from MDPI · 2024Article
- Pervasive under-dominance in gene expression underlying emergent growth trajectories in Arabidopsis thaliana hybrids.Genome biology · 2023Article
- Transcriptional misexpression in hybrids between species linked by gene flow is associated with patterns of sequence divergence.Genome biology and evolution · 2023Article
- Maternal patterns of inheritance alter transcript expression in eggs.BMC genomics · 2023Article
- Regulatory Divergence as a Mechanism for X-Autosome Incompatibilities in Caenorhabditis Nematodes.Genome biology and evolution · 2023Article
- Expression inheritance and constraints on cis- and trans-regulatory mutations underlying lotus color variation.Plant physiology · 2023Article
- The role of non-additive gene action on gene expression variation in plant domestication.EvoDevo · 2023Article
- Cis- and Trans-variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species.Molecular biology and evolution · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Nuclear-specific gene expression in heterokaryons of the filamentous ascomyceteProceedings. Biological sciences · 2022Article
- Article
- Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage.BMC plant biology · 2022Article
- Gene expression variation explains maize seed germination heterosis.BMC plant biology · 2022Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed. Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative single-nucleotide polymorphism sites, respectively. Of the 17% of sites exhibiting both cis- and trans-effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele, whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.
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