Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Genetics

• Publication date

  2006-01-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1534/genetics.105.047894PMID 16172500PMCID PMC1456178
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Plant Speciation

  2007cited by this paper
• Reversible Histone Acetylation and Deacetylation Mediate Genome-Wide, Promoter-Dependent and Locus-Specific Changes in Gene Expression During Plant Development

  2005influential reference
• Nonadditive Gene Expression in Diploid and Triploid Hybrids of Maize

  2005influential reference
• Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation

  2005influential reference
• Methods for genome-wide analysis of gene expression changes in polyploids.

  2005cited by this paper
• The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects.

  2004influential reference
• Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid

  2004cited by this paper
• Allelic Variation of Gene Expression in Maize Hybrids

  2004cited by this paper
• Evolution by polyploidy and gene regulation in Anura.

  2004cited by this paper
• The ethylene signaling pathway: new insights.

  2004cited by this paper
• Evolutionary changes in cis and trans gene regulation

  2004cited by this paper
• Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution

  2004cited by this paper
• Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids

  2004influential reference
• FISH analysis of meiosis in Arabidopsis allopolyploids

  2004cited by this paper
• Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species.

  2004influential reference
• Extensive Sex-Specific Nonadditivity of Gene Expression in Drosophila melanogaster

  2004influential reference
• Genome evolution in polyploids

  2004influential reference
• Understanding mechanisms of novel gene expression in polyploids.

  2003influential reference
• Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing

  2003influential reference
• Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat

  2003cited by this paper
• Allopolyploidy alters gene expression in the highly stable hexaploid wheat

  2003cited by this paper
• A rapidly evolving MYB-related protein causes species isolation in Drosophila

  2003cited by this paper
• In Search of the Molecular Basis of Heterosis

  2003cited by this paper
• Dissection of floral induction pathways using global expression analysis

  2003cited by this paper
• Sex-Dependent Gene Expression and Evolution of the Drosophila Transcriptome

  2003influential reference
• Statistical issues in the design and analysis of spotted microarray experiments

  2002cited by this paper
• Hsp90 as a capacitor of phenotypic variation

  2002cited by this paper
• Remodeling of DNA Methylation and Phenotypic and Transcriptional Changes in Synthetic Arabidopsis Allotetraploids1

  2002influential reference
• Gene loss, silencing and activation in a newly synthesized wheat allotetraploid.

  2002influential reference
• Protein-coding genes are epigenetically regulated in Arabidopsis polyploids

  2001cited by this paper
• Yesterday's polyploids and the mystery of diploidization

  2001cited by this paper
• Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits.

  2001influential reference
• Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group

  2001cited by this paper
• Protein-coding genes are epigenetically regulated in Arabidopsis polyploids.

  2001cited by this paper
• Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae).

  2000influential reference
• The role of genetic and genomic attributes in the success of polyploids.

  2000influential reference
• The probability of duplicate gene preservation by subfunctionalization.

  2000cited by this paper
• Phenotypic Instability and Rapid Gene Silencing in Newly Formed Arabidopsis Allotetraploids

  2000influential reference
• Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

  2000influential reference
• Nucleolar dominance and silencing of transcription.

  1999influential reference
• Ploidy regulation of gene expression.

  1999cited by this paper
• PATHWAYS, MECHANISMS, AND RATES OF POLYPLOID FORMATION IN FLOWERING PLANTS

  1998cited by this paper
• Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome.

  1998cited by this paper
• Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids.

  1998cited by this paper
• Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica.

  1997influential reference
• Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance.

  1997influential reference
• Dosage effects on gene expression in a maize ploidy series.

  1996cited by this paper
• Gentleman R: R: A language for data analysis and graphics

  1996cited by this paper
• Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution.

  1995cited by this paper
• Controlling the false discovery rate: a practical and powerful approach to multiple testing

  1995cited by this paper
• Stomatal Size in Fossil Plants: Evidence for Polyploidy in Majority of Angiosperms

  1994cited by this paper
• Biological applications of the SAS system: an overview

  1988cited by this paper
• The significance of responses of the genome to challenge.

  1984influential reference
• Rate of turnover of structural variants in the rDNA gene family of Drosophila melanogaster

  1982cited by this paper
• Chromosomal evolution in higher plants

  1971influential reference
• Stomatal Size in Fossil Plants : Evidence for Polyploidy in Majority of Angiosperms

  year unknowncited by this paper

• Defense heterosis as a novel plant protection strategy: From theory to breeding practice

  2026cites this paper
• Integrated Transcriptomic, Proteomic, and Metabolomic Analyses Reveal Mechanisms Underlying Day–Night Differences in Carbohydrate Metabolism between Diploid and Tetraploid Rice

  2025cites this paper
• How drought and ploidy level shape gene expression and DNA methylation in Phragmites australis

  2025cites this paper
• Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression

  2025cites this paper
• Subgenome-informed statistical modeling of transcriptomes in 25 common wheat accessions reveals cis- and trans- regulation architectures.

  2025cites this paper
• Empowering plant epigenetics to breed resilience of crops: From nucleolar dominance to transgenerational epigenetic inheritance

  2025cites this paper
• Differential Gene Expression and Unbalanced Homeolog Expression Bias in 4 Million-Year-Old Allopolyploids of Nicotiana Section Repandae

  2025cites this paper
• Development of Brassica rapa-nigra monosomic alien addition lines: cytology, genetics, and morphology

  2025cites this paper
• Comparative Morphological, Physiological, and Transcriptomic Analyses of Diploid and Tetraploid Wucai (Brassica campestris L.)

  2024cites this paper
• Centromere sequence-independent but biased loading of subgenome-specific CENH3 variants in allopolyploid Arabidopsis suecica

  2024cites this paper
• Morphological Characteristics, Genetic Diversity, and Microsatellite Analysis of the Progenies (F1, F2, and Backcross Descendant) of Siniperca chuatsi and Siniperca scherzeri

  2024cites this paper
• HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

  2024cites this paper
• Deep learning can predict subgenome dominance in ancient but not in neo/synthetic polyploidized genomes.

  2024cites this paper
• Unraveling the Genetic Mechanisms of Maize Ear Diameter Heterosis

  2024cites this paper
• Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

  2024cites this paper
• Transgenerational epigenetic inheritance during plant evolution and breeding.

  2024cites this paper
• Understanding the genetic landscape of flowering time variation in Brassica juncea (L.) Czern. and its diploid progenitors: unravelling the role of selection and cytoplasmic backgrounds

  2024cites this paper
• Refining polyploid breeding in sweet potato through allele dosage enhancement

  2024cites this paper
• Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq.

  2023cites this paper
• The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

  2023cites this paper
• Effects of Allopolyploidization and Homoeologous Chromosomal Segment Exchange on Homoeolog Expression in a Synthetic Allotetraploid Wheat under Variable Environmental Conditions

  2023cites this paper
• Protein nonadditive expression and solubility in Arabidopsis hybrids and allotetraploids

  2023cites this paper
• PART OF A SPECIAL ISSUE ON POLYPLOIDY IN ECOLOGY AND EVOLUTION VIEWPOINT Does one subgenome become dominant in the formation and evolution of a polyploid?

  2023cites this paper
• Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid tilapia (Oreochromi niloticus ♀×Oreochromi aureus ♂)

  2023cites this paper
• The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids

  2023cites this paper
• Protein nonadditive expression and solubility contribute to heterosis in Arabidopsis hybrids and allotetraploids

  2023influential citation
• Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid Brassica napus

  2023cites this paper
• Nonadditive and allele-specific expression of ghrelin in hybrid tilapia

  2023influential citation
• Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris

  2023cites this paper
• Global identification of natural antisense transcripts in Gossypium hirsutum and Gossypium barbadense under chilling stress

  2023cites this paper
• The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation

  2022cites this paper
• Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View

  2022influential citation
• Double-haploid induction generates extensive differential DNA methylation in Arabidopsis.

  2022cites this paper
• Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole‐genome duplication

  2022cites this paper
• Chromosome-scale genome assemblies of five different Brassica oleracea morphotypes provide insights in intraspecific diversification

  2022cites this paper
• Cross‐kingdom transcriptomic trends in the evolution of hybrid gene expression

  2022influential citation
• The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits

  2022cites this paper
• miRNA expression differentiation induced by polyploidization in newly formed triploids of black poplar

  2022cites this paper
• Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the Invasive Sphagneticola trilobata and the Native S. calendulacea in South China, and Implications for Its Invasiveness

  2022cites this paper
• The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio

  2022cites this paper
• Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize

  2022cites this paper
• Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species.

  2022cites this paper
• Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance

  2022cites this paper
• High Stability of the Epigenome in Drosophila Interspecific Hybrids

  2022cites this paper
• Subgenome dominance and its evolutionary implications in crop domestication and breeding

  2022cites this paper
• Accession-speci c Parent-of-origin Dependent and Independent Genome Dosage Effects on Salt Tolerance in Arabidopsis Thaliana

  2022cites this paper
• Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspeci c hybridization

  2022cites this paper
• Genomic and Meiotic Changes Accompanying Polyploidization

  2022cites this paper
• Accession-specific parent-of-origin dependent and independent genome dosage effects on salt tolerance in Arabidopsis thaliana

  2022cites this paper
• Genomic Instability in Somatic Hybridization between Poncirus and Citrus Species Aiming to Create New Rootstocks

  2022cites this paper
• Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization

  2022cites this paper
• Integrated Analysis of Hi-C and RNA-Seq Reveals the Molecular Mechanism of Autopolyploid Growth Advantages in Pak Choi (Brassica rapa ssp. chinensis)

  2022cites this paper
• Advances in Research on the Mechanism of Heterosis in Plants

  2021cites this paper
• Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

  2021cites this paper
• MiRNA Identification, Characterization and Integrated Network Analysis for Flavonoid Biosynthesis in Brassicacoraphanus

  2021cites this paper
• Transcriptome analysis reveals the molecular mechanisms of heterosis on thermal resistance in hybrid abalone

  2021cites this paper
• A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

  2021cites this paper
• Whole‐Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization

  2021cites this paper
• Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids

  2021cites this paper
• Polyploidy and mutation in Arabidopsis

  2021cites this paper
• Polyploidy affects the development of Venturia inaequalis in scab-resistant and -susceptible apple cultivars

  2021cites this paper
• Potential of Wild Relatives of Wheat: Ideal Genetic Resources for Future Breeding Programs

  2021cites this paper
• Global insights into homoeolog gene expression in upland cotton under intraspecific hybridization

  2021cites this paper
• The Asymmetrical Evolution of the Mesopolyploid Brassica oleracea Genome

  2021cites this paper
• A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources

  2021cites this paper
• Homoploid F1 hybrids and segmental allotetraploids of rice subspecies are similarly more tolerant to N-deficiency than are parental lines.

  2021cites this paper
• Altered chromatin architecture and gene expression during polyploidization and domestication of soybean.

  2021cites this paper
• DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance

  2021cites this paper
• Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

  2021cites this paper
• Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa

  2021cites this paper
• Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins

  2021influential citation
• Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

  2021cites this paper
• Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids.

  2021cites this paper
• One Hundred Years of Gene Balance: How Stoichiometric Issues Affect Gene Expression, Genome Evolution, and Quantitative Traits

  2021cites this paper
• Genetic characteristics and ploidy trigger the high inducibility of double haploid (DH) inducer in Brassica napus

  2021cites this paper
• Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica

  2021cites this paper
• Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica

  2021cites this paper
• Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition

  2021cites this paper
• Heterosis in Genomic Era: Advances in the Molecular Understanding and Techniques for Rapid Exploitation

  2021influential citation
• Comparative transcriptome analysis revealed differential gene expression in multiple signaling pathways at flowering in polyploid Brassica rapa

  2021cites this paper
• Genomic asymmetry of the Brassica napus seed: Epigenetic contributions of DNA methylation and small RNAs to subgenome bias

  2020cites this paper
• Transcriptome analysis of biological pathways associated with heterosis in Chinese cabbage.

  2020cites this paper
• The Transcriptional and Splicing Changes Caused by Hybridization Can Be Globally Recovered by Genome Doubling during Allopolyploidization

  2020cites this paper
• Parental legacy and regulatory novelty in Brachypodium diurnal transcriptomes accompanying their polyploidy

  2020cites this paper
• Transcriptome Dynamics of the Inflorescence in Reciprocally Formed Allopolyploid Tragopogon miscellus (Asteraceae)

  2020cites this paper
• Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

  2020influential citation
• The effect of cross direction and ploidy level on phenotypic variation of reciprocal diploid and triploid mandarin hybrids

  2020cites this paper
• Speciation Dynamics Of Diverging Allopolyploid Monkeyflower (Mimulus)

  2020cites this paper
• Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus

  2020cites this paper
• Expression Dominance and Homeolog Expression Bias Upon Chilling Stress in A Hybrid Weed Between the Invasive Sphagneticola Trilobata and the Native S. Calendulacea in South China and its Implications for Invasiveness

  2020cites this paper
• The effects of hybridization and genome doubling in plant evolution via allopolyploidy

  2020cites this paper
• Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes

  2020cites this paper
• Synthetic Polyploidy in Grafted Crops

  2020cites this paper
• Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum

  2020cites this paper
• Triploid Citrus Genotypes Have a Better Tolerance to Natural Chilling Conditions of Photosynthetic Capacities and Specific Leaf Volatile Organic Compounds

  2020cites this paper
• In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F1 Hybrid Population

  2020cites this paper
• Genes gained and lost during the evolution and domestication of Brassica napus

  2020influential citation
• High-throughput sequencing reveals the change of microRNA expression caused by allopolyploidization in Cucumis

  2020cites this paper
• Coexpression of parental homeologs of leaf dissection related genes are associated with intermediate leaf forms of two allotetraploid yarrows (Achillea, Asteraceae)

  2020cites this paper
• Cotton genome evolution and features of its structural and functional organization

  2020cites this paper