mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat[W][OPEN]

No abstract is available for this paper.

• Publication year

  2014

• Venue

  The Plant Cell

• Publication date

  2014-05-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1105/tpc.114.124388PMID 24838975PMCID PMC4079356
• 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.

• Differential expression analysis

  2015cited by this paper
• Polyploids as a “model system” for the study of heterosis

  2014cited by this paper
• Differential Expression Analysis

  2014cited by this paper
• Two evolutionarily distinct classes of paleopolyploidy.

  2014cited by this paper
• Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice

  2014cited by this paper
• Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

  2013cited by this paper
• Genomic and epigenetic insights into the molecular bases of heterosis

  2013cited by this paper
• Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation

  2013cited by this paper
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

  2013cited by this paper
• Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes

  2013cited by this paper
• Genomic dosage effects on heterosis in triploid maize

  2013cited by this paper
• Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat

  2013cited by this paper
• Regulation of FLOWERING LOCUS T by a MicroRNA in Brachypodium distachyon[C][W]

  2013influential reference
• Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat

  2013cited by this paper
• Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis

  2013influential reference
• Production of hexaploid triticale by a synthetic hexaploid wheat-rye hybrid method

  2013cited by this paper
• Prevalence of gene expression additivity in genetically stable wheat allohexaploids.

  2013cited by this paper
• Draft genome of the wheat A-genome progenitor Triticum urartu

  2013cited by this paper
• Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids

  2013cited by this paper
• Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes.

  2013cited by this paper
• A GH 3 family m mber , OsGH 3-2 , modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice

  2012cited by this paper
• Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds

  2012cited by this paper
• Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

  2012influential reference
• Genomic asymmetry in allopolyploid plants: wheat as a model.

  2012cited by this paper
• Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines

  2012influential reference
• Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants.

  2012cited by this paper
• Analysis of the bread wheat genome using whole genome shotgun sequencing

  2012cited by this paper
• Homoeolog expression bias and expression level dominance in allopolyploids.

  2012influential reference
• Homoeolog expression bias and expression level dominance in allopolyploid cotton

  2012influential reference
• PsRobot: a web-based plant small RNA meta-analysis toolbox

  2012influential reference
• Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility.

  2012influential reference
• Polyploidy and its effect on evolutionary success: old questions revisited with new tools

  2012cited by this paper
• A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes

  2012cited by this paper
• RSeQC: quality control of RNA-seq experiments

  2012influential reference
• Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat1[W][OA]

  2012cited by this paper
• Trans Chromosomal Methylation in Arabidopsis hybrids

  2012cited by this paper
• Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

  2011cited by this paper
• Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

  2011influential reference
• Chromosomal and genome-wide molecular changes associated with initial stages of allohexaploidization in wheat can be transit and incidental.

  2011cited by this paper
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  2011cited by this paper
• Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

  2011cited by this paper
• Frequent occurrence of unreduced gametes in Triticum turgidum–Aegilops tauschii hybrids

  2010cited by this paper
• Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids.

  2010influential reference
• Monovalent and unpoised status of most genes in undifferentiated cell-enriched Drosophila testis

  2010cited by this paper
• Molecular mechanisms of polyploidy and hybrid vigor.

  2010cited by this paper
• Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation.

  2010cited by this paper
• Differential expression analysis for sequence count data

  2010cited by this paper
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010influential reference
• Profiling of cold-stress-responsive miRNAs in rice by microarrays.

  2010cited by this paper
• Genomic and expression plasticity of polyploidy.

  2010cited by this paper
• DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

  2010influential reference
• miRBase: integrating microRNA annotation and deep-sequencing data

  2010cited by this paper
• De novo assembly of human genomes with massively parallel short read sequencing.

  2010cited by this paper
• Homoeolog-specific transcriptional bias in allopolyploid wheat

  2010cited by this paper
• Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity.

  2010influential reference
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  2009cited by this paper
• The frequency of polyploid speciation in vascular plants

  2009cited by this paper
• Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

  2009cited by this paper
• Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

  2009cited by this paper
• The Sequence Alignment/Map format and SAMtools

  2009cited by this paper
• Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

  2009cited by this paper
• Genomic expression dominance in allopolyploids

  2009cited by this paper
• Duplicate genes increase expression diversity in closely related species and allopolyploids

  2009influential reference
• Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

  2009cited by this paper
• Synthetic hexaploid wheat and its utilization for wheat genetic improvement in China.

  2009cited by this paper
• Biolistics transformation of wheat.

  2009cited by this paper
• Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv

  2009influential reference
• Polyploidy and angiosperm diversification.

  2009cited by this paper
• Gene expression analysis at the intersection of ploidy and hybridity in maize

  2009cited by this paper
• Using RepeatMasker to Identify Repetitive Elements in Genomic

  2009cited by this paper
• MicroRNA expression profiling using microarrays

  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
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• Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

  2007influential reference
• Meiotic restriction in emmer wheat is controlled by one or more nuclear genes that continue to function in derived lines

  2007cited by this paper
• Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids.

  2007influential reference
• Genome Plasticity a Key Factor in the Success of Polyploid Wheat Under Domestication

  2007cited by this paper
• Homoeologous gene silencing in hexaploid wheat.

  2006cited by this paper
• Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids

  2006influential reference
• Post-transcriptional small RNA pathways in plants: mechanisms and regulations.

  2006cited by this paper
• ‘Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells’

  2006cited by this paper
• Use of wild relatives to improve salt tolerance in wheat.

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• The advantages and disadvantages of being polyploid

  2005cited by this paper
• The auxin-responsive GH3 gene family in rice (Oryza sativa)

  2005cited by this paper
• Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences

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  2003cited by this paper
• Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat

  2003cited by this paper
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  2002cited by this paper
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  2000cited by this paper
• The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering.

  1998cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997influential reference

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