title: Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.
abstract: BACKGROUND
  Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression.
  
  
  RESULTS
  We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss.
  
  
  CONCLUSIONS
  We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.
authors.forename: Lindsey J
authors.initials: LJ
authors.lastname: Leach
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Belfield
authors.forename: Caifu
authors.initials: C
authors.lastname: Jiang
authors.forename: Carly
authors.initials: C
authors.lastname: Brown
authors.forename: Aziz
authors.initials: A
authors.lastname: Mithani
authors.affiliation: Department of Plant Sciences, University of Oxford, Oxford, UK. nicholas.harberd@plants.ox.ac.uk.
authors.forename: Nicholas P
authors.initials: NP
authors.lastname: Harberd
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant; D020224:Expressed Sequence Tags; D017353:Gene Deletion; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D020868:Gene Silencing; D017343:Genes, Plant; D018745:Genome, Plant; D006239:Haplotypes; D009928:Organ Specificity / Q000235:genetics; D011123:Polyploidy; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014908:Triticum / Q000235:genetics*
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