Patterns of Homoeologous Gene Expression Shown by RNA Sequencing in Hexaploid Bread Wheat

BMC Genomics. 2014 Apr 11;15:276. doi: 10.1186/1471-2164-15-276.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromosomes, Plant*
  • Expressed Sequence Tags
  • Gene Deletion
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Gene Library
  • Gene Silencing
  • Genes, Plant
  • Genome, Plant*
  • Haplotypes
  • Organ Specificity / genetics
  • Polyploidy*
  • Quantitative Trait Loci
  • Reproducibility of Results
  • Sequence Alignment
  • Sequence Analysis, RNA
  • Transcriptome*
  • Triticum / genetics*