Homoeolog-specific transcriptional bias in allopolyploid wheat

BMC Genomics. 2010 Sep 17;11:505. doi: 10.1186/1471-2164-11-505.


Background: Interaction between parental genomes is accompanied by global changes in gene expression which, eventually, contributes to growth vigor and the broader phenotypic diversity of allopolyploid species. In order to gain a better understanding of the effects of allopolyploidization on the regulation of diverged gene networks, we performed a genome-wide analysis of homoeolog-specific gene expression in re-synthesized allohexaploid wheat created by the hybridization of a tetraploid derivative of hexaploid wheat with the diploid ancestor of the wheat D genome Ae. tauschii.

Results: Affymetrix wheat genome arrays were used for both the discovery of divergent homoeolog-specific mutations and analysis of homoeolog-specific gene expression in re-synthesized allohexaploid wheat. More than 34,000 detectable parent-specific features (PSF) distributed across the wheat genome were used to assess AB genome (could not differentiate A and B genome contributions) and D genome parental expression in the allopolyploid transcriptome. In re-synthesized polyploid 81% of PSFs detected mid-parent levels of gene expression, and only 19% of PSFs showed the evidence of non-additive expression. Non-additive expression in both AB and D genomes was strongly biased toward up-regulation of parental type of gene expression with only 6% and 11% of genes, respectively, being down-regulated. Of all the non-additive gene expression, 84% can be explained by differences in the parental genotypes used to make the allopolyploid. Homoeolog-specific co-regulation of several functional gene categories was found, particularly genes involved in photosynthesis and protein biosynthesis in wheat.

Conclusions: Here, we have demonstrated that the establishment of interactions between the diverged regulatory networks in allopolyploids is accompanied by massive homoeolog-specific up- and down-regulation of gene expression. This study provides insights into interactions between homoeologous genomes and their role in growth vigor, development, and fertility of allopolyploid species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Bias
  • Chromosomes, Plant / genetics
  • DNA Probes / metabolism
  • Diploidy
  • Down-Regulation / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Models, Genetic
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis
  • Polyploidy*
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid*
  • Transcription, Genetic*
  • Triticum / genetics*
  • Up-Regulation / genetics


  • DNA Probes