Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.
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AbstractBACKGROUND: 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.
CitationLeach LJ, Belfield EJ, Jiang C, Brown C, Mithani A, et al. (2014) Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics 15: 276. Available: http://dx.doi.org/10.1186/1471-2164-15-276.
SponsorsWe thank Dr Nils Stein and Dr Thomas Wicker for kindly providing their dataset of assembled chromosome 1 wheat genes. We also thank Steve Reader (John Innes Centre, Norwich, UK) for provision of wheat materials and David Buck and his team at the Wellcome Trust Centre for Human Genetics (WTCHG, Oxford) for performing all of the RNA sequencing and providing valuable support and assistance. This work was supported through funding (of authors LJL, EJB, CJ, CB and AM) in a grant from King Abdullah University of Science and Technology (KAUST) in Saudi Arabia to NPH and through funding from the Biotechnology and Biological Sciences Research Council (BB/F020759/1) to NPH.
PubMed Central IDPMC4023595
CollectionsPublications Acknowledging KAUST Support
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