title: Identification and characterization of rye genes not expressed in allohexaploid triticale.
abstract: BACKGROUND
  One of the most important evolutionary processes in plants is polyploidization. The combination of two or more genomes in one organism often initially leads to changes in gene expression and extensive genomic reorganization, compared to the parental species. Hexaploid triticale (x Triticosecale) is a synthetic hybrid crop species generated by crosses between T. turgidum and Secale cereale. Because triticale is a recent synthetic polyploid it is an important model for studying genome evolution following polyploidization. Molecular studies have demonstrated that genomic sequence changes, consisting of sequence elimination or loss of expression of genes from the rye genome, are common in triticale. High-throughput DNA sequencing allows a large number of genes to be surveyed, and transcripts from the different homeologous copies of the genes that have high sequence similarity can be better distinguished than hybridization methods previously employed.
  
  
  RESULTS
  The expression levels of 23,503 rye cDNA reference contigs were analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye, as well as in five 454-cDNA data sets created from triticale seedling shoot, ovary, stigma, pollen and seed tissues to identify the classes of rye genes silenced or absent in the recent synthetic hexaploid triticale. Comparisons between diploid rye and hexaploid triticale detected 112 rye cDNA contigs (~0.5%) that were totally undetected by expression analysis in all triticale tissues, although their expression was relatively high in rye tissues. Non-expressed rye genes were found to be strikingly less similar to their closest BLASTN matches in the wheat genome or in the other Triticum genomes than a test set of 200 random rye genes. Genes that were not detected in the RNA-seq data were further characterized by testing for their presence in the triticale genome by PCR using genomic DNA as a template.
  
  
  CONCLUSIONS
  Genes with low similarity between rye sequences and their closest matches in the Triticum genome have a higher probability to be repressed or absent in the allopolyploid genome.
authors.affiliation: Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, Quebec, H4B 1R6, Canada. halabadr111@yahoo.com.|Present addresses: Department of Genetics, Faculty of Agriculture, Ain-Shams University, Shoubra El-khema, Cairo, Egypt. halabadr111@yahoo.com.|Agriculture and Agri-Food Canada, Pacific Agri-Food Research Center, Summerland, BC, V0H 1Z0, Canada. halabadr111@yahoo.com.
authors.forename: Hala Badr
authors.initials: HB
authors.lastname: Khalil
authors.affiliation: Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, Quebec, H4B 1R6, Canada. mrzehda@yahoo.com.
authors.forename: Mohammad-Reza
authors.initials: MR
authors.lastname: Ehdaeivand
authors.affiliation: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada. xuyhanghang@gmail.com.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, T1J 4B1, Canada. Andre.Laroche@AGR.GC.CA.
authors.forename: André
authors.initials: A
authors.lastname: Laroche
authors.affiliation: Department of Biology, Concordia University, 7141 Sherbrooke W., Montreal, Quebec, H4B 1R6, Canada. patrick.gulick@concordia.ca.
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Gulick
mesh_terms: D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D011123:Polyploidy; D012434:Secale / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome; D000066889:Triticale / Q000235:genetics* / Q000378:metabolism; D014908:Triticum / Q000235:genetics / Q000378:metabolism