title: Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines.
abstract: BACKGROUND
  Alteration in gene expression resulting from allopolyploidization is a prominent feature in plants, but its spectrum and extent are not fully known. Common wheat (Triticum aestivum) was formed via allohexaploidization about 10,000 years ago, and became the most important crop plant. To gain further insights into the genome-wide transcriptional dynamics associated with the onset of common wheat formation, we conducted microarray-based genome-wide gene expression analysis on two newly synthesized allohexaploid wheat lines with chromosomal stability and a genome constitution analogous to that of the present-day common wheat.
  
  
  RESULTS
  Multi-color GISH (genomic in situ hybridization) was used to identify individual plants from two nascent allohexaploid wheat lines between Triticum turgidum (2n=4x=28; genome BBAA) and Aegilops tauschii (2n=2x=14; genome DD), which had a stable chromosomal constitution analogous to that of common wheat (2n=6x=42; genome BBAADD). Genome-wide analysis of gene expression was performed for these allohexaploid lines along with their parental plants from T. turgidum and Ae. tauschii, using the Affymetrix Gene Chip Wheat Genome-Array. Comparison with the parental plants coupled with inclusion of empirical mid-parent values (MPVs) revealed that whereas the great majority of genes showed the expected parental additivity, two major patterns of alteration in gene expression in the allohexaploid lines were identified: parental dominance expression and non-additive expression. Genes involved in each of the two altered expression patterns could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Strikingly, whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes was highly stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms. Nonetheless, those genes showing non-additive expression exhibited a significant enrichment for vesicle-function.
  
  
  CONCLUSIONS
  Our results show that two patterns of global alteration in gene expression are conditioned by allohexaploidization in wheat, that is, parental dominance expression and non-additive expression. Both altered patterns of gene expression but not the identity of the genes involved are likely to play functional roles in stabilization and establishment of the newly formed allohexaploid plants, and hence, relevant to speciation and evolution of T. aestivum.
authors.affiliation: Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
authors.forename: Bao
authors.initials: B
authors.lastname: Qi
authors.forename: Wei
authors.initials: W
authors.lastname: Huang
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Zhong
authors.forename: Jianhua
authors.initials: J
authors.lastname: Guo
authors.forename: Na
authors.initials: N
authors.lastname: Zhao
authors.forename: Chunming
authors.initials: C
authors.lastname: Xu
authors.forename: Huakun
authors.initials: H
authors.lastname: Zhang
authors.forename: Jinsong
authors.initials: J
authors.lastname: Pang
authors.forename: Fangpu
authors.initials: F
authors.lastname: Han
authors.forename: Bao
authors.initials: B
authors.lastname: Liu
mesh_terms: D019143:Evolution, Molecular; D015870:Gene Expression; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D014644:Genetic Variation; D017403:In Situ Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011123:Polyploidy; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014908:Triticum / Q000145:classification / Q000235:genetics*