title: Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus.
abstract: Brassica napus (AACC, 2n = 38, oilseed rape) is a relatively recent allotetraploid species derived from the putative progenitor diploid species Brassica rapa (AA, 2n = 20) and Brassica oleracea (CC, 2n = 18). To determine the influence of intensive breeding conditions on the evolution of its genome, we analysed structure and copy number of rDNA in 21 cultivars of B. napus, representative of genetic diversity.
  
  
  
  We used next-generation sequencing genomic approaches, Southern blot hybridization, expression analysis and fluorescence in situ hybridization (FISH). Subgenome-specific sequences derived from rDNA intergenic spacers (IGS) were used as probes for identification of loci composition on chromosomes.
  
  
  
  Most B. napus cultivars (18/21, 86 %) had more A-genome than C-genome rDNA copies. Three cultivars analysed by FISH ('Darmor', 'Yudal' and 'Asparagus kale') harboured the same number (12 per diploid set) of loci. In B. napus 'Darmor', the A-genome-specific rDNA probe hybridized to all 12 rDNA loci (eight on the A-genome and four on the C-genome) while the C-genome-specific probe showed weak signals on the C-genome loci only. Deep sequencing revealed high homogeneity of arrays suggesting that the C-genome genes were largely overwritten by the A-genome variants in B. napus 'Darmor'. In contrast, B. napus 'Yudal' showed a lack of gene conversion evidenced by additive inheritance of progenitor rDNA variants and highly localized hybridization signals of subgenome-specific probes on chromosomes. Brassica napus 'Asparagus kale' showed an intermediate pattern to 'Darmor' and 'Yudal'. At the expression level, most cultivars (95 %) exhibited stable A-genome nucleolar dominance while one cultivar ('Norin 9') showed co-dominance.
  
  
  
  The B. napus cultivars differ in the degree and direction of rDNA homogenization. The prevalent direction of gene conversion (towards the A-genome) correlates with the direction of expression dominance indicating that gene activity may be needed for interlocus gene conversion.
authors.affiliation: Laboratory of Molecular Epigenetics, Institute of Biophysics, Královopolská 135, 61265 Brno, Czech Academy of Science, v.v.i., Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Sochorová
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1349 IGEPP, BP 35327, F-35653 Le Rheu cedex, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Coriton
authors.affiliation: Laboratory of Molecular Epigenetics, Institute of Biophysics, Královopolská 135, 61265 Brno, Czech Academy of Science, v.v.i., Czech Republic.
authors.forename: Alena
authors.initials: A
authors.lastname: Kuderová
authors.affiliation: Laboratory of Molecular Epigenetics, Institute of Biophysics, Královopolská 135, 61265 Brno, Czech Academy of Science, v.v.i., Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Lunerová
authors.affiliation: Institut National de la Recherche Agronomique (INRA), UMR 1349 IGEPP, BP 35327, F-35653 Le Rheu cedex, France.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Chèvre
authors.affiliation: Laboratory of Molecular Epigenetics, Institute of Biophysics, Královopolská 135, 61265 Brno, Czech Academy of Science, v.v.i., Czech Republic kovarik@ibp.cz.
authors.forename: Aleš
authors.initials: A
authors.lastname: Kovařík
mesh_terms: D015139:Blotting, Southern; D029688:Brassica napus / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics*; D005785:Gene Conversion / Q000235:genetics*; D020869:Gene Expression Profiling; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D017404:In Situ Hybridization, Fluorescence
chemical_list: D004275:DNA, Ribosomal
keywords: Brassica napus; allopolyploidy; chromosome evolution; gene conversion; rDNA