Polyploidization as a retraction force in plant genome evolution: sequence rearrangements in triticale

• Published in: PloS one Vol. 3; no. 1; p. e1402
• Main Authors: Bento, Miguel, Pereira, H Sofia, Rocheta, Margarida, Gustafson, Perry, Viegas, Wanda, Silva, Manuela
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 02-01-2008; Public Library of Science (PLoS)
• Subjects: Aegilops; Arabidopsis; Banding; Barley; Base Sequence; Binding sites; Cellular biology; Chromatin; Chromosome Mapping; Chromosomes; Comparative analysis; Condensates; Cytogenetics; Cytological research; Deoxyribonucleic acid; DNA; DNA methylation; DNA sequencing; DNA, Plant; Edible Grain - classification; Edible Grain - genetics; Epigenetic inheritance; Epigenetics; Evolution, Molecular; Fluorescence; Fluorescence in situ hybridization; Fragments; Gene Rearrangement; Gene sequencing; Genes; Genetic aspects; Genetic research; Genetics and Genomics/Comparative Genomics; Genome, Plant; Genomes; Genomics; Glycoproteins; Goat grass; Homology; Hordeum; Hordeum bulbosum; Hybridization; Hydroxyproline; Inbreeding; Microsatellites; Molecular Biology/Chromosome Structure; Molecular Biology/Molecular Evolution; Molecular Sequence Data; Nucleotide sequence; Parents; Phylogeny; Pinus pinaster; Plant Biology/Plant Cell Biology; Plant Biology/Plant Genomes and Evolution; Plant evolution; Plant genetics; Polymorphism; Polyploidy; Proteins; Retroelements; Ribosomal DNA; Rye; Sequence Homology, Nucleic Acid; Transposons; Triticale; Triticum; Wheat; United States > US; Missouri
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0001402

Polyploidization is a major evolutionary process in plants where hybridization and chromosome doubling induce enormous genomic stress and can generate genetic and epigenetic modifications. However, proper evaluation of DNA sequence restructuring events and the precise characterization of sequences involved are still sparse.
Inter Retrotransposons Amplified Polymorphism (IRAP), Retrotransposons Microsatellite Amplified Polymorphism (REMAP) and Inter Simple Sequence Repeat (ISSR) largely confirmed the absence of any intraspecific variation in wheat, rye and triticale. The comparative analysis of banding profiles between wheat and rye inbred lines revealed 34% of monomorphic (common to both parental species) bands for the ten different primer combinations used. The analysis of triticale plants uncovered nearly 51% of rearranged bands in the polyploid, being the majority of these modifications, due to the loss of rye bands (83%). Sequence analysis of rye fragments absent in triticale revealed for instance homology with hydroxyproline-rich glycoproteins (HRGP), a protein that belongs to a major family of inducible defence response proteins. Conversely, a wheat-specific band absent in triticale comprises a nested structure of copia-like retrotransposons elements, namely Claudia and Barbara. Sequencing of a polyploid-specific band (absent in both parents) revealed a microsatellite related sequence. Cytological studies using Fluorescent In Situ Hybridization (FISH) with REMAP products revealed a widespread distribution of retrotransposon and/or microsatellite flanking sequences on rye chromosomes, with a preferential accumulation in heterochromatic sub-telomeric domains.
Here, we used PCR-based molecular marker techniques involving retrotransposons and microsatellites to uncover polyploidization induced genetic restructuring in triticale. Sequence analysis of rearranged genomic fragments either from rye or wheat origin showed these to be retrotransposon-related as well as coding sequences. Further FISH analysis revealed possible chromosome hotspots for sequence rearrangements. The role of chromatin condensation on the origin of genomic rearrangements mediated by polyploidization in triticale is also discussed.