Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale

Abstract

BackgroundPolyploidization 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.Methodology/Principal FindingsInter 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.Conclusions/SignificanceHere, 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.

Genomic changes at the early stage of somatic hybridization

“…For the japonica/indica somatic hybrids, LTR primers were used for IRAP assays, while for REMAP, these same primers were combined with the primers RM50R, RM202R, or RM202F (Tables 4 and 5). For the japonica/ wheat somatic hybrids, the IRAP assays described by Bento et al (2008) were used. All polymerase chain reaction (PCR) products were resolved by electrophoresis on either 6% denaturing polyacrylamide or on 2% agarose gels.…”

“…At the cytological level, a common method is genomic in situ hybridization (GISH), a technique that is able to identify alien chromosomes and chromatin, as well as chromosomal rearrangements, especially those resulting from the formation of mosaic chromosomes (Gernand et al, 2005). At the DNA sequence level, various marker platforms have proven informative, especially those targeting retrotransposons (Bento et al, 2008;Kraitshtein et al, 2010). Several genomic variations induced by genomic shock from F1 to successful generations have been discovered (Feldman et al, 1997;Liu et al, 1998;Ozkan et al, 2001); however, the specific timing of the elimination is hard to establish in sexual hybrids because of the technical difficulty of collecting sufficient DNA for analytical purposes from very young zygotes.…”

Genetic and Epigenetic Changes in Somatic Hybrid Introgression Lines Between Wheat and Tall Wheatgrass

“…The activity of retrotransposons needs to be tightly controlled to ensure viability and survival of the host, and a major control step involves the inhibition of transcription. Reactivation of transposons has been observed either as a response to stress or to genomic shock (Bennetzen 2000;Liu and Wendel 2000;Kashkush et al 2002Kashkush et al , 2003Shan et al 2005Shan et al , 2009Bento et al 2008Bento et al , 2010. Our MSAP analysis of the introgression lines indicates that alteration in C methylation involves repetitive sequences.…”

Detection of genetic relationships among spring and winter triticale (× Triticosecale Witt.) and rye cultivars (Secale cereale L.) by using retrotransposon-based markers

“…Molecular marker techniques such as SSAP (Sequence-Specific Amplification Polymorphism) and the related IRAP (Inter-Retrotransposons Amplified Polymorphism) and the REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) are based on retrotransposon activity, and are widely used today. The IRAP technique examines the polymorphism of retrotransposons themselves (Todorovska 2007) and largely confirmed absence of any intraspecific variation in wheat, rye and triticale (Bento et al 2008). Smýkal (2006) mentioned as the major advantage of IRAP (over the other methods used in pea) the high information content gained per single PCR analysis, which substantially cuts time and cost.…”