Triticeae Genome Structure and Evolution

Dvořák, Jan

doi:10.1007/978-0-387-77489-3_23

Cited by 41 publications

(24 citation statements)

References 146 publications

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“…The technique shows a widespread distribution of FISH signals throughout prophase chromosomes (Figure 3). This result confirms that retrotransposon-related sequences are usually dispersed on plant species with large genomes like V. faba [53] and Triticeae species [54,55] or on plants with median size genomes like O. sativa [53] or Vitis vinifera [29], as opposed to the preferential clustering of retrotransposons in pericentromeric domains observed in plant species with small genomes like Arabidopsis thaliana [56]. The detailed analysis of IRAP Athila FISH labelling reveals signals on DAPI-positive domains with less condensed chromatin as well as on domains with more intense DAPI staining (heterochromatin) (arrowhead in Figure 3b), although some of these heterochromatic domains do not present any FISH labeling (small arrow in Figure 3c).…”

Section: Irap Analysis Of Genomic Diversitysupporting

confidence: 77%

Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

et al. 2016

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Faba bean have been grown in Portugal for a long time and locally adapted populations are still maintained on farm. The genetic diversity of four Portuguese faba bean populations that are still cultivated in some regions of the country was evaluated using the Inter Retrotransposons Amplified Polymorphism (IRAP) technique. It was shown that molecular markers based on retrotransposons previously identified in other species can be efficiently used in the genetic variability assessment of Vicia faba. The IRAP experiment targeting Athila yielded the most informative banding patterns. Cluster analysis using the neighbor-joining algorithm generated a dendrogram that clearly shows the distribution pattern of V. faba samples. The four equina accessions are separated from each other and form two distinct clades while the two major faba bean accessions are not unequivocally separated by the IRAP. Fluorescent In Situ Hybridization (FISH) analysis of sequences amplified by IRAP Athila revealed a wide distribution throughout V. faba chromosomes, confirming the whole-genome coverage of this molecular marker. Morphological characteristics were also assessed through cluster analysis of seed characters using the unweighted pair group method arithmetic average (UPGMA) and principal component analysis (PCA), showing a clear discrimination between faba bean major and equina groups. It was also found that the seed character most relevant to distinguish accessions was 100 seed weight. Seed morphological traits and IRAP evaluation give similar results supporting the potential of IRAP analysis for genetic diversity studies.

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Section: Irap Analysis Of Genomic Diversitysupporting

confidence: 77%

Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

et al. 2016

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“…Adapted from [Parisod et al, 2010a]. Dvořák, 2009]. Such nested arrangements of retrotransposons are rarely observed in Arabidopsis and Brassica species, which is in clear contrast to evidence from Triticeae [Arabidopsis Genome Initiative, 2000;PetersonBurch et al, 2004;Alix et al, 2005;Wang et al, 2011].…”

Section: Retrotransposon Classes and Abundance In Plant Genomesmentioning

confidence: 40%

“…In Triticeae, retrotransposons may be clustered in heterochromatin domains but are also present in high copy number all over chromosome arms, frequently in complex nested insertions. Chromosomes are not drawn to scale [Li et al, 2004;Peterson-Burch et al, 2004;Dvořák, 2009]. model allopolyploid species with both large and small genomes, independent of their distinct abundance and distribution patterns. However, the understanding of the real causes for the discrepancy between AFLP and IRAP in detecting rearrangement frequencies in triticale and A. suecica requires further research to extensively characterise the restructured bands at the sequence level.…”

Section: Irap Totalmentioning

confidence: 99%

“…Such a tendency for an increase in retrotransposon copy number is counteracted by sequence deletions such as illegitimate retrotransposon recombination, which results in retrotransposon excision [Devos et al, 2002]. Thus, the ratio between TE insertions and deletions modulates the amount of repeated DNA in a genome and ultimately is largely responsible for the size of the genome [Dvořák, 2009].…”

mentioning

confidence: 99%

“…Retrotransposons transpose via RNA intermediates without excising the original copy, are ubiquitously dispersed in all plant species and represent more than 50% of the genomic sequence in some cases [Kumar and Bennetzen, 1999;Lisch, 2013]. The retrotransposon 'copy-and-paste' mechanism of transposition introduces new copies of the original retroelement into the genome and may rapidly increase the frequency of repetitive elements in plant genomes [Schulman et al, 2004;Dvořák, 2009]. Such a tendency for an increase in retrotransposon copy number is counteracted by sequence deletions such as illegitimate retrotransposon recombination, which results in retrotransposon excision [Devos et al, 2002].…”

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confidence: 99%

See 2 more Smart Citations

Retrotransposons Represent the Most Labile Fraction for Genomic Rearrangements in Polyploid Plant Species

Bento¹,

Tomás²,

Viegas³

et al. 2013

Cytogenet Genome Res

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Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue.

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Targeted Mutagenesis in Hexaploid Bread Wheat Using the TALEN and CRISPR/Cas Systems

Wang

Zong

Gao

2017

Methods in Molecular Biology

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The use of sequence-specific transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats-associated system (CRISPR/Cas9) have provided powerful reverse genetic approaches to the targeted modification of genomes in numerous organisms. Both systems have been employed to generate loss-of-function alleles in bread wheat, by targeting multiple and single copies of genes. Here we present protocols for modifying the wheat genome using the two systems. The protocols include the design of TALEN and CRISPR/Cas9 target sites and their construction, evaluation of their activities in protoplasts, transformation of plants, and mutation screening.

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Triticeae Genome Structure and Evolution

Cited by 41 publications

References 146 publications

Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

Genetic Diversity Assessment of Portuguese Cultivated Vicia faba L. through IRAP Markers

Retrotransposons Represent the Most Labile Fraction for Genomic Rearrangements in Polyploid Plant Species

Targeted Mutagenesis in Hexaploid Bread Wheat Using the TALEN and CRISPR/Cas Systems

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