Genomic analysis of Grapevine Retrotransposon 1 (Gret1) in Vitis vinifera

Pereira, H. Sofia; Barão, Augusta; Delgado, Margarida; Morais-Cecílio, Leonor; Viegas, Wanda

doi:10.1007/s00122-005-0009-0

Cited by 36 publications

(21 citation statements)

References 29 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: 73%

“…The correspondence between quantitative and molecular data on the evaluation of V. faba diversity was also recently confirmed on distinct accessions of a Sicilian major faba bean landrace [48], contrasting therefore with previous reports suggesting no correlation between diversity assessed by molecular tools and morphology traits [25,58]. The importance of IRAP methodology on studies of genetic diversity was already well established for several crops like Avena sativa and A. strigosa [34], H. vulgare [38], P. sativum [27,28], O. sativa [31], V. vinifera [29] and Z. mays [30]. The present study therefore emphasizes the fact that the separation of the faba bean classes extends to more than just morphological seed traits.…”

Section: Seed Morphological Characterizationmentioning

confidence: 87%

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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: 73%

Section: Seed Morphological Characterizationmentioning

confidence: 87%

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

et al. 2016

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“…The absence of IRAP bands for the Gret1 retrotransposon has already been reported by Pereira et al (2005).…”

Section: Discussionmentioning

confidence: 74%

“…Furthermore, they have been utilised to distinguish species across a genus (Kalendar et al 1999), as well as to study genetic diversification in vegetatively propagated crop species (Bretó et al 2001;Natali et al 2007). In grapevine, REMAP and IRAP techniques have been applied by Pereira et al (2005) for discriminating cultivars using primers designed to amplify polymorphisms associated with Gret1 LTR retrotransposons. The effectiveness of the SSAP technique in distinguishing grapevine varieties was also tested by Pelsy et al (2003) and Labra et al (2004) using Tvv1 and Vine-1 RTs, respectively.…”

Section: Introductionmentioning

confidence: 99%

Retrotransposon-based molecular markers for grapevine species and cultivars identification

D’Onofrio

Lorenzis

Giordani

et al. 2010

Tree Genetics & Genomes

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Insertional polymorphisms of two copia-like (Vine-1, Tvv1) and one gypsy-like (Gret1) retrotransposon found in the grapevine genome were studied in 29 Vitis genotypes (Vitis arizonica, Vitis cinerea, Vitis labrusca, Vitis rupestis, Vitis rotundifolia, Vitis vinifera subsp. sylvestris and 23 V. vinifera subsp. sativa) using interretrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and sequence-specific amplified polymorphism (SSAP) techniques. IRAP, REMAP and SSAP polymorphisms were compared with amplified fragment length polymorphism (AFLP), Inter-single sequence repeats (ISSR) and SSR polymorphisms by evaluating the information content, the number of loci simultaneously analysed per experiment, the effectiveness of the analyses in assessing the relationship between accessions and the number of loci needed to obtain a coefficient of variation of 10%. The UPGMA dendrograms of each molecular marker system were compared and the Mantel matrix correspondence test was applied. Furthermore, the corresponding insertion ages of the transposable elements were estimated for each retrotransposon subfamily analysed. The presence of Gret1, Tvv1 and Vine-1 retrotransposons in all analysed genotypes suggests that copia-like and gypsylike retrotransposons are widespread in Vitis genus. The results indicate that these retrotransposons were active before Vitis speciation and contributed to Vitis genus evolution. IRAP, REMAP and SSAP markers allow the discrimination of Vitis species and V. vinifera subsp. sativa cultivars with certainty as has been shown with AFLP, ISSR and SSR analyses, but phylogenetic trees obtained by retrotransposonbased molecular markers polymorphisms show some significant differences in the allocation of the analysed accessions compare to those obtained by ISSR, AFLP and SSR molecular markers. The phylogenetic tree resulting from REMAP polymorphism appeared the most representative of the effective relationship between all analysed accessions

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“…Retrotransposons are mutation inducers but are suitable to develop molecular markers like retroelement-microsatellite-amplified-polymorphism and inter-retroelement-amplified-polymorphism markers (Pereira et al 2005;Fujita et al 2009, Wegscheider et al 2009) and were able to show diversity within Vitis species and subspecies collections (D'Onofrio et al 2010).…”

Section: Introductionmentioning

confidence: 97%

Dynamic grapevine clones—an AFLP-marker study of the Vitis vinifera cultivar Riesling comprising 86 clones

Anhalt

Martínez

Rühl

et al. 2011

Tree Genetics & Genomes

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Grapevine cultivars are planted in worldwide viticulture and are asexually propagated. Horticultural clones are asexually derived from a single individual, and clonal variation can only occur through mutations. Molecular markers are an important tool for the differentiation and identification of clones and mutations. For breeding purposes and clonal selection, knowledge upon the variability of a given clone is essential. The aim of this study was to assess amplified fragment length polymorphism (AFLP) markers for classifying mutations in 86 Riesling clones of Vitis vinifera and to enhance our understanding on the dynamic of grapevine clones analysed by AFLP fingerprints. AFLP markers detected 135 polymorphic bands of a total amount of 305 bands. AFLP markers detected two different types of mutations: single-event mutations, only detected once in one clone, displaying the variation of the grape genome and specific loci mutations where the mutation could be found frequently in the set of clones and therefore stand for the stability of grapevine genome. A general grouping of clones according to age, sub-clonal lineage or origin could not be determined by the set of AFLP markers employed.

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Genomic analysis of Grapevine Retrotransposon 1 (Gret1) in Vitis vinifera

Cited by 36 publications

References 29 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

Retrotransposon-based molecular markers for grapevine species and cultivars identification

Dynamic grapevine clones—an AFLP-marker study of the Vitis vinifera cultivar Riesling comprising 86 clones

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