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Retrotransposon-based molecular markers for grapevine species and cultivars identification

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Abstract

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 inter-retrotransposon 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 gypsy-like 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 retrotransposon-based 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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Abbreviations

AFLP:

Amplified fragment length polymorphism

CV:

Coefficient of variation

He:

Expected heterozygosity

Ho:

Observed heterozygosity

IRAP:

Inter-retrotransposon amplified polymorphism

ISSR:

Inter-SSR

LTRs:

Long terminal repeats

MI:

Marker index

PI:

Probability of identity

PIC:

Polymorphic information content

PICav :

Polymorphic information content arithmetic mean

RBIP:

Retrotransposon-based insertional polymorphism

REMAP:

Retrotransposon-microsatellite amplified polymorphism

RTs:

Retrotransposons

SI:

Shannon’s index

SSAP:

Sequence-specific amplified polymorphism

SSRs:

Single sequence repeats

TEs:

Transposable elements

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Acknowledgements

The authors would like to thank INTERREG III A, C projects and Dept. of Fruit Science and Plant Protection of Woody Species “G. Scaramuzzi”, “G. Scaramuzzi” University of Pisa for funded this work, IASMA (Trento) for supplying V. rupestris, V. cinerea, V. cordifolia and V. champinii genotypes, IVV-CNR (Torino) for the V. rotundifolia genotype, Tos.Co.Vit. (Pisa) for the ‘Sangiovese’ selected clones and ‘Prugnolo gentile’ genotypes. We also thank CIBIACI (Firenze) for the detection of PCR products on an ABI 310 sequencer.

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Authors and Affiliations

  1. Department of Fruit Science and Plant Protection of Woody Species “G. Scaramuzzi”, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy

    Claudio D’Onofrio, Gabriella De Lorenzis & Giancarlo Scalabrelli

  2. Department of Crop Plant Biology, University of Pisa, Via Matteotti 1/B, I-56124, Pisa, Italy

    Tommaso Giordani, Lucia Natali & Andrea Cavallini

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  1. Claudio D’Onofrio
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  2. Gabriella De Lorenzis
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  3. Tommaso Giordani
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  4. Lucia Natali
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  5. Andrea Cavallini
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  6. Giancarlo Scalabrelli
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Correspondence to Claudio D’Onofrio.

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Communicated by R. Velasco

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D’Onofrio, C., De Lorenzis, G., Giordani, T. et al. Retrotransposon-based molecular markers for grapevine species and cultivars identification. Tree Genetics & Genomes 6, 451–466 (2010). https://doi.org/10.1007/s11295-009-0263-4

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