| Summary: | Molecular markers, based on DNA polymorphisms, are useful tools for identifying individuals, establishing phylogenetic relationships, managing collections of genetic material or assisting breeding. In the present study, we developed a marker set to differentiate Vitis species, grapevine varieties or clones belonging to the same variety. This novel marker set combines, in four PCR amplifications, the presence/absence of a remarkable retrotransposon, Tvv1-Δ3460, inserted at its single locus and the SSR polymorphism present within its two LTRs. By studying a collection of Vitaceaeaccessions, we showed the prevalence of two allelic forms of Tvv1-Δ3460 - one of which was partially truncated - in Vitis species. Out of the twenty-five studied Vitis species, the insertion of a Tvv1-Δ3460 element was detected in twenty, including Vitis vinifera. The homozygous vs heterozygous state of the element insertion was determined by amplifying the empty site. Additionally, each Tvv1-Δ3460 LTRs included a microsatellite sequence useful for designing markers based on LTR length. The LTR-SSR markers distinguished most of the fifty-two cultivars and revealed polymorphism within five of the seven varieties studied.
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