Retrotransposon-based molecular markers in grapevine species and cultivars identification and phylogenetic analysis

In this study we analysed the polymorphisms of retrotransposon based molecular markers (IRAP, REMAP, SSAP) in 22 Vitis genotypes: 16 Vitis vinifera genotypes (eight different 'Sangiovese' clones, four different 'Niellucciu' clones, 'Prugnolo gentile', 'Ciliegiolo', 'Trebbiano toscano', 'Vermentino') Vitis vinifera subsp. sylvestris, Vitis rupestris du Lot, Vitis cinerea, Vitis cordifolia, Vitis champinii, and Vitis rotundifolia. In particular, we studied the polymorphisms of three different retrotransposons found in the grapevine genome, two copia-like, Vine-1 and Tvvl, and one gypsy-like, Gret1. Among these, Tvv1 showed the highest polymorphisms and allowed us to clearly distinguish among Vitis species and Vitis vinifera varieties analysed. On the same genotypes, we also analysed some SSR, I-SSR, and AFLP polymorphisms. The phylogenetic tree obtained from the Tvv1 polymorphisms and those obtained from I-SSR, AFLP, and 10 microsatellite loci polymorphisms show some significant differences in the allocation of the analysed accessions. The presence of Tvv1 in all the analysed genotypes suggests that this retrotransposon element is widespread in Vitis genus and indicates that it was active before Vitis speciation and contributed the evolution of this genus.