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20Microsatellite markers are valuable tool to facilitate management of germplasm 21 collections and to access the genetic diversity. In this study, the genetic characterization 22 of a large collection of 379 rootstocks and other non-vinifera accessions maintained at 23 the University of Milan (Italy) has been reported. Accessions were genotyped with 22 24 2 highly polymorphic microsatellite markers (including the nine 'international' loci used 25 for grapevine identification, three VMC, three VrZAG and seven VChr loci), but only 26 17 loci were retained for cultivar identification, to investigate genetic diversity, for 27 pedigree analysis, to infer population structure and to design a core collection. Two 28 hundred thirty-two unique genotypes were identified. The allelic profiles of sixty-nine 29 rootstocks were confirmed according to literature and databases, while the profiles of 44 30 rootstocks were proposed for the first time. Pedigree analysis highlighted 77 parent-31 offspring (PO) trios and XX PO relationships, some of them already known and some 32 other new. Analysis of the genetic structure showed a more likely number of three 33 ancestral groups, with a high percentage of admixed samples. A structure based on the 34 genetic background of genotypes was not observed. A core collection of seventy 35 genotypes captured 100% of the entire number (373) of detected alleles. Most of these 36 genotypes were unidentified or poorly characterized genotypes. The information 37 provided in this paper could assist breeders in better addressing their efforts in the 38 exploitation of still unexplored individuals useful for long-term breeding plans. 39 40 population structure, VVMD25 and VVMD32. 42 43 1855), a phytophage that attacks V. vinifera roots, by importing American vines, nearly 47 cultivar identification (Migliaro et al. 2013); iii) the three VrZAG loci are obtained from 132 V. riparia (Sefc et al. 1999); iv) the seven VChr loci are suggested for an easier 133 genotyping in V. vinifera (Cipriani et al. 2008) and not yet tested on non-vinifera 134 varieties. 135 PCR reactions were performed using forward primers labeled with fluorescent dyes (6-136 FAM, PET, VIC, or NED); three multiplex panels of fluorescent-labeled microsatellite 137 loci were used. Simultaneous PCR amplifications were conducted in a final volume of 138 595

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Background and Aims: Somatic mutations are the major source of intra-varietal variability in some species such as grapevine (Vitis vinifera L.) that are propagated vegetatively. Aglianico and Muscat of Alexandria are two cultivars mostly cultivated in the south of Italy, showing great intra-varietal diversity. The variability of 15 clones of Aglianico belonging to three biotypes, Taburno, Taurasi and Vulture, and 21 clones of Muscat of Alexandria, coming from France, Greece, Italy and Spain, was investigated. Methods and Results: The intra-varietal diversity was investigated by ampelographic and eno-carpological (berry characteristics of oenological interest) methods (nine OIV descriptors, related to bunch and berry morphology, sugar content, total acid content and pH of must), chemical (anthocyanins, aromatic compounds and phenolic substances) and genetic analysis [18 K SNPs, single nucleotide polymorphisms (SNP)]. Intra-varietal diversity has been detected in both cultivars, mainly based on differences in the accumulation of secondary metabolites. The Taurasi biotype was discriminated by linear discrimination analysis mainly for the proportion of malvidin-3-O-glucoside acetate and methoxylated anthocyanins, while the Spanish Muscat biotype was discriminated based on the proportion of flavanols and hydroxycinnamic acids. Conclusions: Ampelography and the concentration of secondary metabolites have proved to be the best tools for the characterisation of the intra-varietal variability of grapevine germplasm. The high-throughput genetic analysis based on 18 K SNP loci did not highlight a polymorphism sufficient to distinguish among biotypes of the same cultivar, suggesting that a different molecular approach has to be adopted. Significance of the Study: This study confirms that intra-varietal diversity is better examined with a multidisciplinary approach.

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