A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers

Abstract

The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

“…Tetranucleotide repeats are scarce in the grapevine genome but a list of potentially useful microsatellites with a core length of four nucleotides was recently identified . While SNPs avoid stuttering problems and do not require an allelic ladder for standardized genotyping, we concur with Santos that long core repeat microsatellites and a forensic standardization approach to their profiling still has considerable unexploited potential in grapevine genetics. It remains to be seen whether massively parallel sequencing‐based technologies offer sufficient advantages over STRs.…”

“…This can be attributed to the use of dinucleotide instead of tetranucleotide repeats. Tetranucleotide repeats are scarce in the grapevine genome but a list of potentially useful microsatellites with a core length of four nucleotides was recently identified [46,66]. While SNPs [67,68] avoid stuttering problems and do not require an allelic ladder for standardized genotyping, we concur with Santos [46] that long core repeat microsatellites and a forensic standardization approach [49] to their profiling still has considerable unexploited potential in grapevine genetics.…”

“…Although denaturing CE is one of the most precise and reliable sizing techniques currently available, it can still be subject to run-to-run variation resulting from differences between instruments, running conditions, the internal standards that are used, and variations in buffer composition among other things [44]. Therefore, every CE experiment performed in this work included an analysis of an allelic ladder prepared by mixing microsatellite amplicons as suggested by Butler et al for human microsatellites [45] and by Santos et al for grapevines [46].…”

Forensic genetics and genomics: Much more than just a human affair

“…These genetic markers have been applied to perform identification in a variety of food products such as olive oil [e.g., 209 , 210 ], grapevine cultivars [e.g., 211 , 212 , 213 ], composition of honey [e.g., 214 , 215 , 216 ], mushrooms [e.g., 217 , 218 , 219 ], dairy products [e.g., 220 , 221 , 222 ], seafood products [ 20 ], or meat species adulteration [ 223 ]. Additional documented cases include: i ) identification of cultivars of basmati rice [ 224 ], pome [ 225 ] and stone fruits [ 226 ], leguminosae [ 227 , 228 ], coffee [ 229 ], and tea and infusions [ 230 ]; ii ) patent misappropriation of strawberry cultivars [ 231 ]; iii ) confirmation of Protected Designation of Origin (PDO), Protected Geographical Indication (PGI), or Traditional Speciality Guaranteed (TSG) in olive [ 232 ] and grape [ 213 , 233 ] products; iv ) adulteration of traditional medicines [ 234 , 235 ] and herbs or spices [ 236 ]; v ) insufficient and erroneous food labelling, including the presence of some hidden allergens [ 237 , 238 ] or genetically modified organisms [ 239 ] (GMOs; see section Genetically modified organisms).…”

Determination of downy and powdery mildew resistance of some Vitis spp.

“…Grapes are one of the most important fruits in the world and are believed to have been cultivated in different regions globally for thousands of years (Santos et al, 2014). It is widely known that Turkey is an important centre of origin both for cultivated Vitis vinifera ssp.…”