Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Abstract

The use of microsatellite markers in large-scale genetic studies is limited by its low throughput and high cost and labor requirements. Here, we provide a panel of 45 multiplex PCRs for fast and cost-efficient genome-wide fluorescencebased microsatellite analysis in grapevine. The developed multiplex PCRs panel (with up to 15-plex) enables the scoring of 270 loci covering all the grapevine genome (9 to 20 loci/chromosome) using only 45 PCRs and sequencer runs. The 45 multiplex PCRs were validated using a diverse grapevine collection of 207 accessions, selected to represent most of the cultivated Vitis vinifera genetic diversity. Particular attention was paid to quality control throughout the whole process (assay replication, null allele detection, ease of scoring). Genetic diversity summary statistics and features of electrophoretic profiles for each studied marker are provided, as are the genotypes of 25 common cultivars that could be used as references in other studies.

Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs

“…A set of 17 grapevine SSR markers well characterized in previous studies [22,[29][30][31][32] were used, including ten developed by Merdinoglu et al (2005) [33] (VVIn74, VVIr09, VVIp25b, VVIn56, VVIn52, VVIq57, VVIp31, VVIp77, VVIv36, VVIr21) and seven suggested by the guidelines of the European scientific community for universal grapevine identification, characterization, standardization, and exchange of information [34,35]: VVS2 [36], VVMD5, VVMD7 [37], VVMD25, VVMD27 [38], VrZAG62, and VrZAG79 [39]. One primer in each primer pair was 5' labeled with one of the following fluorescent dyes: 6-FAM, PET, NED, or VIC.…”

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).…”

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

“…A panel of 45 multiplex microsatellite PCRs was recently suggested by Zarouri et al. but needs validation.…”

“…This lack of discrimination is unsurprising given that the Combined DNA index system for human identification uses 13 microsatellite loci [58] and at least nine microsatellites are recommended for kinship studies in grapevine [50,59]. A panel of 45 multiplex microsatellite PCRs was recently suggested by Zarouri et al [60] but needs validation.…”