Using Simple Sequence Repeats (SSRs) for DNA Fingerprinting Germplasm Accessions of Grape (Vitis L.) Species

Abstract

<jats:p>The USDA-ARS <jats:italic>Vitis</jats:italic> genetic resources collections in Geneva, N.Y., and Davis, Calif., contain ≈3600 accessions of &gt;35 species. Accurate and unambiguous identification of these grapes is essential for efficient and effective use of this germplasm. Previous workers have successfully used polymerase chain reaction (PCR)-generated SSRs to fingerprint cultivars of the wine and table grape species, <jats:italic>V. vinifera.</jats:italic> Building on this work, we conducted a test of five previously characterized SSR loci on 110 accessions of 25 grape taxa (21 <jats:italic>Vitis</jats:italic> species and 4 hybrids) to determine if they would satisfy our need for identifying cultivars within the USDA-ARS grape collections. Scorable SSR fragments were produced with all 550 primer-accession combinations, with no null loci observed. The loci were highly polymorphic, with 16 to 38 different alleles found at a locus. Heterozygosity values ranged from 0.464 to 0.818, while gene diversity values ranged from 0.875 to 0.955. Discrimination power at a locus varied from a low of 0.947 to a high of 0.987. Combined discrimination power of all loci was effectively 1.000, with 2 chances in 100,000,000 that two sexually, independently derived grape accessions would not be distinguishable using this set of five SSR loci. Two plants in the study that had previously been classified as belonging to different grape species were shown to have identical SSR fingerprints, showing that they almost certainly possessed the same genotype. Because SSR markers are codominant and highly polymorphic and SSR loci are generally conserved across a range of related species, we strongly recommend SSRs for fingerprinting not only grape, but other clonal genetic resources collections as well.</jats:p>

Development of a standard set of microsatellite reference alleles for identification of grape cultivars

“…For example, in a work on 105 accessions of 16 American Vitis species (found in the pedigrees of almost every known hybrid), 25 and 23 alleles were observed for VVS2 and VVMD7, respectively (Lamboy and Alpha 1998). The allele ranges, however, were very similar compared to our work.…”

“…Polymorphism information content (PIC) and discrimination power were calculated according to Lamboy and Alpha (1998).…”

Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm

“…Levels of polymorphism in our study were considerably higher than 2-4 alleles per locus, reported by Cipriani et al (1999) andSosinski et al (2000) for the predominantly self-pollinating peach. Higher values have been reported for outcrossing, fruit-bearing perennials such as apple, with 8.2 and 12.1 (Gianfranceschi et al 1998;Hokanson et al 1998 respectively); sour cherry, 10.7 (Cantini et al 2001); and grape, 27.4 alleles per locus (Lamboy and Alpha 1998). In our study, observed heterozygosity averaged over the 14 loci was 0.517, higher than the mean value reported for SSRs in peach (0.32, Cipriani et al 1999) and lower than values detected in apple (0.693, Hokanson et al 1998;0.78, Gianfranceschi et al 1998) andcherry (0.946, Cantini et al 2001).…”

Molecular linkage maps of Vitis vinifera L. and Vitis riparia Mchx

“…Within the Vitaceae, a high degree of conservation in the microsatellites flanking regions from V. vinifera is observed across a number of taxa (Sefc et al 1999;Di Gaspero et al 2000;Rossetto et al 2002). The versatility of grape SSRs (Thomas and Scott 1993) has been widely explored for typing grapevine cultivars in order to facilitate the management of grapevine collections and control the trade of plant material (Grando and Frisinghelli 1998;Lamboy and Alpha 1998;Franks et al 2002). Currently, the development of new microsatellite sequences and the increasing number of mapping projects are exploiting the potential of SSRs to integrate genetic maps and to generate a common reference map for grape.…”