Open Access Research article

A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

Guido Cipriani1*, Maria Teresa Marrazzo1, Gabriele Di Gaspero12, Antonella Pfeiffer1, Michele Morgante12 and Raffaele Testolin12

Author Affiliations

1 Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy

2 Istituto di Genomica Applicata, Parco Scientifico e Tecnologico 'Luigi Danieli' Udine, Italy

For all author emails, please log on.

BMC Plant Biology 2008, 8:127  doi:10.1186/1471-2229-8-127

Published: 16 December 2008

Abstract

Background

Individual fingerprinting based on molecular markers has become a popular tool for studies of population genetics and analysis of genetic diversity in germplasm collections, including the solution of synonymy/homonymy and analysis of paternity and kinship.

Genetic profiling of individuals is nowadays based on SSR (Simple Sequence Repeat) markers, which have a number of positive features that make them superior to any other molecular marker developed so far. In humans, SSRs with core repeats three to five nucleotides long are preferred because neighbour alleles are more easily separated and distinguished from each other; while in plants, SSRs with shorter repeats, namely two-nucleotides long, are still in use although they suffer lower separation of neighbour alleles and uncomfortable stuttering.

Results

New microsatellite markers, containing tri-, tetra-, and penta-nucleotide repeats, were selected from a total of 26,962 perfect microsatellites in the genome sequence of nearly homozogous grapevine PN40024, assembled from reads covering 8.4 X genome equivalents.

Long nucleotide repeats were selected for fingerprinting, as previously done in many species including humans. The new grape SSR markers were tested for their reproducibility and information content in a panel of 48 grape cultivars. Allelic segregation was tested in progenies derived from two controlled crosses.

Conclusion

A list of 38 markers with excellent quality of peaks, high power of discrimination, and uniform genome distribution (1–3 markers/chromosome), is proposed for grape genotyping. The reasons for exclusion are given for those that were discarded. The construction of marker-specific allelic ladders is also described, and their use is recommended to harmonise allelic calls and make the data obtained with different equipment and by different laboratories fully comparable.