A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2008-12-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/8/127 |
| _version_ | 1818520569394495488 |
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| author | Pfeiffer Antonella Di Gaspero Gabriele Marrazzo Maria Cipriani Guido Morgante Michele Testolin Raffaele |
| author_facet | Pfeiffer Antonella Di Gaspero Gabriele Marrazzo Maria Cipriani Guido Morgante Michele Testolin Raffaele |
| author_sort | Pfeiffer Antonella |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-11T01:39:15Z |
| format | Article |
| id | doaj.art-ce63d4c1a2c943c29247620f6b917e8f |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-11T01:39:15Z |
| publishDate | 2008-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-ce63d4c1a2c943c29247620f6b917e8f2022-12-22T01:25:07ZengBMCBMC Plant Biology1471-22292008-12-018112710.1186/1471-2229-8-127A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotypingPfeiffer AntonellaDi Gaspero GabrieleMarrazzo MariaCipriani GuidoMorgante MicheleTestolin Raffaele<p>Abstract</p> <p>Background</p> <p>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.</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2229/8/127 |
| spellingShingle | Pfeiffer Antonella Di Gaspero Gabriele Marrazzo Maria Cipriani Guido Morgante Michele Testolin Raffaele A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping BMC Plant Biology |
| title | A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping |
| title_full | A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping |
| title_fullStr | A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping |
| title_full_unstemmed | A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping |
| title_short | A set of microsatellite markers with long core repeat optimized for grape (<it>Vitis </it>spp.) genotyping |
| title_sort | set of microsatellite markers with long core repeat optimized for grape it vitis it spp genotyping |
| url | http://www.biomedcentral.com/1471-2229/8/127 |
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