PCR-mediated recombination in development of microsatellite markers: mechanism and implications
Protocols for microsatellite-enrichment libraries have been widely applied to several species in order to supply the most informative molecular markers for population and inbreeding studies. One drawback of these protocols is the ratio of designed primer pairs that fail to amplify the expected fragm...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Sociedade Brasileira de Genética
2008-01-01
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| Series: | Genetics and Molecular Biology |
| Subjects: | |
| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000100012 |
| _version_ | 1818198400116457472 |
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| author | Paula A. Roratto Darine Buchmann Sandro Santos Marlise L. Bartholomei-Santos |
| author_facet | Paula A. Roratto Darine Buchmann Sandro Santos Marlise L. Bartholomei-Santos |
| author_sort | Paula A. Roratto |
| collection | DOAJ |
| description | Protocols for microsatellite-enrichment libraries have been widely applied to several species in order to supply the most informative molecular markers for population and inbreeding studies. One drawback of these protocols is the ratio of designed primer pairs that fail to amplify the expected fragment, even after exhaustive optimization attempts. A possible cause of unsuccessful microsatellite primers may be that such loci are artifacts resulting from chimeric PCR products, instead of real genomic sequences. The microsatellite-enriched library constructed for Aegla longirostri (Crustacea, Decapoda, Anomura) showed that 29% of sequenced clones were chimeric products because these sequences shared one of the flanking regions around the same repeat motif but not the other. PCR-mediated recombination is a well-known event described for several procedures in which related sequences are used as a template. We have associated this phenomenon with microsatellite marker development. This study explained the high ratio of recombinant sequences generated in the A. longirostri microsatellite-enriched library. We discuss the mechanism and implications of PCR chimeric-product formation during microsatellite isolation. |
| first_indexed | 2024-12-12T02:05:16Z |
| format | Article |
| id | doaj.art-98fcf01785db4590a31cd480f60f5d85 |
| institution | Directory Open Access Journal |
| issn | 1415-4757 1678-4685 |
| language | English |
| last_indexed | 2024-12-12T02:05:16Z |
| publishDate | 2008-01-01 |
| publisher | Sociedade Brasileira de Genética |
| record_format | Article |
| series | Genetics and Molecular Biology |
| spelling | doaj.art-98fcf01785db4590a31cd480f60f5d852022-12-22T00:42:04ZengSociedade Brasileira de GenéticaGenetics and Molecular Biology1415-47571678-46852008-01-01311586310.1590/S1415-47572008000100012PCR-mediated recombination in development of microsatellite markers: mechanism and implicationsPaula A. RorattoDarine BuchmannSandro SantosMarlise L. Bartholomei-SantosProtocols for microsatellite-enrichment libraries have been widely applied to several species in order to supply the most informative molecular markers for population and inbreeding studies. One drawback of these protocols is the ratio of designed primer pairs that fail to amplify the expected fragment, even after exhaustive optimization attempts. A possible cause of unsuccessful microsatellite primers may be that such loci are artifacts resulting from chimeric PCR products, instead of real genomic sequences. The microsatellite-enriched library constructed for Aegla longirostri (Crustacea, Decapoda, Anomura) showed that 29% of sequenced clones were chimeric products because these sequences shared one of the flanking regions around the same repeat motif but not the other. PCR-mediated recombination is a well-known event described for several procedures in which related sequences are used as a template. We have associated this phenomenon with microsatellite marker development. This study explained the high ratio of recombinant sequences generated in the A. longirostri microsatellite-enriched library. We discuss the mechanism and implications of PCR chimeric-product formation during microsatellite isolation.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000100012chimeric PCR productmicrosatellite isolationrecombinationsimple sequence repeats (SSR) |
| spellingShingle | Paula A. Roratto Darine Buchmann Sandro Santos Marlise L. Bartholomei-Santos PCR-mediated recombination in development of microsatellite markers: mechanism and implications Genetics and Molecular Biology chimeric PCR product microsatellite isolation recombination simple sequence repeats (SSR) |
| title | PCR-mediated recombination in development of microsatellite markers: mechanism and implications |
| title_full | PCR-mediated recombination in development of microsatellite markers: mechanism and implications |
| title_fullStr | PCR-mediated recombination in development of microsatellite markers: mechanism and implications |
| title_full_unstemmed | PCR-mediated recombination in development of microsatellite markers: mechanism and implications |
| title_short | PCR-mediated recombination in development of microsatellite markers: mechanism and implications |
| title_sort | pcr mediated recombination in development of microsatellite markers mechanism and implications |
| topic | chimeric PCR product microsatellite isolation recombination simple sequence repeats (SSR) |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000100012 |
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