Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia
The rubber crops profitability depends largely on genotypes established in plantations, meaning that clone identity must be ascertained. This work was aimed at identifying commercial clones Hevea sp. by microsatellites. Primers were designed from sequences reported in Genbank using Primer3, PrimerQu...
- Autores:
-
García R., Ibonne Aydee
González S., Sandra Milena
Montoya C., Dolly
Aristizabal, Fabio
- Tipo de recurso:
- Article of journal
- Fecha de publicación:
- 2011
- Institución:
- Universidad Nacional de Colombia
- Repositorio:
- Universidad Nacional de Colombia
- Idioma:
- spa
- OAI Identifier:
- oai:repositorio.unal.edu.co:unal/29762
- Acceso en línea:
- https://repositorio.unal.edu.co/handle/unal/29762
http://bdigital.unal.edu.co/19810/
- Palabra clave:
- 63 Agricultura y tecnologías relacionadas / Agriculture
polymorphism
molecular markers
Hevea brasiliensis
SSR
clone
PCR
natural rubber.
- Rights
- openAccess
- License
- Atribución-NoComercial 4.0 Internacional
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| dc.title.spa.fl_str_mv |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| title |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| spellingShingle |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia 63 Agricultura y tecnologías relacionadas / Agriculture polymorphism molecular markers Hevea brasiliensis SSR clone PCR natural rubber. |
| title_short |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| title_full |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| title_fullStr |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| title_full_unstemmed |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| title_sort |
Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia |
| dc.creator.fl_str_mv |
García R., Ibonne Aydee González S., Sandra Milena Montoya C., Dolly Aristizabal, Fabio |
| dc.contributor.author.spa.fl_str_mv |
García R., Ibonne Aydee González S., Sandra Milena Montoya C., Dolly Aristizabal, Fabio |
| dc.subject.ddc.spa.fl_str_mv |
63 Agricultura y tecnologías relacionadas / Agriculture |
| topic |
63 Agricultura y tecnologías relacionadas / Agriculture polymorphism molecular markers Hevea brasiliensis SSR clone PCR natural rubber. |
| dc.subject.proposal.spa.fl_str_mv |
polymorphism molecular markers Hevea brasiliensis SSR clone PCR natural rubber. |
| description |
The rubber crops profitability depends largely on genotypes established in plantations, meaning that clone identity must be ascertained. This work was aimed at identifying commercial clones Hevea sp. by microsatellites. Primers were designed from sequences reported in Genbank using Primer3, PrimerQuest and OlgoPerfect software for PCR amplification of microsatellites. The primers so obtained were thermodynamically analysed by Oligo Analyzer 3.1 software and experimentally evaluated on 12 Hevea sp. clones. The 15 of the 561 microsatellite markers were selected; they had 2- and 3-bp repeat motifs and 11- to 23-bp repeat extension ranges. The most informative ones were microsatellites amplified with SSRH103, SSRH134, SSRH510 and SSRH516 primers with seven alleles and SSRH403 primers with eight alleles. Four microsatellite markers were sufficient for discriminating 10 of the 12 clones. Clustering analysis involved all the markers on the clones evaluated here, showing Brazilian clones’ narrow genetic base compared to Asiatic ones. The current work provides new markers and joins work published by other authors for identifying and diversity studies of natural rubber clone. |
| publishDate |
2011 |
| dc.date.issued.spa.fl_str_mv |
2011-09-01 |
| dc.date.accessioned.spa.fl_str_mv |
2019-06-26T13:46:06Z |
| dc.date.available.spa.fl_str_mv |
2019-06-26T13:46:06Z |
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Artículo de revista |
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http://purl.org/coar/resource_type/c_2df8fbb1 |
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info:eu-repo/semantics/article |
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info:eu-repo/semantics/publishedVersion |
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http://purl.org/coar/resource_type/c_6501 |
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http://purl.org/coar/version/c_970fb48d4fbd8a85 |
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Text |
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http://purl.org/redcol/resource_type/ART |
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publishedVersion |
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ISSN: 2357-3732 |
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https://repositorio.unal.edu.co/handle/unal/29762 |
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http://bdigital.unal.edu.co/19810/ |
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ISSN: 2357-3732 |
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https://repositorio.unal.edu.co/handle/unal/29762 http://bdigital.unal.edu.co/19810/ |
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spa |
| language |
spa |
| dc.relation.spa.fl_str_mv |
http://revistas.unal.edu.co/index.php/agrocol/article/view/15866 |
| dc.relation.ispartof.spa.fl_str_mv |
Universidad Nacional de Colombia Revistas electrónicas UN Agronomía Colombiana Agronomía Colombiana |
| dc.relation.references.spa.fl_str_mv |
García R., Ibonne Aydee and González S., Sandra Milena and Montoya C., Dolly and Aristizabal, Fabio (2011) Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia. Agronomía Colombiana, 29 (3). pp. 359-366. ISSN 2357-3732 |
| dc.rights.spa.fl_str_mv |
Derechos reservados - Universidad Nacional de Colombia |
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http://purl.org/coar/access_right/c_abf2 |
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Atribución-NoComercial 4.0 Internacional |
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http://creativecommons.org/licenses/by-nc/4.0/ |
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info:eu-repo/semantics/openAccess |
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Atribución-NoComercial 4.0 Internacional Derechos reservados - Universidad Nacional de Colombia http://creativecommons.org/licenses/by-nc/4.0/ http://purl.org/coar/access_right/c_abf2 |
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openAccess |
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application/pdf |
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Universidad Nacional de Colombia, Facultad de Agronomía, Centro Editorial |
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Atribución-NoComercial 4.0 InternacionalDerechos reservados - Universidad Nacional de Colombiahttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2García R., Ibonne Aydeed0fca09d-2eb5-44e8-bc86-cd69da96a619300González S., Sandra Milena2844d89d-d4eb-4767-a2e9-5d3207e62544300Montoya C., Dolly28d84c2f-dcda-4d8b-8dde-97b465b9ce5b300Aristizabal, Fabio1a65ab32-171b-4bfd-a380-30a133498fbb3002019-06-26T13:46:06Z2019-06-26T13:46:06Z2011-09-01ISSN: 2357-3732https://repositorio.unal.edu.co/handle/unal/29762http://bdigital.unal.edu.co/19810/The rubber crops profitability depends largely on genotypes established in plantations, meaning that clone identity must be ascertained. This work was aimed at identifying commercial clones Hevea sp. by microsatellites. Primers were designed from sequences reported in Genbank using Primer3, PrimerQuest and OlgoPerfect software for PCR amplification of microsatellites. The primers so obtained were thermodynamically analysed by Oligo Analyzer 3.1 software and experimentally evaluated on 12 Hevea sp. clones. The 15 of the 561 microsatellite markers were selected; they had 2- and 3-bp repeat motifs and 11- to 23-bp repeat extension ranges. The most informative ones were microsatellites amplified with SSRH103, SSRH134, SSRH510 and SSRH516 primers with seven alleles and SSRH403 primers with eight alleles. Four microsatellite markers were sufficient for discriminating 10 of the 12 clones. Clustering analysis involved all the markers on the clones evaluated here, showing Brazilian clones’ narrow genetic base compared to Asiatic ones. The current work provides new markers and joins work published by other authors for identifying and diversity studies of natural rubber clone.La rentabilidad del cultivo de caucho depende en gran medida de los genotipos establecidos en plantación, por lo tanto es necesario asegurar la identidad de los clones. Este trabajo tuvo como objetivo identificar clones comerciales de Hevea sp. mediante microsatélites. Se diseñaron primers a partir de secuencias reportadas en el Genbank con los programas Primer3, PrimerQuestSM y OlgoPerfectSM para amplificación por PCR de microsatélites. Los primers obtenidos se analizaron termodinámicamente mediante el programa Oligo Analizer 3.1 y se evaluaron experimentalmente sobre 12 clones de Hevea sp. Se seleccionaron 15 de 561 marcadores microsatélites con motivos de repetición de 2 y 3 pb y rangos de extensión entre 11 y 23 repeticiones. Los más informativos fueron: con siete alelos los microsatélites amplificados con lo primers SSRH103, SSRH134, SSRH510 y SSRH516, con ocho alelos los primers SSRH403. Cuatro marcadores microsatélites fueron suficientes para discriminar diez de los 12 clones. El análisis de agrupamiento realizado con la totalidad de los marcadores sobre los clones evaluados, evidencia la estrecha base genética de los clones brasileños respecto a los asiáticos. Este trabajo aporta nuevos marcadores y se suma a los publicados por otros autores, para la identificación y estudios de diversidad de clones de caucho natural.application/pdfspaUniversidad Nacional de Colombia, Facultad de Agronomía, Centro Editorialhttp://revistas.unal.edu.co/index.php/agrocol/article/view/15866Universidad Nacional de Colombia Revistas electrónicas UN Agronomía ColombianaAgronomía ColombianaGarcía R., Ibonne Aydee and González S., Sandra Milena and Montoya C., Dolly and Aristizabal, Fabio (2011) Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombia. Agronomía Colombiana, 29 (3). pp. 359-366. ISSN 2357-373263 Agricultura y tecnologías relacionadas / Agriculturepolymorphismmolecular markersHevea brasiliensisSSRclonePCRnatural rubber.Identification in silico of ssr markers for genotyping hevea sp. clone gardens in colombiaArtículo de revistainfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1http://purl.org/coar/version/c_970fb48d4fbd8a85Texthttp://purl.org/redcol/resource_type/ARTORIGINAL15866-115255-2-PB.pdfapplication/pdf513892https://repositorio.unal.edu.co/bitstream/unal/29762/1/15866-115255-2-PB.pdf5105e84119d46a6adb29066797ebcf74MD51THUMBNAIL15866-115255-2-PB.pdf.jpg15866-115255-2-PB.pdf.jpgGenerated Thumbnailimage/jpeg8679https://repositorio.unal.edu.co/bitstream/unal/29762/2/15866-115255-2-PB.pdf.jpgedfa9f7087429325f626547d8b2cb62dMD52unal/29762oai:repositorio.unal.edu.co:unal/297622023-11-22 23:05:22.558Repositorio Institucional Universidad Nacional de Colombiarepositorio_nal@unal.edu.co |