Genomic profiling of plastid DNA variation in the Mediterranean olive tree

[Background] Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened...

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Autores: Besnard, Guillaume, Hernández Molina, Pilar, Khadari, Bouchaib, Dorado, Gabriel, Savolainen, Vincent
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2011
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/39023
Acceso en línea:http://hdl.handle.net/10261/39023
Access Level:acceso abierto
Palabra clave:Olive trees
Plastid Genome
Microsatellite Motif
cpDNA haplotypes
cpDNA Variation
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spelling Genomic profiling of plastid DNA variation in the Mediterranean olive treeBesnard, GuillaumeHernández Molina, PilarKhadari, BouchaibDorado, GabrielSavolainen, VincentOlive treesPlastid GenomeMicrosatellite MotifcpDNA haplotypescpDNA Variation[Background] Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.[Results] Eight complete cpDNA genomes of Olea were sequenced de novo. The nucleotide divergence between olive cpDNA lineages was low and not exceeding 0.07%. Based on these sequences, markers were developed for studying two single nucleotide substitutions and length polymorphism of 62 regions (with variable microsatellite motifs or other indels). They were then used to genotype the cpDNA variation in cultivated and wild Mediterranean olive trees (315 individuals). Forty polymorphic loci were detected on this sample, allowing the distinction of 22 haplotypes belonging to the three Mediterranean cpDNA lineages known as E1, E2 and E3. The discriminating power of cpDNA variation was particularly low for the cultivated olive tree with one predominating haplotype, but more diversity was detected in wild populations.[Conclusions] We propose a method for a rapid characterisation of the Mediterranean olive germplasm. The low variation in the cultivated olive tree indicated that the utility of cpDNA variation for forensic analyses is limited to rare haplotypes. In contrast, the high cpDNA variation in wild populations demonstrated that our markers may be useful for phylogeographic and populations genetic studies in O. europaea.This work was funded by the Intra- European fellowship PIEF-GA-2008-220813 to GB. PH was supported by MICINN grant AGL2010-17316 from the Spanish Ministry of Science and Innovation. GD was supported by projects 041/C/2007, 75/C/2009 & 56/C/ 2010 of “Consejería de Agricultura y Pesca, Junta de Andalucía"; “Grupo PAI” AGR-248 of “Junta de Andalucía"; and “Ayuda a Grupos” of “Universidad de Córdoba” (Spain). VS was supported by grants from the ERC, Leverhulme Trust, NERC and the Royal Society.Peer ReviewedBioMed CentralEuropean CommissionMinisterio de Ciencia e Innovación (España)Junta de AndalucíaUniversidad de Córdoba (España)European Research CouncilLeverhulme TrustNatural Environment Research Council (UK)Royal Society of Chemistry (UK)2011201120112011info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/39023reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1186/1471-2229-11-80info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/390232026-05-22T06:33:51Z
dc.title.none.fl_str_mv Genomic profiling of plastid DNA variation in the Mediterranean olive tree
title Genomic profiling of plastid DNA variation in the Mediterranean olive tree
spellingShingle Genomic profiling of plastid DNA variation in the Mediterranean olive tree
Besnard, Guillaume
Olive trees
Plastid Genome
Microsatellite Motif
cpDNA haplotypes
cpDNA Variation
title_short Genomic profiling of plastid DNA variation in the Mediterranean olive tree
title_full Genomic profiling of plastid DNA variation in the Mediterranean olive tree
title_fullStr Genomic profiling of plastid DNA variation in the Mediterranean olive tree
title_full_unstemmed Genomic profiling of plastid DNA variation in the Mediterranean olive tree
title_sort Genomic profiling of plastid DNA variation in the Mediterranean olive tree
dc.creator.none.fl_str_mv Besnard, Guillaume
Hernández Molina, Pilar
Khadari, Bouchaib
Dorado, Gabriel
Savolainen, Vincent
author Besnard, Guillaume
author_facet Besnard, Guillaume
Hernández Molina, Pilar
Khadari, Bouchaib
Dorado, Gabriel
Savolainen, Vincent
author_role author
author2 Hernández Molina, Pilar
Khadari, Bouchaib
Dorado, Gabriel
Savolainen, Vincent
author2_role author
author
author
author
dc.contributor.none.fl_str_mv European Commission
Ministerio de Ciencia e Innovación (España)
Junta de Andalucía
Universidad de Córdoba (España)
European Research Council
Leverhulme Trust
Natural Environment Research Council (UK)
Royal Society of Chemistry (UK)
dc.subject.none.fl_str_mv Olive trees
Plastid Genome
Microsatellite Motif
cpDNA haplotypes
cpDNA Variation
topic Olive trees
Plastid Genome
Microsatellite Motif
cpDNA haplotypes
cpDNA Variation
description [Background] Characterisation of plastid genome (or cpDNA) polymorphisms is commonly used for phylogeographic, population genetic and forensic analyses in plants, but detecting cpDNA variation is sometimes challenging, limiting the applications of such an approach. In the present study, we screened cpDNA polymorphism in the olive tree (Olea europaea L.) by sequencing the complete plastid genome of trees with a distinct cpDNA lineage. Our objective was to develop new markers for a rapid genomic profiling (by Multiplex PCRs) of cpDNA haplotypes in the Mediterranean olive tree.
publishDate 2011
dc.date.none.fl_str_mv 2011
2011
2011
2011
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/39023
url http://hdl.handle.net/10261/39023
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1186/1471-2229-11-80
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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