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Abstract
Restriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling. This has become one of the most popular genotyping approaches for breeding, conservation, and evolution studies in model and non-model plant species. However, universal protocols do not always adapt well to non-model species. Herein, this study [ver mas...]
dc.contributor.authorAguirre, Natalia Cristina
dc.contributor.authorFilippi, Carla Valeria
dc.contributor.authorZaina, Giusi
dc.contributor.authorRivas, Juan Gabriel
dc.contributor.authorAcuña, Cintia Vanesa
dc.contributor.authorVillalba, Pamela Victoria
dc.contributor.authorGarcia, Martin Nahuel
dc.contributor.authorGonzalez, Sergio
dc.contributor.authorRivarola, Maximo Lisandro
dc.contributor.authorMartinez, Maria Carolina
dc.contributor.authorPuebla, Andrea Fabiana
dc.contributor.authorMorgante, Michele
dc.contributor.authorHopp, Horacio Esteban
dc.contributor.authorPaniego, Norma Beatriz
dc.contributor.authorMarcucci Poltri, Susana Noemi
dc.date.accessioned2019-10-31T15:36:37Z
dc.date.available2019-10-31T15:36:37Z
dc.date.issued2019-08
dc.identifier.issn2073-4395
dc.identifier.otherhttps://doi.org/10.3390/agronomy9090484
dc.identifier.urihttps://www.mdpi.com/2073-4395/9/9/484/htm
dc.identifier.urihttp://hdl.handle.net/20.500.12123/6254
dc.description.abstractRestriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling. This has become one of the most popular genotyping approaches for breeding, conservation, and evolution studies in model and non-model plant species. However, universal protocols do not always adapt well to non-model species. Herein, this study reports the development of an optimized and detailed ddRADseq protocol in Eucalyptus dunnii, a non-model species, which combines different aspects of published methodologies. The initial protocol was established using only two samples by selecting the best combination of enzymes and through optimal size selection and simplifying lab procedures. Both single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were determined with high accuracy after applying stringent bioinformatics settings and quality filters, with and without a reference genome. To scale it up to 24 samples, we added barcoded adapters. We also applied automatic size selection, and therefore obtained an optimal number of loci, the expected SNP locus density, and genome-wide distribution. Reliability and cross-sequencing platform compatibility were verified through dissimilarity coefficients of 0.05 between replicates. To our knowledge, this optimized ddRADseq protocol will allow users to go from the DNA sample to genotyping data in a highly accessible and reproducible way.eng
dc.formatapplication/pdfes_AR
dc.language.isoenges_AR
dc.publisherMDPIes_AR
dc.relationinfo:eu-repograntAgreement/INTA/PNBIO/1131042/AR./Genómica aplicada al mejoramiento molecular.es_AR
dc.rightsinfo:eu-repo/semantics/openAccesses_AR
dc.sourceAgronomy 9 (9) : 484 (Agosto 2019)es_AR
dc.subjectSingle Nucleotide Polymorphismeng
dc.subjectPolimorfismo de un Solo Nucleótidoes_AR
dc.subjectGenotypeseng
dc.subjectGenotiposes_AR
dc.subjectEucalyptuses_AR
dc.subjectGenetic Markerseng
dc.subjectMarcadores Genéticoseng
dc.subjectDNA Sequenceeng
dc.subjectSecuencia de ADNes_AR
dc.subject.otherEucalyptus dunnii
dc.titleOptimizing ddRADseq in non-model species: a case study in Eucalyptus dunnii maidenes_AR
dc.typeinfo:ar-repo/semantics/artículoes_AR
dc.typeinfo:eu-repo/semantics/articlees_AR
dc.typeinfo:eu-repo/semantics/publishedVersiones_AR
dc.description.origenInstituto de Biotecnologíaes_AR
dc.description.filFil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Zaina, Giusi. University of Udine. Department of Agricultural, Food, Environmental and Animal Sciences; Italiaes_AR
dc.description.filFil: Rivas, Juan Gabriel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Villalba, Pamela Victoria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Garcia, Martin Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Gonzalez, Sergio Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Martinez, Maria Carolina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Morgante, Michele. University of Udine. Department of Agricultural, Food, Environmental and Animal Sciences; Italiaes_AR
dc.description.filFil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.description.filFil: Marcucci Poltri, Susana Noemi. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentinaes_AR
dc.subtypecientifico


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