Fine-tuning the performance of ddRAD-seq in the peach genome

Autores
Aballay, Maximiliano Martín; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Valentini, Gabriel Hugo; Sanchez, Gerardo
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina.
Fil: Aballay, Maximiliano Martín. Consejo Nacional de Investigaciones Científica y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.
Fil: Aguirre, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina.
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fuente
Scientific reports 11 : 6298 (2021)
Materia
Durazno
Prunus persica
Marcadores Genéticos
Genómica
Fitomejoramiento
Genética
Peaches
Genetic Markers
Genomics
Plant Breeding
Genetics
Secuenciación
Sequencing
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/8987
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network_name_str INTA Digital (INTA)
spelling Fine-tuning the performance of ddRAD-seq in the peach genomeAballay, Maximiliano MartínAguirre, Natalia CristinaFilippi, Carla ValeriaValentini, Gabriel HugoSanchez, GerardoDuraznoPrunus persicaMarcadores GenéticosGenómicaFitomejoramientoGenéticaPeachesGenetic MarkersGenomicsPlant BreedingGeneticsSecuenciaciónSequencingThe advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.EEA San PedroFil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina.Fil: Aballay, Maximiliano Martín. Consejo Nacional de Investigaciones Científica y Técnicas; ArgentinaFil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.Fil: Aguirre, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina.Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaSpringer Nature2021-03-29T11:19:42Z2021-03-29T11:19:42Z2021-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/8987https://www.nature.com/articles/s41598-021-85815-02045-2322https://doi.org/10.1038/s41598-021-85815-0Scientific reports 11 : 6298 (2021)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:48:49Zoai:localhost:20.500.12123/8987instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:48:49.838INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Fine-tuning the performance of ddRAD-seq in the peach genome
title Fine-tuning the performance of ddRAD-seq in the peach genome
spellingShingle Fine-tuning the performance of ddRAD-seq in the peach genome
Aballay, Maximiliano Martín
Durazno
Prunus persica
Marcadores Genéticos
Genómica
Fitomejoramiento
Genética
Peaches
Genetic Markers
Genomics
Plant Breeding
Genetics
Secuenciación
Sequencing
title_short Fine-tuning the performance of ddRAD-seq in the peach genome
title_full Fine-tuning the performance of ddRAD-seq in the peach genome
title_fullStr Fine-tuning the performance of ddRAD-seq in the peach genome
title_full_unstemmed Fine-tuning the performance of ddRAD-seq in the peach genome
title_sort Fine-tuning the performance of ddRAD-seq in the peach genome
dc.creator.none.fl_str_mv Aballay, Maximiliano Martín
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Valentini, Gabriel Hugo
Sanchez, Gerardo
author Aballay, Maximiliano Martín
author_facet Aballay, Maximiliano Martín
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Valentini, Gabriel Hugo
Sanchez, Gerardo
author_role author
author2 Aguirre, Natalia Cristina
Filippi, Carla Valeria
Valentini, Gabriel Hugo
Sanchez, Gerardo
author2_role author
author
author
author
dc.subject.none.fl_str_mv Durazno
Prunus persica
Marcadores Genéticos
Genómica
Fitomejoramiento
Genética
Peaches
Genetic Markers
Genomics
Plant Breeding
Genetics
Secuenciación
Sequencing
topic Durazno
Prunus persica
Marcadores Genéticos
Genómica
Fitomejoramiento
Genética
Peaches
Genetic Markers
Genomics
Plant Breeding
Genetics
Secuenciación
Sequencing
dc.description.none.fl_txt_mv The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina.
Fil: Aballay, Maximiliano Martín. Consejo Nacional de Investigaciones Científica y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.
Fil: Aguirre, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina.
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
description The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.
publishDate 2021
dc.date.none.fl_str_mv 2021-03-29T11:19:42Z
2021-03-29T11:19:42Z
2021-03
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/8987
https://www.nature.com/articles/s41598-021-85815-0
2045-2322
https://doi.org/10.1038/s41598-021-85815-0
url http://hdl.handle.net/20.500.12123/8987
https://www.nature.com/articles/s41598-021-85815-0
https://doi.org/10.1038/s41598-021-85815-0
identifier_str_mv 2045-2322
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv Scientific reports 11 : 6298 (2021)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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score 12.623145

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