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

Autores
Aballay, Maximiliano Martín; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Valentini, Gabriel Hugo; Sánchez, 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.
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Sánchez, Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina
Materia
Prunus persica
SNPs
Genotyping by sequencing
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/182275
Acceder
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Fine-tuning the performance of ddRAD-seq in the peach genomeAballay, Maximiliano MartínAguirre, Natalia CristinaFilippi, Carla ValeriaValentini, Gabriel HugoSánchez, GerardoPrunus persicaSNPsGenotyping by sequencinghttps://purl.org/becyt/ford/4.1https://purl.org/becyt/ford/4https://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4The 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.Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Sánchez, Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; ArgentinaNature Publishing Group2021-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/182275Aballay, Maximiliano Martín; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Valentini, Gabriel Hugo; Sánchez, Gerardo; Fine-tuning the performance of ddRAD-seq in the peach genome; Nature Publishing Group; Scientific Reports; 11; 1; 3-2021; 1-132045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/s41598-021-85815-0info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-85815-0info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:03:07Zoai:ri.conicet.gov.ar:11336/182275instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:03:07.776CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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
Prunus persica
SNPs
Genotyping by 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
Sánchez, Gerardo
author Aballay, Maximiliano Martín
author_facet Aballay, Maximiliano Martín
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Valentini, Gabriel Hugo
Sánchez, Gerardo
author_role author
author2 Aguirre, Natalia Cristina
Filippi, Carla Valeria
Valentini, Gabriel Hugo
Sánchez, Gerardo
author2_role author
author
author
author
dc.subject.none.fl_str_mv Prunus persica
SNPs
Genotyping by sequencing
topic Prunus persica
SNPs
Genotyping by sequencing
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.1
https://purl.org/becyt/ford/4
https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
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.
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación En Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Sánchez, Gerardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Norte. 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
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/11336/182275
Aballay, Maximiliano Martín; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Valentini, Gabriel Hugo; Sánchez, Gerardo; Fine-tuning the performance of ddRAD-seq in the peach genome; Nature Publishing Group; Scientific Reports; 11; 1; 3-2021; 1-13
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/182275
identifier_str_mv Aballay, Maximiliano Martín; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Valentini, Gabriel Hugo; Sánchez, Gerardo; Fine-tuning the performance of ddRAD-seq in the peach genome; Nature Publishing Group; Scientific Reports; 11; 1; 3-2021; 1-13
2045-2322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.nature.com/articles/s41598-021-85815-0
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-021-85815-0
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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