Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach

Autores
Aballay, Maximiliano Martín; Valentini, Gabriel Hugo; Aguirre, Natalia Cristina; Filippi, Carla Valeria; Daorden, Maria Elena; Sanchez, Gerardo
Año de publicación
2019
Idioma
inglés
Tipo de recurso
Estado
versión aceptada
Descripción
Peach is a diploid (2n=2x=16) specie with a small genome (265Mb), compared to other economically important crops. Due to its self-compatibility and long generation periods, modern peach cultivars have a narrow genetic variability. Therefore novel germoplasms are continuously pursued for breeding purposes. The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost but in the case of peach, were scarcely developed. At present, a standard Genotyping By Sequencing (GBS), based in a single restriction with ApekI to reduce genome complexity, was applied in peach. We compared 6 double restrictions with the restriction generated with ApeKI to find that the combination of PstI/MboI retained the highest number of loci in concordance with in silico analysis. With this novel GBS platform, a diverse peach germoplasm collection composed of 190 genotypes was analysed. The libraries were sequenced (HiSeq 1500 Illumina) to obtain a total of 207052814 of paired-end (2x250bp) reads. The mapping against peach genome allowed the identification of 107760 SNP. Phylogenetic and population structure analyses sugested that a group of Bolivian traditional peaches and feral germoplasms of Argentine shares a common origin that probably goes back from the colony period where this specie was introduced in the American continent by the Spanish. Principal Component Analysis (PCA) from genomic data showed that these ancestral germoplasms differ largely from modern peach cultivars. Our results in combination with some outstanding trait of these genotypes (high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage their use in peach breeding programs.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Daorden, María Elena. 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
International Plant and Animal Genome XXVII Conference. San Diego, USA, 12-16 January 2019
Materia
Biotecnología Vegetal
Prunus Persica
Durazno
Fitomejoramiento
Genómica
Mapas Genéticos
Plant Biotechnology
Peaches
Plant Breeding
Genomics
Genetics Maps
Tecnología NGS
Next Generation Sequencing Technologies
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:20.500.12123/4682
Acceder
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oai_identifier_str oai:localhost:20.500.12123/4682
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network_name_str INTA Digital (INTA)
spelling Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peachAballay, Maximiliano MartínValentini, Gabriel HugoAguirre, Natalia CristinaFilippi, Carla ValeriaDaorden, Maria ElenaSanchez, GerardoBiotecnología VegetalPrunus PersicaDuraznoFitomejoramientoGenómicaMapas GenéticosPlant BiotechnologyPeachesPlant BreedingGenomicsGenetics MapsTecnología NGSNext Generation Sequencing TechnologiesPeach is a diploid (2n=2x=16) specie with a small genome (265Mb), compared to other economically important crops. Due to its self-compatibility and long generation periods, modern peach cultivars have a narrow genetic variability. Therefore novel germoplasms are continuously pursued for breeding purposes. The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost but in the case of peach, were scarcely developed. At present, a standard Genotyping By Sequencing (GBS), based in a single restriction with ApekI to reduce genome complexity, was applied in peach. We compared 6 double restrictions with the restriction generated with ApeKI to find that the combination of PstI/MboI retained the highest number of loci in concordance with in silico analysis. With this novel GBS platform, a diverse peach germoplasm collection composed of 190 genotypes was analysed. The libraries were sequenced (HiSeq 1500 Illumina) to obtain a total of 207052814 of paired-end (2x250bp) reads. The mapping against peach genome allowed the identification of 107760 SNP. Phylogenetic and population structure analyses sugested that a group of Bolivian traditional peaches and feral germoplasms of Argentine shares a common origin that probably goes back from the colony period where this specie was introduced in the American continent by the Spanish. Principal Component Analysis (PCA) from genomic data showed that these ancestral germoplasms differ largely from modern peach cultivars. Our results in combination with some outstanding trait of these genotypes (high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage their use in peach breeding programs.EEA San PedroFil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Daorden, María Elena. 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; Argentina2019-03-20T13:45:23Z2019-03-20T13:45:23Z2019info:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6670info:ar-repo/semantics/posterinfo:eu-repo/semantics/conferencePosterapplication/pdfhttp://hdl.handle.net/20.500.12123/4682International Plant and Animal Genome XXVII Conference. San Diego, USA, 12-16 January 2019reponame: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)2025-10-23T11:16:52Zoai:localhost:20.500.12123/4682instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-23 11:16:53.3INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
title Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
spellingShingle Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
Aballay, Maximiliano Martín
Biotecnología Vegetal
Prunus Persica
Durazno
Fitomejoramiento
Genómica
Mapas Genéticos
Plant Biotechnology
Peaches
Plant Breeding
Genomics
Genetics Maps
Tecnología NGS
Next Generation Sequencing Technologies
title_short Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
title_full Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
title_fullStr Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
title_full_unstemmed Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
title_sort Novel NGS-Based genomic platform reveals unexploited variability of Prunus persica (L. Batch) for future genetic breeding of peach
dc.creator.none.fl_str_mv Aballay, Maximiliano Martín
Valentini, Gabriel Hugo
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Daorden, Maria Elena
Sanchez, Gerardo
author Aballay, Maximiliano Martín
author_facet Aballay, Maximiliano Martín
Valentini, Gabriel Hugo
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Daorden, Maria Elena
Sanchez, Gerardo
author_role author
author2 Valentini, Gabriel Hugo
Aguirre, Natalia Cristina
Filippi, Carla Valeria
Daorden, Maria Elena
Sanchez, Gerardo
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Biotecnología Vegetal
Prunus Persica
Durazno
Fitomejoramiento
Genómica
Mapas Genéticos
Plant Biotechnology
Peaches
Plant Breeding
Genomics
Genetics Maps
Tecnología NGS
Next Generation Sequencing Technologies
topic Biotecnología Vegetal
Prunus Persica
Durazno
Fitomejoramiento
Genómica
Mapas Genéticos
Plant Biotechnology
Peaches
Plant Breeding
Genomics
Genetics Maps
Tecnología NGS
Next Generation Sequencing Technologies
dc.description.none.fl_txt_mv Peach is a diploid (2n=2x=16) specie with a small genome (265Mb), compared to other economically important crops. Due to its self-compatibility and long generation periods, modern peach cultivars have a narrow genetic variability. Therefore novel germoplasms are continuously pursued for breeding purposes. The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost but in the case of peach, were scarcely developed. At present, a standard Genotyping By Sequencing (GBS), based in a single restriction with ApekI to reduce genome complexity, was applied in peach. We compared 6 double restrictions with the restriction generated with ApeKI to find that the combination of PstI/MboI retained the highest number of loci in concordance with in silico analysis. With this novel GBS platform, a diverse peach germoplasm collection composed of 190 genotypes was analysed. The libraries were sequenced (HiSeq 1500 Illumina) to obtain a total of 207052814 of paired-end (2x250bp) reads. The mapping against peach genome allowed the identification of 107760 SNP. Phylogenetic and population structure analyses sugested that a group of Bolivian traditional peaches and feral germoplasms of Argentine shares a common origin that probably goes back from the colony period where this specie was introduced in the American continent by the Spanish. Principal Component Analysis (PCA) from genomic data showed that these ancestral germoplasms differ largely from modern peach cultivars. Our results in combination with some outstanding trait of these genotypes (high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage their use in peach breeding programs.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Aguirre, Natalia Cristina. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Daorden, María Elena. 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 Peach is a diploid (2n=2x=16) specie with a small genome (265Mb), compared to other economically important crops. Due to its self-compatibility and long generation periods, modern peach cultivars have a narrow genetic variability. Therefore novel germoplasms are continuously pursued for breeding purposes. The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost but in the case of peach, were scarcely developed. At present, a standard Genotyping By Sequencing (GBS), based in a single restriction with ApekI to reduce genome complexity, was applied in peach. We compared 6 double restrictions with the restriction generated with ApeKI to find that the combination of PstI/MboI retained the highest number of loci in concordance with in silico analysis. With this novel GBS platform, a diverse peach germoplasm collection composed of 190 genotypes was analysed. The libraries were sequenced (HiSeq 1500 Illumina) to obtain a total of 207052814 of paired-end (2x250bp) reads. The mapping against peach genome allowed the identification of 107760 SNP. Phylogenetic and population structure analyses sugested that a group of Bolivian traditional peaches and feral germoplasms of Argentine shares a common origin that probably goes back from the colony period where this specie was introduced in the American continent by the Spanish. Principal Component Analysis (PCA) from genomic data showed that these ancestral germoplasms differ largely from modern peach cultivars. Our results in combination with some outstanding trait of these genotypes (high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage their use in peach breeding programs.
publishDate 2019
dc.date.none.fl_str_mv 2019-03-20T13:45:23Z
2019-03-20T13:45:23Z
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6670
info:ar-repo/semantics/poster
info:eu-repo/semantics/conferencePoster
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/4682
url http://hdl.handle.net/20.500.12123/4682
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.source.none.fl_str_mv International Plant and Animal Genome XXVII Conference. San Diego, USA, 12-16 January 2019
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 12.982451

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