The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces

Autores
Aballay, Maximiliano Martín; Ksouri, Najla; Valentini, Gabriel Hugo; Puebla, Andrea Fabiana; Gogorcena Aoiz, Yolanda; Sanchez, Gerardo
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión borrador
Descripción
The advance of next generation sequencing (NGS) technologies allows the implementation of high-throughput genotyping at a reasonable cost. This open the possibility to learn more about phylogenetic relationships, genetic variability, and the development of new genetic markers for breeding purposes. In this work a previous developed ddRAD-seq platform was applied for the genotyping of two peach collections curated at the EEA San Pedro (237 genotypes) and the EE Aula Dei (89 genotypes). Here we present a joint analysis of a total of 798×106 of paired-end (2×250 bp) reads belonging to 326 genotypes (2,45M reads genotype-1). A total of 564,382 SNPs were discovered and a reduced data set composed of 10,576 SNP (MAF >1% and missing data <10%) was used in a combination of analyses (principal component analysis, population structure and phylogeny). The results showed that the ancestral germplasms differ largely from modern peach cultivars. In addition, genetic relationships between American landraces (North American and Bolivian), American ferals (Argentinian) and European landraces (Spanish and Italian) were revealed suggesting a common origin which probably reflect the introduction of germplasm by the Spaniards during the colonization period. These results with some outstanding traits of ancestral genotypes (fruit quality, high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage the usage of this germplasm on breeding programs for the development of new varieties with agricultural impact.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.
Fil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fuente
Acta horticulturae 1352 : 81-88. (Dec. 2022)
Materia
Prunus persica
Filogenética
Variación Genética
Secuenciación de Alto Rendimiento
Fitomejoramiento
Durazno
Biotecnología Vegetal
Phylogenetics
Genetic Variation
High-throughput Sequencing
Plant Breeding
Peaches
Plant Biotechnology
NGS
Next Generation Sequencing
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/13837
Acceder
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oai_identifier_str oai:localhost:20.500.12123/13837
network_acronym_str INTADig
repository_id_str l
network_name_str INTA Digital (INTA)
spelling The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landracesAballay, Maximiliano MartínKsouri, NajlaValentini, Gabriel HugoPuebla, Andrea FabianaGogorcena Aoiz, YolandaSanchez, GerardoPrunus persicaFilogenéticaVariación GenéticaSecuenciación de Alto RendimientoFitomejoramientoDuraznoBiotecnología VegetalPhylogeneticsGenetic VariationHigh-throughput SequencingPlant BreedingPeachesPlant BiotechnologyNGSNext Generation SequencingThe advance of next generation sequencing (NGS) technologies allows the implementation of high-throughput genotyping at a reasonable cost. This open the possibility to learn more about phylogenetic relationships, genetic variability, and the development of new genetic markers for breeding purposes. In this work a previous developed ddRAD-seq platform was applied for the genotyping of two peach collections curated at the EEA San Pedro (237 genotypes) and the EE Aula Dei (89 genotypes). Here we present a joint analysis of a total of 798×106 of paired-end (2×250 bp) reads belonging to 326 genotypes (2,45M reads genotype-1). A total of 564,382 SNPs were discovered and a reduced data set composed of 10,576 SNP (MAF >1% and missing data <10%) was used in a combination of analyses (principal component analysis, population structure and phylogeny). The results showed that the ancestral germplasms differ largely from modern peach cultivars. In addition, genetic relationships between American landraces (North American and Bolivian), American ferals (Argentinian) and European landraces (Spanish and Italian) were revealed suggesting a common origin which probably reflect the introduction of germplasm by the Spaniards during the colonization period. These results with some outstanding traits of ancestral genotypes (fruit quality, high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage the usage of this germplasm on breeding programs for the development of new varieties with agricultural impact.EEA San PedroFil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; EspañaFil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.Fil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; EspañaFil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaISHS2023-01-06T10:48:47Z2023-01-06T10:48:47Z2022-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/drafthttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/13837https://www.actahort.org/books/1352/1352_11.htm978-94-62613-52-2 2406-6168https://doi.org/10.17660/ActaHortic.2022.1352.11Acta horticulturae 1352 : 81-88. (Dec. 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.info:eu-repo/semantics/restrictedAccess2025-09-04T09:49:41Zoai:localhost:20.500.12123/13837instacron: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 09:49:41.496INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
title The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
spellingShingle The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
Aballay, Maximiliano Martín
Prunus persica
Filogenética
Variación Genética
Secuenciación de Alto Rendimiento
Fitomejoramiento
Durazno
Biotecnología Vegetal
Phylogenetics
Genetic Variation
High-throughput Sequencing
Plant Breeding
Peaches
Plant Biotechnology
NGS
Next Generation Sequencing
title_short The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
title_full The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
title_fullStr The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
title_full_unstemmed The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
title_sort The genomic analysis of a wide peach germplasm collection revealed genetic relationships between European landraces and American ferals and landraces
dc.creator.none.fl_str_mv Aballay, Maximiliano Martín
Ksouri, Najla
Valentini, Gabriel Hugo
Puebla, Andrea Fabiana
Gogorcena Aoiz, Yolanda
Sanchez, Gerardo
author Aballay, Maximiliano Martín
author_facet Aballay, Maximiliano Martín
Ksouri, Najla
Valentini, Gabriel Hugo
Puebla, Andrea Fabiana
Gogorcena Aoiz, Yolanda
Sanchez, Gerardo
author_role author
author2 Ksouri, Najla
Valentini, Gabriel Hugo
Puebla, Andrea Fabiana
Gogorcena Aoiz, Yolanda
Sanchez, Gerardo
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Prunus persica
Filogenética
Variación Genética
Secuenciación de Alto Rendimiento
Fitomejoramiento
Durazno
Biotecnología Vegetal
Phylogenetics
Genetic Variation
High-throughput Sequencing
Plant Breeding
Peaches
Plant Biotechnology
NGS
Next Generation Sequencing
topic Prunus persica
Filogenética
Variación Genética
Secuenciación de Alto Rendimiento
Fitomejoramiento
Durazno
Biotecnología Vegetal
Phylogenetics
Genetic Variation
High-throughput Sequencing
Plant Breeding
Peaches
Plant Biotechnology
NGS
Next Generation Sequencing
dc.description.none.fl_txt_mv The advance of next generation sequencing (NGS) technologies allows the implementation of high-throughput genotyping at a reasonable cost. This open the possibility to learn more about phylogenetic relationships, genetic variability, and the development of new genetic markers for breeding purposes. In this work a previous developed ddRAD-seq platform was applied for the genotyping of two peach collections curated at the EEA San Pedro (237 genotypes) and the EE Aula Dei (89 genotypes). Here we present a joint analysis of a total of 798×106 of paired-end (2×250 bp) reads belonging to 326 genotypes (2,45M reads genotype-1). A total of 564,382 SNPs were discovered and a reduced data set composed of 10,576 SNP (MAF >1% and missing data <10%) was used in a combination of analyses (principal component analysis, population structure and phylogeny). The results showed that the ancestral germplasms differ largely from modern peach cultivars. In addition, genetic relationships between American landraces (North American and Bolivian), American ferals (Argentinian) and European landraces (Spanish and Italian) were revealed suggesting a common origin which probably reflect the introduction of germplasm by the Spaniards during the colonization period. These results with some outstanding traits of ancestral genotypes (fruit quality, high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage the usage of this germplasm on breeding programs for the development of new varieties with agricultural impact.
EEA San Pedro
Fil: Aballay, Maximiliano Martín. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Valentini, Gabriel Hugo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina.
Fil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
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 the implementation of high-throughput genotyping at a reasonable cost. This open the possibility to learn more about phylogenetic relationships, genetic variability, and the development of new genetic markers for breeding purposes. In this work a previous developed ddRAD-seq platform was applied for the genotyping of two peach collections curated at the EEA San Pedro (237 genotypes) and the EE Aula Dei (89 genotypes). Here we present a joint analysis of a total of 798×106 of paired-end (2×250 bp) reads belonging to 326 genotypes (2,45M reads genotype-1). A total of 564,382 SNPs were discovered and a reduced data set composed of 10,576 SNP (MAF >1% and missing data <10%) was used in a combination of analyses (principal component analysis, population structure and phylogeny). The results showed that the ancestral germplasms differ largely from modern peach cultivars. In addition, genetic relationships between American landraces (North American and Bolivian), American ferals (Argentinian) and European landraces (Spanish and Italian) were revealed suggesting a common origin which probably reflect the introduction of germplasm by the Spaniards during the colonization period. These results with some outstanding traits of ancestral genotypes (fruit quality, high yield/vigour, pathogen resistance, thermal requirements, etc.) encourage the usage of this germplasm on breeding programs for the development of new varieties with agricultural impact.
publishDate 2022
dc.date.none.fl_str_mv 2022-12
2023-01-06T10:48:47Z
2023-01-06T10:48:47Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/draft
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str draft
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/13837
https://www.actahort.org/books/1352/1352_11.htm
978-94-62613-52-2 
2406-6168
https://doi.org/10.17660/ActaHortic.2022.1352.11
url http://hdl.handle.net/20.500.12123/13837
https://www.actahort.org/books/1352/1352_11.htm
https://doi.org/10.17660/ActaHortic.2022.1352.11
identifier_str_mv 978-94-62613-52-2 
2406-6168
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv ISHS
publisher.none.fl_str_mv ISHS
dc.source.none.fl_str_mv Acta horticulturae 1352 : 81-88. (Dec. 2022)
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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