Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

Autores
Calderón, Luciano; Mauri, Nuria; Muñoz, Claudio; Carbonell Bejerano, Pablo; Bree, Laura; Bergamin, Daniel; Sola, Cristóbal; Gomez Talquenca, Gonzalo; Royo, Carolina; Ibáñez, Javier; Martínez Zapater, José Miguel; Lijavetzky, Diego
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.
EEA Mendoza
Fil: Calderón, Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Calderón, Luciano. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Mauri, Nuria. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; Argentina
Fil: Muñoz, Claudio. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Carbonell Bejerano, Pablo. Max Planck Institute for Developmental Biology; Alemania
Fil: Bree, Laura. Vivero Mercier; Argentina
Fil: Bergamin, Daniel. Vivero Mercier; Argentina
Fil: Sola, Cristóbal. Vivero Mercier; Argentina
Fil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Royo, Carolina. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Ibáñez, Javier. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Martínez Zapater, José Miguel. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Lijavetzky, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Lijavetzky, Diego. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fuente
Scientific reports, 11 : 7775. (08 April 2021)
Materia
Vid
Clones
Identificación
Genotipos
Variación Genética
Grapevines
Identification
Genotypes
Genetic Variation
Malbec
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:20.500.12123/9295
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oai_identifier_str oai:localhost:20.500.12123/9295
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network_name_str INTA Digital (INTA)
spelling Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)Calderón, LucianoMauri, NuriaMuñoz, ClaudioCarbonell Bejerano, PabloBree, LauraBergamin, DanielSola, CristóbalGomez Talquenca, GonzaloRoyo, CarolinaIbáñez, JavierMartínez Zapater, José MiguelLijavetzky, DiegoVidClonesIdentificaciónGenotiposVariación GenéticaGrapevinesIdentificationGenotypesGenetic VariationMalbecGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.EEA MendozaFil: Calderón, Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Calderón, Luciano. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Mauri, Nuria. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; ArgentinaFil: Muñoz, Claudio. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; ArgentinaFil: Carbonell Bejerano, Pablo. Max Planck Institute for Developmental Biology; AlemaniaFil: Bree, Laura. Vivero Mercier; ArgentinaFil: Bergamin, Daniel. Vivero Mercier; ArgentinaFil: Sola, Cristóbal. Vivero Mercier; ArgentinaFil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Mendoza; ArgentinaFil: Royo, Carolina. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; EspañaFil: Ibáñez, Javier. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; EspañaFil: Martínez Zapater, José Miguel. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; EspañaFil: Lijavetzky, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Lijavetzky, Diego. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaSpringer Nature2021-05-06T17:08:52Z2021-05-06T17:08:52Z2021-04-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/9295https://www.nature.com/articles/s41598-021-87445-yCalderón, L., Mauri, N., Muñoz, C. et al. Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.). Sci Rep 11, 7775 (2021). https://doi.org/10.1038/s41598-021-87445-y2045-2322 (Online)https://doi.org/10.1038/s41598-021-87445-yScientific reports, 11 : 7775. (08 April 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)2025-09-29T13:45:12Zoai:localhost:20.500.12123/9295instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:45:12.801INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
title Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
spellingShingle Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
Calderón, Luciano
Vid
Clones
Identificación
Genotipos
Variación Genética
Grapevines
Identification
Genotypes
Genetic Variation
Malbec
title_short Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
title_full Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
title_fullStr Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
title_full_unstemmed Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
title_sort Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
dc.creator.none.fl_str_mv Calderón, Luciano
Mauri, Nuria
Muñoz, Claudio
Carbonell Bejerano, Pablo
Bree, Laura
Bergamin, Daniel
Sola, Cristóbal
Gomez Talquenca, Gonzalo
Royo, Carolina
Ibáñez, Javier
Martínez Zapater, José Miguel
Lijavetzky, Diego
author Calderón, Luciano
author_facet Calderón, Luciano
Mauri, Nuria
Muñoz, Claudio
Carbonell Bejerano, Pablo
Bree, Laura
Bergamin, Daniel
Sola, Cristóbal
Gomez Talquenca, Gonzalo
Royo, Carolina
Ibáñez, Javier
Martínez Zapater, José Miguel
Lijavetzky, Diego
author_role author
author2 Mauri, Nuria
Muñoz, Claudio
Carbonell Bejerano, Pablo
Bree, Laura
Bergamin, Daniel
Sola, Cristóbal
Gomez Talquenca, Gonzalo
Royo, Carolina
Ibáñez, Javier
Martínez Zapater, José Miguel
Lijavetzky, Diego
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Vid
Clones
Identificación
Genotipos
Variación Genética
Grapevines
Identification
Genotypes
Genetic Variation
Malbec
topic Vid
Clones
Identificación
Genotipos
Variación Genética
Grapevines
Identification
Genotypes
Genetic Variation
Malbec
dc.description.none.fl_txt_mv Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.
EEA Mendoza
Fil: Calderón, Luciano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Calderón, Luciano. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Mauri, Nuria. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; Argentina
Fil: Muñoz, Claudio. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias; Argentina
Fil: Carbonell Bejerano, Pablo. Max Planck Institute for Developmental Biology; Alemania
Fil: Bree, Laura. Vivero Mercier; Argentina
Fil: Bergamin, Daniel. Vivero Mercier; Argentina
Fil: Sola, Cristóbal. Vivero Mercier; Argentina
Fil: Gomez Talquenca, Gonzalo. Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Mendoza; Argentina
Fil: Royo, Carolina. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Ibáñez, Javier. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Martínez Zapater, José Miguel. Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja). Finca La Grajera; España
Fil: Lijavetzky, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Lijavetzky, Diego. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
description Grapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.
publishDate 2021
dc.date.none.fl_str_mv 2021-05-06T17:08:52Z
2021-05-06T17:08:52Z
2021-04-08
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/20.500.12123/9295
https://www.nature.com/articles/s41598-021-87445-y
Calderón, L., Mauri, N., Muñoz, C. et al. Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.). Sci Rep 11, 7775 (2021). https://doi.org/10.1038/s41598-021-87445-y
2045-2322 (Online)
https://doi.org/10.1038/s41598-021-87445-y
url http://hdl.handle.net/20.500.12123/9295
https://www.nature.com/articles/s41598-021-87445-y
https://doi.org/10.1038/s41598-021-87445-y
identifier_str_mv Calderón, L., Mauri, N., Muñoz, C. et al. Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.). Sci Rep 11, 7775 (2021). https://doi.org/10.1038/s41598-021-87445-y
2045-2322 (Online)
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 : 7775. (08 April 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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