Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
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...
| Autores principales: | , , , , , , , , , , , |
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| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
Springer Nature
2021
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| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855484367734833152 |
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| author | 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_browse | Bergamin, Daniel Bree, Laura Calderón, Luciano Carbonell Bejerano, Pablo Gomez Talquenca, Gonzalo Ibáñez, Javier Lijavetzky, Diego Martínez Zapater, José Miguel Mauri, Nuria Muñoz, Claudio Royo, Carolina Sola, Cristóbal |
| 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_sort | Calderón, Luciano |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA9295 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | INTA92952025-09-15T11:38:27Z Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.) 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 Vid Clones Identificación Genotipos Variación Genética Grapevines Identification Genotypes Genetic Variation Malbec 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 2021-05-06T17:08:52Z 2021-05-06T17:08:52Z 2021-04-08 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf Springer Nature Scientific reports, 11 : 7775. (08 April 2021) |
| spellingShingle | Vid Clones Identificación Genotipos Variación Genética Grapevines Identification Genotypes Genetic Variation Malbec 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 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.) |
| 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_short | 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 |
| topic | Vid Clones Identificación Genotipos Variación Genética Grapevines Identification Genotypes Genetic Variation Malbec |
| 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 |
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