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

Abstract 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...

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Autores principales:	Luciano Calderón, Nuria Mauri, Claudio Muñoz, Pablo Carbonell-Bejerano, Laura Bree, Daniel Bergamin, Cristobal Sola, Sebastian Gomez-Talquenca, Carolina Royo, Javier Ibáñez, José Miguel Martínez-Zapater, Diego Lijavetzky
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/457623389726453aa29658a1d1ccf41e
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spelling	oai:doaj.org-article:457623389726453aa29658a1d1ccf41e2021-12-02T18:15:25ZWhole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)10.1038/s41598-021-87445-y2045-2322https://doaj.org/article/457623389726453aa29658a1d1ccf41e2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87445-yhttps://doaj.org/toc/2045-2322Abstract 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.Luciano CalderónNuria MauriClaudio MuñozPablo Carbonell-BejeranoLaura BreeDaniel BergaminCristobal SolaSebastian Gomez-TalquencaCarolina RoyoJavier IbáñezJosé Miguel Martínez-ZapaterDiego LijavetzkyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Luciano Calderón Nuria Mauri Claudio Muñoz Pablo Carbonell-Bejerano Laura Bree Daniel Bergamin Cristobal Sola Sebastian Gomez-Talquenca Carolina Royo Javier Ibáñez José Miguel Martínez-Zapater Diego Lijavetzky Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)
description	Abstract 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	article
author	Luciano Calderón Nuria Mauri Claudio Muñoz Pablo Carbonell-Bejerano Laura Bree Daniel Bergamin Cristobal Sola Sebastian Gomez-Talquenca Carolina Royo Javier Ibáñez José Miguel Martínez-Zapater Diego Lijavetzky
author_facet	Luciano Calderón Nuria Mauri Claudio Muñoz Pablo Carbonell-Bejerano Laura Bree Daniel Bergamin Cristobal Sola Sebastian Gomez-Talquenca Carolina Royo Javier Ibáñez José Miguel Martínez-Zapater Diego Lijavetzky
author_sort	Luciano Calderón
title	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_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.)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/457623389726453aa29658a1d1ccf41e
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Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

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