Genomic variation and clone genotyping in Vitis vinifera L. Malbec

Autores
Calderón, Pablo Luciano Sebastian; Mauri Panadero, Nuria; Muñoz, Claudio Javier; Bree, Laura; Carbonell Bejerano, Pablo; Royo, Carolina; Sola, Cristobal; Martínez Zapater, José M.; Lijavetzky, Diego Claudio
Año de publicación
2019
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentinean viticulture, showing a notorious phenotypic variation on many traits of technological interest, for example the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones exhibiting different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based protocol for clones? discrimination. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align these reads to the Pinot noir reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele); these variants allow distinguishing Malbec from the reference genome. On the other hand, we identified 458 non-shared SNVs (i.e. at least one of the clones has the same allele than the reference); these were of particular interest to us because they allow for clone discrimination. From the latter set we picked 48 SNVs to validate them through Sanger sequencing. After validation these same 48 SNVs were employ to build a chip for the high throughput genotyping platform FLUIDIGM. We genotyped 221 plants, including clones of known origin as well as plants belonging to five different mass selections. We were able to classify all genotyped plants in 10 different haplo-groups; showing that with a small but informative number of SNVs it is possible to discriminate among clones of the same cultivar in an efficient manner.
Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Mauri Panadero, Nuria. Instituto de Ciencias de la Vid y el Vino; España
Fil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Bree, Laura. Instituto de Ciencias de la Vid y el Vino; España
Fil: Carbonell Bejerano, Pablo. No especifíca;
Fil: Royo, Carolina. Instituto de Ciencias de la Vid y el Vino; España
Fil: Sola, Cristobal. No especifíca;
Fil: Martínez Zapater, José M.. Instituto de Ciencias de la Vid y el Vino; España
Fil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
63rd Italian Society of Agricultural Genetics Annual Congress
Napoli
Italia
Italian Society of Agricultural Genetics
Materia
GRAPEVINE
MALBEC
GENOMICS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/155209
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/155209
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genomic variation and clone genotyping in Vitis vinifera L. MalbecCalderón, Pablo Luciano SebastianMauri Panadero, NuriaMuñoz, Claudio JavierBree, LauraCarbonell Bejerano, PabloRoyo, CarolinaSola, CristobalMartínez Zapater, José M.Lijavetzky, Diego ClaudioGRAPEVINEMALBECGENOMICShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentinean viticulture, showing a notorious phenotypic variation on many traits of technological interest, for example the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones exhibiting different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based protocol for clones? discrimination. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align these reads to the Pinot noir reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele); these variants allow distinguishing Malbec from the reference genome. On the other hand, we identified 458 non-shared SNVs (i.e. at least one of the clones has the same allele than the reference); these were of particular interest to us because they allow for clone discrimination. From the latter set we picked 48 SNVs to validate them through Sanger sequencing. After validation these same 48 SNVs were employ to build a chip for the high throughput genotyping platform FLUIDIGM. We genotyped 221 plants, including clones of known origin as well as plants belonging to five different mass selections. We were able to classify all genotyped plants in 10 different haplo-groups; showing that with a small but informative number of SNVs it is possible to discriminate among clones of the same cultivar in an efficient manner.Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Mauri Panadero, Nuria. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Bree, Laura. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Carbonell Bejerano, Pablo. No especifíca;Fil: Royo, Carolina. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Sola, Cristobal. No especifíca;Fil: Martínez Zapater, José M.. Instituto de Ciencias de la Vid y el Vino; EspañaFil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina63rd Italian Society of Agricultural Genetics Annual CongressNapoliItaliaItalian Society of Agricultural GeneticsItalian Society of Agricultural Genetics2019info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/mswordapplication/pdfhttp://hdl.handle.net/11336/155209Genomic variation and clone genotyping in Vitis vinifera L. Malbec; 63rd Italian Society of Agricultural Genetics Annual Congress; Napoli; Italia; 2019; 7.24CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://www.geneticagraria.it/congress_abstract.asp?a_pag=4&Indice=310&id=63Internacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:41:19Zoai:ri.conicet.gov.ar:11336/155209instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:41:19.255CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genomic variation and clone genotyping in Vitis vinifera L. Malbec
title Genomic variation and clone genotyping in Vitis vinifera L. Malbec
spellingShingle Genomic variation and clone genotyping in Vitis vinifera L. Malbec
Calderón, Pablo Luciano Sebastian
GRAPEVINE
MALBEC
GENOMICS
title_short Genomic variation and clone genotyping in Vitis vinifera L. Malbec
title_full Genomic variation and clone genotyping in Vitis vinifera L. Malbec
title_fullStr Genomic variation and clone genotyping in Vitis vinifera L. Malbec
title_full_unstemmed Genomic variation and clone genotyping in Vitis vinifera L. Malbec
title_sort Genomic variation and clone genotyping in Vitis vinifera L. Malbec
dc.creator.none.fl_str_mv Calderón, Pablo Luciano Sebastian
Mauri Panadero, Nuria
Muñoz, Claudio Javier
Bree, Laura
Carbonell Bejerano, Pablo
Royo, Carolina
Sola, Cristobal
Martínez Zapater, José M.
Lijavetzky, Diego Claudio
author Calderón, Pablo Luciano Sebastian
author_facet Calderón, Pablo Luciano Sebastian
Mauri Panadero, Nuria
Muñoz, Claudio Javier
Bree, Laura
Carbonell Bejerano, Pablo
Royo, Carolina
Sola, Cristobal
Martínez Zapater, José M.
Lijavetzky, Diego Claudio
author_role author
author2 Mauri Panadero, Nuria
Muñoz, Claudio Javier
Bree, Laura
Carbonell Bejerano, Pablo
Royo, Carolina
Sola, Cristobal
Martínez Zapater, José M.
Lijavetzky, Diego Claudio
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv GRAPEVINE
MALBEC
GENOMICS
topic GRAPEVINE
MALBEC
GENOMICS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentinean viticulture, showing a notorious phenotypic variation on many traits of technological interest, for example the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones exhibiting different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based protocol for clones? discrimination. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align these reads to the Pinot noir reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele); these variants allow distinguishing Malbec from the reference genome. On the other hand, we identified 458 non-shared SNVs (i.e. at least one of the clones has the same allele than the reference); these were of particular interest to us because they allow for clone discrimination. From the latter set we picked 48 SNVs to validate them through Sanger sequencing. After validation these same 48 SNVs were employ to build a chip for the high throughput genotyping platform FLUIDIGM. We genotyped 221 plants, including clones of known origin as well as plants belonging to five different mass selections. We were able to classify all genotyped plants in 10 different haplo-groups; showing that with a small but informative number of SNVs it is possible to discriminate among clones of the same cultivar in an efficient manner.
Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Mauri Panadero, Nuria. Instituto de Ciencias de la Vid y el Vino; España
Fil: Muñoz, Claudio Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
Fil: Bree, Laura. Instituto de Ciencias de la Vid y el Vino; España
Fil: Carbonell Bejerano, Pablo. No especifíca;
Fil: Royo, Carolina. Instituto de Ciencias de la Vid y el Vino; España
Fil: Sola, Cristobal. No especifíca;
Fil: Martínez Zapater, José M.. Instituto de Ciencias de la Vid y el Vino; España
Fil: Lijavetzky, Diego Claudio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina
63rd Italian Society of Agricultural Genetics Annual Congress
Napoli
Italia
Italian Society of Agricultural Genetics
description Somatic mutations are a major force introducing novel genetic variation; this role becomes enhanced in systems lacking of sexual reproduction. The later is the case of grapevines used in the wine industry. Even though clonal propagation is a normal practice in this industry, a remarkable phenotypic variation has been reported at the intra-cultivar level. However, less is known about the genetic variability among clones. Malbec is the main cultivar for the Argentinean viticulture, showing a notorious phenotypic variation on many traits of technological interest, for example the biochemical composition of berries. Therefore, it turns relevant to develop a formal protocol to discriminate among clones exhibiting different properties. Here we performed a genomic analysis in order to test if the genetic variability is in agreement with the phenotypic variability, and also to develop a genetic-based protocol for clones? discrimination. For this aim we obtained Illumina reads at a 35x depth for four different Malbec clones (MB53, MB59, Cot143 and Cot225). Bioinformatic tools were employed to align these reads to the Pinot noir reference genome (PN40024) and to perform variant calling analysis for single nucleotide variants (SNVs) discovery. Afterwards, strict quality and frequency filters were applied to obtain a set of reliable SNVs. We discovered 2 million of shared SNVs (i.e. all clones shared the same allele); these variants allow distinguishing Malbec from the reference genome. On the other hand, we identified 458 non-shared SNVs (i.e. at least one of the clones has the same allele than the reference); these were of particular interest to us because they allow for clone discrimination. From the latter set we picked 48 SNVs to validate them through Sanger sequencing. After validation these same 48 SNVs were employ to build a chip for the high throughput genotyping platform FLUIDIGM. We genotyped 221 plants, including clones of known origin as well as plants belonging to five different mass selections. We were able to classify all genotyped plants in 10 different haplo-groups; showing that with a small but informative number of SNVs it is possible to discriminate among clones of the same cultivar in an efficient manner.
publishDate 2019
dc.date.none.fl_str_mv 2019
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Congreso
Book
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/155209
Genomic variation and clone genotyping in Vitis vinifera L. Malbec; 63rd Italian Society of Agricultural Genetics Annual Congress; Napoli; Italia; 2019; 7.24
CONICET Digital
CONICET
url http://hdl.handle.net/11336/155209
identifier_str_mv Genomic variation and clone genotyping in Vitis vinifera L. Malbec; 63rd Italian Society of Agricultural Genetics Annual Congress; Napoli; Italia; 2019; 7.24
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://www.geneticagraria.it/congress_abstract.asp?a_pag=4&Indice=310&id=63
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/msword
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Italian Society of Agricultural Genetics
publisher.none.fl_str_mv Italian Society of Agricultural Genetics
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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