Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collectio...

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Authors: Zinelabidine, Lalla Hasna, Torres-Pérez, Rafael, Grimplet, Jérôme, Baroja Hernández, Elisa, Ibáñez Pascual, Sergio, Carbonell-Bejerano, Pablo, Martínez-Zapater, José M., Ibáñez Marcos, Javier, Tello, Javier
Format: article
Status:Published version
Publication Date:2021
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/262054
Online Access:http://hdl.handle.net/10261/262054
Access Level:Open access
Keyword:Berry number
Flower number
Single nucleotide polymorphism
Targeted sequencing
Vitis vinifera L.
Yield
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spelling Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevineZinelabidine, Lalla HasnaTorres-Pérez, RafaelGrimplet, JérômeBaroja Hernández, ElisaIbáñez Pascual, SergioCarbonell-Bejerano, PabloMartínez-Zapater, José M.Ibáñez Marcos, JavierTello, JavierBerry numberFlower numberSingle nucleotide polymorphismTargeted sequencingVitis vinifera L.YieldGrapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.This work was supported by the Spanish Ministerio de Economía y Competitividad (MINECO) [project AGL2014−59171-R] and by the Agencia Estatal de Investigación (AEI) [project BIO2017‐86375‐R], both co-funded by FEDER (UE). JT is funded by a Juan de la Cierva-Incorporación grant [IJC2018-035036-I]. LHZ was partially funded by a STSM from the COST Action CA17111 INTEGRAPE, supported by COST (European Cooperation in Science and Technology).Elsevier BVMinisterio de Economía y Competitividad (España)Ministerio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)European CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2022202220212022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/262054reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO//AGL2014-59171-Rinfo:eu-repo/grantAgreement/AEI//BIO2017‐86375‐Rinfo:eu-repo/grantAgreement/AEI//IJC2018-035036-Ihttp://dx.doi.org/10.1016/j.plantsci.2021.110875Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2620542026-05-22T06:33:51Z
dc.title.none.fl_str_mv Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
title Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
spellingShingle Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
Zinelabidine, Lalla Hasna
Berry number
Flower number
Single nucleotide polymorphism
Targeted sequencing
Vitis vinifera L.
Yield
title_short Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
title_full Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
title_fullStr Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
title_full_unstemmed Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
title_sort Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine
dc.creator.none.fl_str_mv Zinelabidine, Lalla Hasna
Torres-Pérez, Rafael
Grimplet, Jérôme
Baroja Hernández, Elisa
Ibáñez Pascual, Sergio
Carbonell-Bejerano, Pablo
Martínez-Zapater, José M.
Ibáñez Marcos, Javier
Tello, Javier
author Zinelabidine, Lalla Hasna
author_facet Zinelabidine, Lalla Hasna
Torres-Pérez, Rafael
Grimplet, Jérôme
Baroja Hernández, Elisa
Ibáñez Pascual, Sergio
Carbonell-Bejerano, Pablo
Martínez-Zapater, José M.
Ibáñez Marcos, Javier
Tello, Javier
author_role author
author2 Torres-Pérez, Rafael
Grimplet, Jérôme
Baroja Hernández, Elisa
Ibáñez Pascual, Sergio
Carbonell-Bejerano, Pablo
Martínez-Zapater, José M.
Ibáñez Marcos, Javier
Tello, Javier
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Berry number
Flower number
Single nucleotide polymorphism
Targeted sequencing
Vitis vinifera L.
Yield
topic Berry number
Flower number
Single nucleotide polymorphism
Targeted sequencing
Vitis vinifera L.
Yield
description Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.
publishDate 2021
dc.date.none.fl_str_mv 2021
2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/262054
url http://hdl.handle.net/10261/262054
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO//AGL2014-59171-R
info:eu-repo/grantAgreement/AEI//BIO2017‐86375‐R
info:eu-repo/grantAgreement/AEI//IJC2018-035036-I
http://dx.doi.org/10.1016/j.plantsci.2021.110875
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier BV
publisher.none.fl_str_mv Elsevier BV
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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