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This research was funded by the Spanish Ministerio de Economia y Competitividad (MINECO), projects AGL2010-15694 and AGL2014-59171-R. J.T. is funded by a Juan de la Cierva-Incorporacion grant (IJC2018-035036-I).

Analysis of institutional authors

Grimplet, JeromeAuthor

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June 11, 2020
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Article

VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine

Publicated to:Genes. 11 (6): E598- - 2020-06-01 11(6), DOI: 10.3390/genes11060598

Authors: Tello, Javier; Torres-Perez, Rafael; Flutre, Timothee; Grimplet, Jerome; Ibanez, Javier

Affiliations

Ctr Invest & Tecnol Agroalimentaria Aragon CITA, Unidad Hortofruticultura, Zaragoza 50059, Spain - Author
Ctr Nacl Biotecnol CNB CSIC, Serv Bioinformat Genom & Proteom BioinfoGP, Madrid 28049, Spain - Author
Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), 26080 Logroño, Spain. - Author
Inst Ciencias Vid & Vino CSIC, Dept Viticultura, UR, Logrono 26080, Spain - Author
Instituto Agroalimentario de Aragón-IA2 (CITA-Universidad de Zaragoza), 50059 Zaragoza, Spain. - Author
Servicio de Bioinformática para Genómica y Proteómica (BioinfoGP), Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain. - Author
Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain. - Author
Univ Paris Saclay, GQE Le Moulon, AgroParisTech, CNRS,INRAE, F-91190 Gif Sur Yvette, France - Author
Univ Zaragoz, Inst Agroalimentario Aragon IA2 CITA, Zaragoza 50059, Spain - Author
Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France. - Author
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Abstract

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.

Keywords

Association geneticsBerry sizeBunchCluster compactnessDisease resistanceFruitGenesGenetic variationGenomeGenotypeGrowth-regulatorsHaplotypesIdentificationInflorescenceLinkage disequilibriumMetalloproteinsPairwise relatednessPhenotypePhytocyaninsPlantPlant diseasesPolymorphism, geneticPolymorphism, single nucleotidePromoter regions, geneticRachis lignificationSingle nucleotide polymorphism (snp)Table grapeTargeted sequencingUclacyaninsVitisVitis vinifera lVitis vinifera l.Vitis viniferal

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Genes due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2020, it was in position 66/176, thus managing to position itself as a Q2 (Segundo Cuartil), in the category Genetics & Heredity. Notably, the journal is positioned en el Cuartil Q2 para la agencia Scopus (SJR) en la categoría Genetics.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 1.9, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-09, the following number of citations:

  • WoS: 9
  • Scopus: 10
  • Europe PMC: 3

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-09:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 24.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 24 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 1.5.
  • The number of mentions on the social network X (formerly Twitter): 2 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: http://hdl.handle.net/10532/5048

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: France.