Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number
Bunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a gene...
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2025-04-01
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| author | Marco Meneses Claudia Muñoz-Espinoza Sofía Reyes-Impellizzeri Erika Salazar Claudio Meneses Katja Herzog Patricio Hinrichsen |
| author_facet | Marco Meneses Claudia Muñoz-Espinoza Sofía Reyes-Impellizzeri Erika Salazar Claudio Meneses Katja Herzog Patricio Hinrichsen |
| author_sort | Marco Meneses |
| collection | DOAJ |
| description | Bunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a genetically diverse collection of 116 <i>Vitis vinifera</i> L. cultivars and lines enriched for table grapes over two seasons. For this, 3D scanning-based morphological data were combined with ground measurements of 14 BC-related traits, observing high correlations among both approaches (R<sup>2</sup> > 0.90–0.97). The multivariate analysis suggests that the attributes ‘berries per bunch’, ‘berry weight and width’, and ‘bunch weight and length’ could be considered as the main descriptors for BC, optimizing evaluation times. Then, GWASs based on a set of 70,335 SNPs revealed that GBS analysis in this same population enabled the detection of several SNPs associated with different sub-traits, with a locus for ‘berries per bunch’ in chromosome (chr) 18 being the most prominent. Enrichment analysis of significant and frequent SNPs found simultaneously in several traits and seasons revealed the over-representation of discrete functions such as alpha-linolenic acid metabolism and glycan degradation. In summary, the utility of 3D automated phenotyping was validated for table grape backgrounds, and new SNPs and candidate genes associated with the BC trait were detected. The latter could eventually become a selection tool for grapevine breeding programs. |
| format | Article |
| id | doaj-art-e2ecb92c8f064fa998811329b5de3ddf |
| institution | DOAJ |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-04-01 |
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| spelling | doaj-art-e2ecb92c8f064fa998811329b5de3ddf2025-08-20T02:58:44ZengMDPI AGPlants2223-77472025-04-01149130810.3390/plants14091308Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry NumberMarco Meneses0Claudia Muñoz-Espinoza1Sofía Reyes-Impellizzeri2Erika Salazar3Claudio Meneses4Katja Herzog5Patricio Hinrichsen6Instituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, ChileAgronomy Faculty, Universidad de Concepción, Chillán 3780000, ChileCentro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8340008, ChileInstituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, ChileAgronomy Faculty, Pontificia Universidad Católica de Chile, Santiago 8331150, ChileJulius Kühn-Institut, Institute for Grapevine Breeding, Geilweilerhof, 76833 Siebeldingen, GermanyInstituto de Investigaciones Agropecuarias, INIA La Platina, Santiago 8831314, ChileBunch compactness (BC) is a complex, multi-trait characteristic that has been studied mostly in the context of wine grapes, with table grapes being scarcely considered. As these groups have marked phenotypic and genetic differences, including BC, the study of this trait is reported here using a genetically diverse collection of 116 <i>Vitis vinifera</i> L. cultivars and lines enriched for table grapes over two seasons. For this, 3D scanning-based morphological data were combined with ground measurements of 14 BC-related traits, observing high correlations among both approaches (R<sup>2</sup> > 0.90–0.97). The multivariate analysis suggests that the attributes ‘berries per bunch’, ‘berry weight and width’, and ‘bunch weight and length’ could be considered as the main descriptors for BC, optimizing evaluation times. Then, GWASs based on a set of 70,335 SNPs revealed that GBS analysis in this same population enabled the detection of several SNPs associated with different sub-traits, with a locus for ‘berries per bunch’ in chromosome (chr) 18 being the most prominent. Enrichment analysis of significant and frequent SNPs found simultaneously in several traits and seasons revealed the over-representation of discrete functions such as alpha-linolenic acid metabolism and glycan degradation. In summary, the utility of 3D automated phenotyping was validated for table grape backgrounds, and new SNPs and candidate genes associated with the BC trait were detected. The latter could eventually become a selection tool for grapevine breeding programs.https://www.mdpi.com/2223-7747/14/9/1308bunch compactnessGBSautomated phenotypingGWASgrapevinetable grape |
| spellingShingle | Marco Meneses Claudia Muñoz-Espinoza Sofía Reyes-Impellizzeri Erika Salazar Claudio Meneses Katja Herzog Patricio Hinrichsen Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number Plants bunch compactness GBS automated phenotyping GWAS grapevine table grape |
| title | Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number |
| title_full | Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number |
| title_fullStr | Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number |
| title_full_unstemmed | Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number |
| title_short | Characterization of Bunch Compactness in a Diverse Collection of <i>Vitis vinifera</i> L. Genotypes Enriched in Table Grape Cultivars Reveals New Candidate Genes Associated with Berry Number |
| title_sort | characterization of bunch compactness in a diverse collection of i vitis vinifera i l genotypes enriched in table grape cultivars reveals new candidate genes associated with berry number |
| topic | bunch compactness GBS automated phenotyping GWAS grapevine table grape |
| url | https://www.mdpi.com/2223-7747/14/9/1308 |
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