Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine
Investigating the genetic architecture of important agronomic traits in grapevine, like berry quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. To address these limitations, this study aimed to develop innovative tools to unravel the complex polygenic genomic architecture of these traits. Specifically, a high-density 200K single nucleotide polymorphism array is developed and validated its effectiveness by genotyping 471 accessions from three F<sub>1</sub> breeding populations. A high-throughput grape phenotyping tool is developed to accurately capture berry color, shape, and size. By integrating data from the two platforms, associated loci are identified over three growing seasons. Association mapping and haplotype analysis identified novel loci and candidate genes for berry shape (bHLH017), soluble sugars (ACT), and organic acids (ALMT1 and FUSC2), as well as vine cold tolerance (NAC08), and fine-mapped the flower sex determination locus. Furthermore, the functional role of NAC08 is validated, demonstrating that it activates the expression of a raffinose synthase gene, thereby increasing raffinose levels and conferring cold tolerance. Together, these augmented tools, the integrated data, and novel loci establish a better foundation for trait aggregation that will enhance breeding efficiency and boost the development of high-quality grape varieties.
Authors
- Pablo Carbonell‐Bejerano (ORCID: https://orcid.org/0000-0002-7266-9665)
- Pierre‐François Bert (ORCID: https://orcid.org/0000-0003-3209-952X)
- Huayang Li (ORCID: https://orcid.org/0000-0002-0364-3234)
- M. Henke (ORCID: https://orcid.org/0000-0003-0673-3873)
- Zhanwu Dai (ORCID: https://orcid.org/0000-0002-7625-8337)
- Yi Wang (ORCID: https://orcid.org/0000-0002-6303-385X)
- Zemin Wang
- Yongjian Wang (ORCID: https://orcid.org/0000-0002-7695-9838)
- Yuyu Zhang (ORCID: https://orcid.org/0000-0003-3095-3083)
- Zhenchang Liang (ORCID: https://orcid.org/0000-0002-4644-4454)
- Peige Fan (ORCID: https://orcid.org/0000-0002-3917-9904)
- Junhua Kong (ORCID: https://orcid.org/0000-0001-6905-2405)
Institutions
- Consejo Superior de Investigaciones Científicas (ES)
- Université de Bordeaux (FR)
- Universidad de La Rioja (ES)
- Chinese Academy of Sciences (CN)
- Beijing Botanical Garden (CN)
- Ecophysiologie et Génomique Fonctionnelle de la Vigne (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- École Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (FR)
- Instituto de Ciencias de la Vid y del Vino (ES)
- Unité mixte de recherche Œnologie (FR)
- Institute of Botany (CN)
- Gobierno de La Rioja (ES)
- University of Chinese Academy of Sciences (CN)
- China National Botanical Garden
- Hunan Agricultural University (CN)
Publication Details
- Journal
- Advanced Science
- Published
- 2025-05-08
- DOI
- https://doi.org/10.1002/advs.202412587
- Citations
- 7
- Primary Topic
- Horticultural and Viticultural Research
- Type
- article
- Field-Weighted Citation Impact
- 12.25
Funders
- National Science Foundation
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- National Key Research and Development Program of China
- Institute of Botany, Chinese Academy of Sciences