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Urra C, Sanhueza D, Pavez C, Tapia P, Núñez-Lillo G, Minio A, Miossec M, Blanco-Herrera F, Gainza F, Castro A, Cantu D, Meneses C. Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study. G3 (Bethesda) 2023; 13:jkad145. [PMID: 37395733 PMCID: PMC10468313 DOI: 10.1093/g3journal/jkad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains unexplored, and tools to discriminate unequivocally clones have been lacking. This study aimed to uncover genetic variations among a group of clonal selections of 4 important Vitis vinifera cultivars: Cabernet sauvignon, Sauvignon blanc, Chardonnay, and Merlot, and use this information to develop genetic markers to discriminate the clones of these cultivars. We sequenced with short-read sequencing technology the genomes of 18 clones, including biological replicates for a total of 46 genomes. Sequences were aligned to their respective cultivar's reference genome for variant calling. We used reference genomes of Cabernet sauvignon, Chardonnay, and Merlot and developed a de novo genome assembly of Sauvignon blanc using long-read sequencing. On average, 4 million variants were detected for each clone, with 74.2% being single nucleotide variants and 25.8% being small insertions or deletions (InDel). The frequency of these variants was consistent across all clones. From these variants, we validated 46 clonal markers using high-throughput amplicon sequencing for 77.7% of the evaluated clones, most of them small InDel. These results represent an advance in grapevine genotyping strategies and will benefit the viticulture industry for the characterization and identification of the plant material.
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Affiliation(s)
- Claudio Urra
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago 8580745, Chile
| | - Dayan Sanhueza
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Catalina Pavez
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Patricio Tapia
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Gerardo Núñez-Lillo
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2263782, Chile
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616-5270, USA
| | - Matthieu Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Francisca Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
| | - Felipe Gainza
- Center for Research and Innovation, Viña Concha y Toro S.A, Pencahue, Talca 3460000, Chile
| | - Alvaro Castro
- UC Davis-Chile, Life Sciences Innovation Center, Santiago 7520424, Chile
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616-5270, USA
| | - Claudio Meneses
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program Millenium Institute Center for Genome Regulation, CRG, Santiago 8331150, Chile
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