Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study

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dc.contributor.authorUrra, Claudio
dc.contributor.authorSanhueza, Dayan
dc.contributor.authorPavez, Catalina
dc.contributor.authorTapia, Patricio
dc.contributor.authorNunez-Lillo, Gerardo
dc.contributor.authorMinio, Andrea
dc.contributor.authorMiossec, Matthieu
dc.contributor.authorBlanco-Herrera, Francisca
dc.contributor.authorGainza, Felipe
dc.contributor.authorCastro, Alvaro
dc.contributor.authorCantu, Dario
dc.contributor.authorMeneses, Claudio
dc.date.accessioned2025-01-20T20:09:14Z
dc.date.available2025-01-20T20:09:14Z
dc.date.issued2023
dc.description.abstractWine 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.
dc.description.abstractWe characterized the genetic variation among clones of the most economically important Vitis vinifera cultivars and developed genetic markers that can be used for clonal discrimination using high-throughput amplicon sequencing.
dc.fuente.origenWOS
dc.identifier.doi10.1093/g3journal/jkad145
dc.identifier.issn2160-1836
dc.identifier.urihttps://doi.org/10.1093/g3journal/jkad145
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/91979
dc.identifier.wosidWOS:001026595500001
dc.issue.numero9
dc.language.isoen
dc.revistaG3-genes genomes genetics
dc.rightsacceso restringido
dc.subjectVitis vinifera
dc.subjectclonal genetic diversity
dc.subjectDNA fingerprinting
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleIdentification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study
dc.typeartículo
dc.volumen13
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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