Whole-genome sequencing data of a diverse grapevine germplasm collection maintained in Bordeaux, France

Grapevine (Vitis vinifera) is one of the worlds most economically important fruit crops and a model species for perennial fruit tree genetics and genomics. The extensive genetic diversity found in cultivated and wild Vitis species provides a valuable resource for studies of domestication, adaptation, trait evolution, and breeding. This article presents a standardized whole-genome variant dataset comprising 547 grapevine accessions maintained in the INRAE Bordeaux grapevine germplasm collection, including 397 domesticated V. vinifera cultivars and 150 wild Vitis accessions. Whole-genome sequencing data were generated at a target sequencing depth of approximately 20x, and sequence variants were identified using a standardized Genome Analysis Toolkit (GATK) workflow against the reference genome PN40024v4 (40X). Variant discovery was carried out simultaneously across the complete sample set to ensure consistent genotype calling. All accessions were sequenced using the same technology and processed using the same reference genome, sequence alignment, variant-calling, and filtering workflow to produce a standardized variant dataset comprising ca. 9.1M SNPs and 0.77M INDELs. The resulting VCF files provide a harmonized genomic resource that can be readily reused for studies of grapevine genetics, germplasm characterization, population genomics, comparative genomics, genome-wide association studies, and the development and benchmarking of bioinformatic methods. SPECIFICATIONS TABLE O_TBL View this table: org.highwire.dtl.DTLVardef@490449org.highwire.dtl.DTLVardef@1b884fborg.highwire.dtl.DTLVardef@12280bforg.highwire.dtl.DTLVardef@32bcceorg.highwire.dtl.DTLVardef@1099221_HPS_FORMAT_FIGEXP M_TBL C_TBL VALUE OF THE DATAO_LIThis dataset provides whole-genome raw sequencing for 118 wild Vitis accessions originating from North America and Asia and a sequencing-derived variant data for these accessions and 429 Vitis vinifera cultivars and wild accessions from the INRAE Bordeaux germplasm collection, previously published by Dong et al. 2023[1]. The dataset captures genetic variation across a total of 547 grapevine accessions, including domesticated and wild grapevine germplasm using a common variant-calling pipeline, facilitating direct comparisons among accessions. C_LIO_LIThe inclusion of wild Vitis species together with cultivated grapevine accessions provides a resource for studies of grapevine diversity, domestication, phylogenetic relationships, and comparative genomics. The dataset enables the investigation of genetic variation across multiple Vitis species using a standardized set of genomic variants. C_LIO_LIThe variant call format (VCF) file can be reused for population genetics, phylogenetic analyses, genetic diversity assessments, introgression analyses, and the identification of genomic regions of interest. The dataset is compatible with widely used bioinformatics software and can be integrated with other publicly available grapevine genomic resources. C_LIO_LIThis dataset constitutes a genomic resource for grapevine breeding and conservation research. Researchers can use these data to identify genetic diversity in wild relatives, compare allelic variation between cultivated and wild germplasm, investigate candidate loci associated with traits of interest, and support the management and characterization of grapevine germplasm collections. C_LI