DOI: 10.5061/dryad.s7h44j1n1
title: Genomic structure and ex situ conservation of the North American grapevine <em>Vitis labrusca</em>

description: Vitis labrusca, a North American wild grapevine, is an important source of
 disease resistance and climate resilience traits for grape breeding, yet
 its genomic diversity is incompletely represented in ex situ germplasm
 collections. We genotyped 314 accessions, which included material
 conserved at the USDA germplasm collection and newly sampled wild
 individuals. Accessions were genotyped using genotyping-by-sequencing, and
 after imputation and filtering, we identified a total of 44,701 SNPs.
 Within the accessions genotyped, we identified extensive mislabelling and
 hybridization, with approximately one-third of accessions classified as
 putative hybrids. We also detected genetically distinct populations from
 Virginia and North Carolina that are not currently conserved. These
 results reveal significant geographic and genomic gaps in ex situ
 conservation of V. labrusca and highlight priority regions for future
 sampling to better safeguard this species for breeding and research.
description: A total of 314 unique samples were sequenced, although 11 of
 these were sequenced twice. Sequencing data were processed and single
 nucleotide polymorphisms (SNPs) identified using the Tassel 5 GBS v2
 Pipeline v5.2.94 (Bradbury et al., 2007). During this process, replicate
 samples with the same IDs were automatically merged. Default parameters
 were used for all steps except the initial GBSSeqToTagDBPlugin() step,
 where a minimum quality score (-mnQS) of 20 was required. Reads were
 aligned to the V. labrusca reference genome for GREM4, version 1 (Li
 & Gschwend, 2023) using BWA v0.7.18 (Li & Durbin, 2009). A
 minimum minor allele frequency (MAF) of 0.01 was set for SNP discovery
 using Tassel, and a total of 154,638 SNPs were identified. These SNPs were
 filtered using VCFTools v0.1.16 to remove indels, retain only biallelic
 sites, and ensure a MAF threshold of 0.01 (Danecek et al., 2011),
 resulting in 145,155 SNPs across the 314 accessions.<br> <br>
 Imputation was performed using LinkImputeR (Money et al., 2017), with
 input filters of MAF 0.01, a maximum missingness by position of 70%, and a
 Hardy-Weinberg equilibrium filter of p &lt; 0.0001. Parameters tested
 included depths of 2 to 6 (increasing by 1) and maximum missingness per
 SNP and sample of 0.2 to 0.6 (increasing by 0.1). The selected imputation
 case applied the filters of PositionMiss(0.6) and SampleMiss(0.6),
 resulting in an accuracy of 0.935 and a correlation value of 0.8091. After
 imputation, 271 accessions and 46,916 SNPs remained. VCFTools (v0.1.16)
 (Danecek et al., 2011) was used to remove SNPs located on unassembled
 contigs in the V. labrusca genome from the SNP set, resulting in a final
 filtered dataset of 44,701 SNPs.<br> <br> PLINK v2.00a5.8
 (Chang et al., 2015; Purcell & Chang, 2025) was used to prune the
 imputed SNP table for linkage disequilibrium (LD). LD-pruning was
 performed by considering a window of 10 SNPs, removing one SNP from a pair
 if the r2 was &gt;0.5 then shifting the window by 3 SNPS and repeating
 the procedure (--indep-pairwise 10 3 0.5). The resulting dataset contained
 271 accessions and 32,267 SNPs.<br> <br> Accessions with
 &gt;0.90 ancestry proportion assignment to Cluster 2 (n = 183) were
 retained as putative “pure” V. labrusca. These accessions were kept using
 PLINK (v2.00a5.8), followed by a filter for MAF 0.01, resulting in 27,071
 SNPs remaining (Chang et al., 2015; Purcell & Chang, 2025).
 LD-pruning was repeated as described above and the final dataset contained
 18,849 SNPs and 183 accessions.
 <strong>References</strong>
 Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M.,
 Ramdoss, Y. & Buckler, E.S. (2007). TASSEL: software for
 association mapping of complex traits in diverse samples. Bioinformatics,
 23(19), pp. 2633–2635. Chang, C.C., Chow, C.C.,
 Tellier, L.C., Vattikuti, S., Purcell, S.M. & Lee, J.J. (2015).
 Second-generation PLINK: rising to the challenge of larger and richer
 datasets. GigaScience, 4(1), pp. s13742-015-0047–8 https://doi.org/10.1186/s13742-015-0047-8. Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., McVean, G., Durbin, R. & Genomes Project Analysis, G. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), pp. 2156–8 https://doi.org/10.1093/bioinformatics/btr330. Li, B. & Gschwend, A.R. (2023). Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes. Frontiers in Plant Science, 14 https://doi.org/10.3389/fpls.2023.1234130. Li, H. & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), pp. 1754–60 https://doi.org/10.1093/bioinformatics/btp324. Money, D., Migicovsky, Z., Gardner, K. & Myles, S. (2017). LinkImputeR: user-guided genotype calling and imputation for non-model organisms. BMC Genomics, 18(1), p. 523 https://doi.org/10.1186/s12864-017-3873-5. Purcell, S. & Chang, C. (2025). PLINK v2.00a5.8 www.cog-genomics.org/plink/2.0/.
description: # Genomic structure and ex situ conservation of the North American
 grapevine *Vitis labrusca* Dataset DOI:
 [10.5061/dryad.s7h44j1n1](https://doi.org/10.5061/dryad.s7h44j1n1) ##
 Description of the data and file structure We examined 314 accessions of
 *V. labrusca*, including accessions conserved in the USDA germplasm
 collection as well as wild-collected accessions. Using
 genotyping-by-sequencing, we identified over 44,000 genetic markers, which
 we used to determine population structure, potential mislabelling or
 hybridization, and the extent to which *ex situ* conserved accessions
 adequately capture this species. ### Files and variables #### File:
 filtered_chr1_19_cluster2_maf01_ld_pca.eigenvec **Description:** PCA
 results for accessions assigned &gt; 0.90 to Cluster 2 (n = 183) after MAF
 1 % filter and LD-pruning (--indep-pairwise 10 3 0.5) using 18,849 SNPs
 #### File: filtered_chr1_19_cluster2_maf01.map **Description:** SNP map
 file (PLINK format) for accessions assigned &gt; 0.90 to Cluster 2 (n =
 183) after MAF 1 % filter for a total of 27,071 SNPs #### File:
 filtered_chr1_19_cluster2_maf01_ld_pca.eigenval **Description:** PCA
 results for accessions assigned &gt; 0.90 to Cluster 2 (n = 183) after MAF
 1 % filter and LD-pruning (--indep-pairwise 10 3 0.5) using 18,849 SNPs
 #### File: filtered_chr1_19_ld_pca.eigenvec **Description:** PCA results
 for all accessions (n = 271) after MAF 1 % filter and
 LD-pruning (--indep-pairwise 10 3 0.5) using 32,267 SNPs #### File:
 filtered_chr1_19_ld_pca.eigenval **Description:** PCA results for all
 accessions (n = 271) after MAF 1 % filter and LD-pruning (--indep-pairwise
 10 3 0.5) using 32,267 SNPs #### File:
 filtered_chr1_19_cluster2_maf01_ld.map **Description:** SNP map file
 (PLINK format) for accessions assigned &gt; 0.90 to Cluster 2 (n = 183)
 after MAF 1 % filter and LD-pruning (--indep-pairwise 10 3 0.5) for a
 total of 18,849 SNPs #### File: filtered_chr1_19_ld.map
 **Description:** SNP map file (PLINK format) for all accessions (n = 271)
 after MAF 1 % filter and LD-pruning (--indep-pairwise 10 3 0.5) for a
 total of 32,267 SNPs #### File: filtered_chr1_19_cluster2_maf01.ped
 **Description:** SNP ped file (PLINK format) for accessions assigned &gt;
 0.90 to Cluster 2 (n = 183) after MAF 1 % filter for a total of 27,071
 SNPs #### File: filtered_chr1_19_cluster2_maf01_ld.ped
 **Description:** SNP ped file (PLINK format) for accessions assigned &gt;
 0.90 to Cluster 2 (n = 183) after MAF 1 % filter and LD-pruning
 (--indep-pairwise 10 3 0.5) for a total of 18,849 SNPs #### File:
 filtered_chr1_19_ld.ped **Description:** SNP ped file (PLINK format) for
 all accessions (n = 271) after MAF 1 % filter and LD-pruning
 (--indep-pairwise 10 3 0.5) for a total of 32,267 SNPs #### File:
 filtered_chr1_19.map **Description:** SNP map file (PLINK format) for all
 accessions (n = 271) after MAF 1 % filter for a total of 44,701 SNPs ####
 File: filtered_chr1_19.ped **Description:** SNP ped file (PLINK format)
 for all accessions (n = 271) after MAF 1 % filter for a total of 44,701
 SNPs ## Code/software Files are provided in PLINK (v2.00a5.8) format
 (ped/map) ## Access information Data was derived from the following
 sources: * Data are from Migicovsky et al. (2025) Genomic structure and ex
 situ conservation of the North American grapevine *Vitis labrusca*,
 *Plants People Planet*