Fig. 6
From: A super-pangenome of the North American wild grape species
Pan-GWAS revealed significant associations with chloride concentration in the leaves. a Workflow to generate the variant file required for the pan-GWAS. The name of the vg module used for each step is indicated in purple, the output type is in black, and the file extension is orange. The PGGB graph is deconstructed to a variant file using V. girdiana haplotype 1 as a reference (1). Vg construct is used to construct a pangenome from the VCF and the reference fasta (2). After merging the IDs (3), xg (4) and post-pruning (6) gcsa (7) indices are created to proceed with the alignments with vg map (8). The snarls are computed from the xg index (5) and the read support (pack) is extracted from the gam files (9) to finally proceed with the variant genotyping (10). b Linkage disequilibrium decay in the SNP dataset used for the pan-GWAS. Half-decay is represented in yellow, while minimum decay with a threshold set to LD < 0.1 is colored in orange. The number of points was randomly down-sampled to 50 k for visual representation. c Manhattan plot representing significant association with the chloride concentration in the leaves. Significant associations are detected using a Bonferroni threshold set to -log10(0.05/n) and colored in orange. The SNPs are represented as light grey points, and the SVs as dark grey triangles. d Manhattan plot focused on the significant region in chromosome 8 outlined by the orange box in c for the association with the leaf chloride concentration. The filling color is based on the pairwise linkage disequilibrium with the SNP located at chr08:13598495. The gene structural annotation of this region is represented at the bottom. e Chloride concentrations (M) in the roots (x-axis) and in the leaves (y-axis) from the different samples used for the GWAS. Samples corresponding to the accessions assembled and used in the pangenome are filled in black. The colors represent the genotype at the significant SNP, homozygous reference (0/0) in green, heterozygous (0/1) in grey, and homozygous alternative (1/1) in orange