Fig. 1

Schematic representation of SLDP and different SNP distributions across the genome. a Schematic representation of SLDP. SNPs (per cycle) marked in light red represent “important SNPs,” while those in light blue represent other SNPs. The set of “important SNPs” is marked according to GWAS prior information. SLDP retains all “important SNPs” in sliding window-based LD pruning. b Schematic illustration of the SNP distribution for different marker sets. The SNPs along the genome are colored according to their GWAS–logP value, with red and gray indicating high or low significance levels in GWAS, respectively. The GBS and chip sets were extracted from the LCS panel and SNPs non-overlapping with the LCS panel nearest and within the 1 kb range were extracted; only autosomal SNPs were retained