Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs - Supporting information

Descriptions of Supplementary Information files: S1 Figure: Phenotyping validation on 350 randomly selected dogs: Strip plot showing original versus re-scored 6 point phenotypes for a random sample of 350 dogs from the discovery sample. The correlation coefficient (Pearson’s Rho) between the original and new phenotype scores is shown in the upper left hand corner of the plot. S2 Figure: Manhattan plots for additional GWAS: A. 6pt phenotype, no covariates. B. Binary phenotype, with covariates. C. Binary phenotype, no covariates. The data used to generate these plots are available in S1 File and S3 File. S3 Figure: Detailed view of regions surrounding the top CFA2 (A), 15 (B), 18 (C), 20 (D), and 21 (e) GWAS markers. Each panel shows the genomic region defined by the positions of the first upstream marker and last downstream marker with r2 ≥ 0.2 with the most significant GWAS marker on the chromosome (indicated by a red “x”). The top panel of each figure shows the GWAS -log10(p-value) and physical position of all GWAS markers in the region, colored by their r2 with the top GWAS marker. The bottom panel of each figure shows the canFam3.1 locations of known dog transcripts in this region. Transcription ranges are shown as dark blue rectangles, each of which is labelled with its Ensembl Genes (version 95) [81] transcript or gene name and its strand orientation (“>” = plus strand, “<” = minus strand). S4 Figure: CFA15 top marker genotype correlates with sequencing coverage in known CNV: A. Boxplots overlaid with strip plots show the distribution of mean normalized depth of coverage across the CFA15 CNV characterized in Weich et al. 2020 [32] (CFA15: 29,821,450-29,832,950 bp) for dogs with each possible BICF2G630433130 genotype. Each point represents a single dog. Kruskal Wallis test p-values are shown for each pair of genotypes. B. SRA run ID and sample name, breed, BICF2G630433130 genotype (coded as number of red-associated alleles), and CFA15 CNV mean normalized depth of coverage for all dogs shown in A. S1 Table (TSV): Full breed ancestry breakdown in discovery and validation datasets. S2 Table (XLXS): Summary of replication of top associations across GWAS using different phenotype encoding, with or without covariates. Columns show, for each top SNP in each GWAS, the marker ID, physical position, gene (if applicable), and the GWAS -log10(p-value), with the red-associated allele and the GWAS beta in parentheses. S3 Table (TSV): Wild canid WGS SRA accession info and genotypes at top GWAS SNPs used to generate Fig3A. S4 Table (XLXS): Data used for Fig 4. The “Fig4A” tab contains genetic dosage values at the top five GWAS SNPs for all dogs in the discovery dataset, as well as their six point phenotype values. The “Fig4B” tab includes the following for each top GWAS SNP: number of dogs genotyped (N), allele 1 frequency (p), allele 0 frequency (q), observed mean standardized 6pt phenotype values for each genotype class, the observed homozygote midpoint phenotype, additive effect (a), dominance effect (d), and the allelic substitution effect. S5 Table (TSV): Data shown in S4 Figure B, including SRA run ID and sample name, breed, BICF2G630433130 genotype, and CFA15 CNV mean normalized depth of coverage for 23 previously published whole genome sequence datasets. S1 File (TSV): Table with phenotype, phenotyping method (photo or breed average), E locus genotype, A locus genotype, K locus genotype, furnishings genotype, and CFA20:55855406 genotype for all dogs in the discovery and validation samples. These data were used to generate Fig3B. S2 File (TSV): Phenotyping validation data used to generate S1 Fig. S3 File (ZIP): Plink binary dataset containing genome-wide genotypes for all 3,057 dogs. S4 File (ZIP): GWAS outputs for discovery sample: GEMMA .assoc and .log files (.txt) for all GWAS using quantitative and binary phenotype encoding. S5 File (TSV): Model coefficients and performance metrics for all predictive models incorporating dominance and epistasis.