Figure 2.

A genome wide association study (GWAS) identifies the locus for mushroom phenotype in Shetland Ponies. (A) Manhattan Plot for the χ² basic allelic association test. (B) Single locus mixed linear model (SLMM) utilizing an F-test to calculate p-values. (A,B) Plotted on the y-axis are the -log 10P values calculated for each test against the chromosomes plotted on the x-axis. The horizontal black line across each plot represents Bonferroni significance (P < 1.4 × 10⁻⁷). (C) A 326 kb region on ECA7 reaching genome wide significance. Plotted in blue are the data points from the SLMM GWAS analysis (N = 24). Plotted in green are the eight SNPs from this region genotyped in our replication sample set, displaying the combined p-values under a recessive model for the GWAS and replication sample sets (N = 40 mushroom ponies, N = 29 chestnut).