Fig. 2

Genome-wide summary of the data mining for the Brown Swiss population. In the outer circles, the identified haplotypes per chromosome with reduced homozygosity for the trio-based approach are indicated in dark blue and their associated haplotypes of the pgp-based approach in light blue. Note that only the haplotypes that were detected through the pgp-based approach are shown if, within the same region, another haplotype was detected by the trio-based approach. The circle with the brown dots indicates LD (r²) between haplotypes and markers on the custom SNP array. Note that the dot size correlates with the extent of LD. The third circle shows the significant haplotype association results. Note that the different colors represent the three groups of evaluated traits and the dot size correlates with the significance values accordingly. The three inner circles present the significant GWAS results across all fertility (purple), birth (red), and growth-related (yellow) traits. Scales are based on the −log10(p-value). Note that the red arrows indicate the previously identified haplotypes BH1 and BH2 [19] and the herein described MRPL55-related haplotype BH14, as well as the BH14, BH24 and BH34 haplotypes and their associated genes that harbor the most likely causative variants