Allelic Heterogeneity of Bovine Polledness Figure 2. DNA sequence variants in Polled and horned Holstein Friesian. (a) Positions of DNA sequence variants (DSV) detected in the eight HF animals are presented by bars for SNPs and inverted triangles for InDels, with red symbols for heterozygous and blue symbols for homozygous differences from the reference sequence. Homozygous polled bulls are PP-HF1, PP-HF2 and PP-HF3. Pp-HF4 is declared as heterozygous polled and pp-HF5, pp-HF6, pp-HF7 and pp-HF8 are horned. Annotated genes and ESTs lying in the re-sequenced region are shown in the green shaded region. The five candidate mutations for polledness are superimposed: three SNPs were outlined by red crosses, 5 bp InDel and the duplicated region P80kbID were highlighted by inverted triangle. The red triangle area above P80kbID marks the duplicated sequence. (b) Within-species conservation. The nucleotide diversity in the re-sequenced region is shown by a density plot of bovine variants from dbSNP per kb. (c) Copy number variations. The ratio of mapped sequence reads between polled and horned animals is plotted with blue dots. The red line represents the result of segmentation analysis, showing the average ratio in the determined bins. (d) Across-species conservation. For each candidate mutation the surrounding base conservation for species without horn, bovid species and all aligned species was determined as PhastCons score calculated from MULTIZ alignments. As an example, here we display the base conservation for the candidate mutation PC1768587A. (e) The underlying multi-species alignment for the across- PLoS ONE | www.plosone.org 4 June 2012 | Volume 7 | Issue 6 | e39477