Mapping statistics of illumina reads.

<p>Mapping statistics of illumina reads.</p

Probe counts by significance and fold-change (fc) in testes of F0 boars.

<p>#significants: Number of significant probes that differ between the two groups on the significance level indicated.</p><p>FDR: False discovery rate.</p

Methylating nutrients contents of the diets fed the F0 boars (per kg diet).

<p>Methylating nutrients contents of the diets fed the F0 boars (per kg diet).</p

Dot plot of human Chr15:27,500,001–29,000,000 against dog Chr3:31,500,001–33,000,000.

<p>The human <i>OCA2</i> gene spans 380 kb. The dot plot illustrates that ~300 kb of dog reference sequence are inverted with respect to the human sequence due to an assembly error in the current CanFam 3.1 assembly. Due to this assembly error the first two exons of the canine <i>OCA2</i> gene are currently in the wrong orientation and annotated as <i>LOC100855460</i>.</p

<i>OCA2</i> splice site variant in German Spitz dogs with oculocutaneous albinism

<div><p>We investigated a German Spitz family where the mating of a black male to a white female had yielded three puppies with an unexpected light brown coat color, lightly pigmented lips and noses, and blue eyes. Combined linkage and homozygosity analysis based on a fully penetrant monogenic autosomal recessive mode of inheritance identified a critical interval of 15 Mb on chromosome 3. We obtained whole genome sequence data from one affected dog, three wolves, and 188 control dogs. Filtering for private variants revealed a single variant with predicted high impact in the critical interval in <i>LOC100855460</i> (XM_005618224.1:c.377+2T>G LT844587.1:c.-45+2T>G). The variant perfectly co-segregated with the phenotype in the family. We genotyped 181 control dogs with normal pigmentation from diverse breeds including 22 unrelated German Spitz dogs, which were all homozygous wildtype. Comparative sequence analyses revealed that <i>LOC100855460</i> actually represents the 5’-end of the canine <i>OCA2</i> gene. The CanFam 3.1 reference genome assembly is incorrect and separates the first two exons from the remaining exons of the <i>OCA2</i> gene. We amplified a canine <i>OCA2</i> cDNA fragment by RT-PCR and determined the correct full-length mRNA sequence (LT844587.1). Variants in the <i>OCA2</i> gene cause oculocutaneous albinism type 2 (OCA2) in humans, pink-eyed dilution in mice, and similar phenotypes in corn snakes, medaka and Mexican cave tetra fish. We therefore conclude that the observed oculocutaneous albinism in German Spitz is most likely caused by the identified variant in the 5’-splice site of the first intron of the canine <i>OCA2</i> gene.</p></div

Estimates of effects on carcass traits of F2 offspring from differentially fed F0 boars.

<p>c: control diet, e: experimental diet, b: barrow, f: female, Est.: Estimate of the effect.</p

Coat color phenotypes in the investigated Giant Spitz family.

<p><b>(A)</b> White mother and black father of the litter. (<b>B)</b> Pictures of two affected puppies and one unaffected sibling on the left at one week of age. <b>(C, E)</b> Affected dog GS103 with green eyes and a light nose at 4 and 5.5 months of age, respectively. <b>(D, F)</b> Affected dog GS104 at 4 and 7 months of age, respectively.</p

Coat color phenotypes in the investigated Giant Spitz family.

<p><b>(A)</b> White mother and black father of the litter. (<b>B)</b> Pictures of two affected puppies and one unaffected sibling on the left at one week of age. <b>(C, E)</b> Affected dog GS103 with green eyes and a light nose at 4 and 5.5 months of age, respectively. <b>(D, F)</b> Affected dog GS104 at 4 and 7 months of age, respectively.</p

Design of the three generation pig feeding experiment.

<p>One group of the F0 boars received a diet enriched with methylating micronutrients (experimental diet E). The F2 offspring were derived from either the F0 boars that received the control diet C or from the F0 boars that received the experimental diet E.</p

Clustering heat maps for the gene expression analysis.

<p>Clustering heat maps for the gene expression analysis in gluteus muscle (GM), liver and kidney of F2 control (C) and F2 experimental (E) pigs are shown. The clustering of significant genes (significance threshold 0.01 and log2 Ratio threshold 1(FC>2)) for GM, liver and kidney with respective 79, 64 and 53 genes are shown. The sex of the pigs and their grouping is given on the top of the heat map of GM for all tissues. The color key of fold change is indicated.</p