Accumulating mutations in series of haplotypes at the KIT and MITF loci are major determinants of white markings in Franches-Montagnes horses.

Coat color and pattern variations in domestic animals are frequently inherited as simple monogenic traits, but a number are known to have a complex genetic basis. While the analysis of complex trait data remains a challenge in all species, we can use the reduced haplotypic diversity in domestic animal populations to gain insight into the genomic interactions underlying complex phenotypes. White face and leg markings are examples of complex traits in horses where little is known of the underlying genetics. In this study, Franches-Montagnes (FM) horses were scored for the occurrence of white facial and leg markings using a standardized scoring system. A genome-wide association study (GWAS) was performed for several white patterning traits in 1,077 FM horses. Seven quantitative trait loci (QTL) affecting the white marking score with p-values p≤10(-4) were identified. Three loci, MC1R and the known white spotting genes, KIT and MITF, were identified as the major loci underlying the extent of white patterning in this breed. Together, the seven loci explain 54% of the genetic variance in total white marking score, while MITF and KIT alone account for 26%. Although MITF and KIT are the major loci controlling white patterning, their influence varies according to the basic coat color of the horse and the specific body location of the white patterning. Fine mapping across the MITF and KIT loci was used to characterize haplotypes present. Phylogenetic relationships among haplotypes were calculated to assess their selective and evolutionary influences on the extent of white patterning. This novel approach shows that KIT and MITF act in an additive manner and that accumulating mutations at these loci progressively increase the extent of white markings

A Mutation in the SUV39H2 Gene in Labrador Retrievers with Hereditary Nasal Parakeratosis (HNPK) Provides Insights into the Epigenetics of Keratinocyte Differentiation.

Peer reviewe

Mutations in MITF and PAX3 Cause “Splashed White” and Other White Spotting Phenotypes in Horses

During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The “splashed white” pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white horses are deaf. We analyzed a Quarter Horse family segregating for the splashed white coat color. Genome-wide linkage analysis in 31 horses gave a positive LOD score of 1.6 in a region on chromosome 6 containing the PAX3 gene. However, the linkage data were not in agreement with a monogenic inheritance of a single fully penetrant mutation. We sequenced the PAX3 gene and identified a missense mutation in some, but not all, splashed white Quarter Horses. Genome-wide association analysis indicated a potential second signal near MITF. We therefore sequenced the MITF gene and found a 10 bp insertion in the melanocyte-specific promoter. The MITF promoter variant was present in some splashed white Quarter Horses from the studied family, but also in splashed white horses from other horse breeds. Finally, we identified two additional non-synonymous mutations in the MITF gene in unrelated horses with white spotting phenotypes. Thus, several independent mutations in MITF and PAX3 together with known variants in the EDNRB and KIT genes explain a large proportion of horses with the more extreme white spotting phenotypes

Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.

Variants in the EDNRB, KIT, MITF, PAX3 and TRPM1 genes are known to cause white spotting phenotypes in horses, which can range from the common white markings up to completely white horses. In this study, we investigated these candidate genes in 169 horses with white spotting phenotypes not explained by the previously described variants. We identified a novel missense variant, PAX3:p.Pro32Arg, in Appaloosa horses with a splashed white phenotype in addition to their leopard complex spotting patterns. We also found three novel variants in the KIT gene. The splice site variant c.1346+1G>A occurred in a Swiss Warmblood horse with a pronounced depigmentation phenotype. The missense variant p.Tyr441Cys was present in several part-bred Arabians with sabino-like depigmentation phenotypes. Finally, we provide evidence suggesting that the common and widely distributed KIT:p.Arg682His variant has a very subtle white-increasing effect, which is much less pronounced than the effect of the other described KIT variants. We termed the new KIT variants W18-W20 to provide a simple and unambiguous nomenclature for future genetic testing applications

Results of the logistic regression model analysis.

<p>Results of the logistic regression model analysis for the relationship between <i>MITF</i> haplotypes, SNPs across the 2 Mb <i>KIT</i> region <i>and KIT</i> haplotypes.</p

Phylogenetic relationship between haplotypes at <i>MITF</i> and <i>KIT</i>.

<p>Phylogenetic relationships between haplotypes at <i>MITF</i> (M1–M6) and <i>KIT</i> (K1–K7). Haplotype combinations (hap1 = haplotype 1, hap2 = haplotype 2) and individuals average total white markings score (aTSC = average Total Score) are shown on the right.</p

Phenotypic variation in the expression of white markings.

<p>Example of phenotypes. Horse (A) has a total score of white markings of 1 (head = 0; foreleg = 0; hind leg = 1); horse (B) has a total score of white markings of 19 (head = 9; foreleg = 2; hind leg = 8).</p

Genetic variance (%) explained by the three major candidate loci.

<p>The contributions of <i>MC1R</i>, <i>KIT</i> and <i>MITF</i> were calculated separately for each locus across a 2 Mb interval.</p

Average total white markings score for <i>MITF-KIT</i> haplotype combinations.

<p>Average total white markings score and standard deviation for <i>MITF-KIT</i> haplotype combinations. Adjacent squares represent haplotypes (red = <i>MITF</i>; blue = <i>KIT</i>); color shades represent haplotypes of the phylogenetic relationship trees (<i>MITF</i>: M1–M6; <i>KIT</i>: K1–K7).</p

GWAS identifies two major loci associated with total white marking scores.

<p>A Manhattan plot showing the negative log of the probability of association (p-value) between individual marker and total white marking score. (A) Analysis included horses of all colors, (B) bay horses only, (C) chestnut horses only. Markers are represented in different colors according to their chromosome. Significance level of p≤1×10⁻⁸ is indicated with a dashed red line; a dashed black line represents association with p≤10⁻⁴.</p