A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses.

The research article is about the identification of variations in the SLC45A2 gene that are responsible for distinct dilution phenotypes, particularly cream and pearl, in domestic horses.

Overview of the Study

The researchers conducted a gene-centric approach to identify variants in the SLC45A2 gene that are associated with certain dilution phenotypes in horses. Specifically, these phenotypes are cream and pearl dilutions. The cream dilution impacts red and black pigments depending on the number of alleles present, while the pearl dilution, which is recessive, also affects these pigments but requires two copies or one paired with a cream allele.

• Dilution traits such as cream and pearl are characteristics that modify the base coat colours in horses.
• The cream allele dilutes both red and black pigments when two copies exist, but only red when one copy is present.
• On the other hand, the pearl allele needs two copies or one copy paired with a cream allele to affect the pigments.

Methods Used

Two horses labelled as ‘false double dilute’, which appeared phenotypically homozygous cream but were found to possess only a single cream allele, were sequenced for the SLC45A2 gene. A known pearl carrier was also sequenced to identify potential causal variants.

• Researchers found a missense variant within the sequenced SLC45A2 gene in one false double dilute horse and the pearl carrier. This was also genotyped in additional 126 horses for statistical evaluation.
• Another variant, a novel missense variant, was found in the second false double dilute horse and one non-dilute offspring. This novel variant, dubbed the C variant after the horse’s name, produces a recessive dilution similar to pearl.

Findings of the Study

The genotype matched the expected phenotype in all horses (P-value = 6.5 x 10) and is identical to a pearl variant found previously.

• This genetic variant in SLC45A2 was associated with the expected diluted colour phenotype in all horses. The p-value indicates that this result is statistically significant.
• The new variant found also resulted in a recessive dilution, demonstrating that multiple alleles of SLC45A2 can cause different dilution phenotypes in horses.

In conclusion, variations in the SLC45A2 gene can cause different dilution phenotypes in horses. This study enhances our understanding of horse coat colour genetics and could be useful for horse breeders and geneticists.