Variant in the RFWD3 gene associated with PATN1, a modifier of leopard complex spotting.

The research is about identifying a variant in the RFWD3 gene that is related to PATN1, a major modifier of Leopard complex spotting (a pattern of depigmentation in horses). It was discovered using whole transcriptome sequencing, Sequenom assays, and linkage analysis and may be useful for breeders selecting for high white patterning.

*Background*

• Leopard complex spotting (LP) is a unique depigmentation pattern in horses caused by an incompletely dominant mutation in the TRPM1 gene.
• While the LP mutation allows for various patterns, other loci – positions on a chromosome – are responsible for modifying the extent of the white color.
• Pedigree analysis of families with high levels of LP patterning suggested a single dominant gene, Pattern-1 (PATN1), as a major modifier of LP.

*Research Process*

• Linkage analysis was conducted in two half-sibling families with PATN1 mutations to identify the locus region for further investigation.
• Whole transcriptome sequencing of skin samples from horses with and without the PATN1 allele was then performed.
• The focus was to identify single nucleotide polymorphisms (SNPs) – differences at a single position in a DNA sequence among individuals – for fine mapping.
• Two Sequenom assays were used to genotype 192 individuals from five LP-carrying breeds.
• The first round identified a 1.6-Mb region without a clear candidate gene, leading to another round of fine mapping.

*Findings*

• The second round of mapping highlighted SNP ECA3:23 658 447T>G in the 3′-UTR of RFWD3.
• The resulting significance level reached was P = 1.063 × 10(-39), meaning it’s statistically highly significant.
• Sequencing of RFWD3 didn’t identify any coding polymorphisms – differences in one base in a DNA sequence – specific to horses with PATN1.
• However, genotyping of the RFWD3 3′-UTR SNP in additional LP animals and horses from other breeds supported the association (P = 4.17 × 10(-115)).

*Conclusion*

• The highlighted variant in the RFWD3 gene is a strong candidate for PATN1.
• This information could be particularly useful for breeders selecting for high levels of white patterning in LP horses.