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

Area of Science:

• Animal Genetics
• Equine Coat Color Genetics
• Molecular Genetics

Background:

• Leopard complex spotting (LP) in horses is caused by a mutation in TRPM1, resulting in depigmentation patterns.
• Modifier loci influence the extent of white patterning, with Pattern-1 (PATN1) identified as a major dominant gene.

Purpose of the Study:

• To identify the genetic basis of the PATN1 modifier locus influencing LP spotting patterns.
• To fine-map the PATN1 locus and identify candidate genes or variants associated with increased white patterning.

Main Methods:

• Pedigree analysis and linkage analysis were used to narrow down the chromosomal region for PATN1 on ECA3p.
• Whole transcriptome sequencing and SNP genotyping were performed on horses with and without the PATN1 allele.
• Fine mapping utilized Sequenom assays and targeted sequencing of candidate genes like RFWD3.

Main Results:

• Linkage analysis identified a 15-Mb region on ECA3p, refined to a 1.6-Mb region.
• A significant association (P = 1.063 × 10(-39)) was found with SNP ECA3:23 658 447T>G in the 3 -UTR of RFWD3.
• Further genotyping confirmed the strong association of this RFWD3 SNP with PATN1 across multiple breeds (P = 4.17 × 10(-115)).

Conclusions:

• The RFWD3 3 -UTR SNP is a strong candidate for the PATN1 locus.
• This genetic variant can be a valuable tool for breeders aiming to select for horses with extensive white patterning in LP breeds.