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Variant in the RFWD 3 gene associated with PATN 1 , a modifier of leopard complex spotting
Author(s) -
Holl H. M.,
Brooks S. A.,
Archer S.,
Brown K.,
Malvick J.,
Penedo M. C. T.,
Bellone R. R.
Publication year - 2016
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12375
Subject(s) - biology , spotting , gene , leopard , genetics , zoology , computer science , artificial intelligence
Summary Leopard complex spotting ( LP ), the result of an incompletely dominant mutation in TRPM 1 , produces a collection of unique depigmentation patterns in the horse. Although the LP mutation allows for expression of the various patterns, other loci are responsible for modification of the extent of white. Pedigree analysis of families segregating for high levels of patterning indicated a single dominant gene, named Pattern‐1 ( PATN 1 ), as a major modifier of LP . Linkage analysis in two half‐sibling families segregating for PATN 1 identified a 15‐Mb region on ECA 3p that warranted further investigation. Whole transcriptome sequencing of skin samples from horses with and without the PATN 1 allele was performed to identify genic SNP s for fine mapping. Two Sequenom assays were utilized to genotype 192 individuals from five LP ‐carrying breeds. The initial panel highlighted a 1.6‐Mb region without a clear candidate gene. In the second round of fine mapping, SNP ECA 3:23 658 447T>G in the 3′‐ UTR of RING finger and WD repeat domain 3 ( RFWD 3 ) reached a significance level of P = 1.063 × 10 −39 . Sequencing of RFWD 3 did not identify any coding polymorphisms specific to PATN 1 horses. Genotyping of the RFWD 3 3′‐ UTR SNP in 54 additional LP animals and 327 horses from nine breeds not segregating for LP further supported the association ( P = 4.17 × 10 −115 ). This variant is a strong candidate for PATN 1 and may be particularly useful for LP breeders to select for high levels of white patterning.