Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse

Rebecca R Bellone,Padmanabhan Mahadevan,Bianca Haase,Johanna L A Paijmans,Janelle Nelson,Michael J Mienaltowski,Nityanand Maddodi,Samantha A Brooks,Sheila Archer,Vijayasaradhi Setaluri,Arne Ludwig,Martina Engensteiner,David L Adelson,Ralf Bortfeldt,Michael Hofreiter,Sulochana Devi,Tosso Leeb,G W Forsyth ,Mélanie Pruvost ,Daniel W Foerster ,Seng Han Lim ,Lynne S Sandmeyer ,Gloria G Fortes ,Heather M Holl ,Monika Reißmann ,Bruce H Grahn

doi:10.1371/journal.pone.0078280

Abstract

Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ2=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.

Highlights

Domestic mammals are selectively bred for variability in coat color and pattern, making pigmentation an attractive system to study
RNA sequencing determined that the three associated SNPs were not detected in a yet uncharacterized exon in horse TRPM1, as no reads were identified covering these SNPs in the five horses sequenced (Figure S1)
congenital stationary night blindness (CSNB) in Leopard complex spotting (LP) horses is explained by lack of normal TRPM1 transcription as night vision in mammals is controlled by depolarizing currents that result from the ON pathway visual system involving TRPM1 (Figure 7)

Summary

Introduction

Domestic mammals are selectively bred for variability in coat color and pattern, making pigmentation an attractive system to study. Leopard complex spotting (LP) is found in several breeds of horse and is characterized by the absence of pigment (white spotting) in the coat (Figure 1B and C), and associated pigmentation characteristics (Figure 2) [14]. These white spotting patterns tend to be symmetrical and centered over the hips. Varnish roaning is the progressive loss of pigment in the coat, as the horse ages, while maintaining full pigment on the bony surfaces of the face, hips, and, lower legs

Methods

Results

Conclusion