Whole genome sequencing identified a 16 kilobase deletion on ECA13 associated with distichiasis in Friesian horses

Abstract

Background Distichiasis, an ocular disorder in which aberrant cilia (eyelashes) grow from the opening of the Meibomian glands of the eyelid, has been reported in Friesian horses. These misplaced cilia can cause discomfort, chronic keratitis, and corneal ulceration, potentially impacting vision due to corneal fibrosis, or, if secondary infection occurs, may lead to loss of the eye. Friesian horses represent the vast majority of reported cases of equine distichiasis, and as the breed is known to be affected with inherited monogenic disorders, this condition was hypothesized to be a simply inherited Mendelian trait. Results A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. An additive single locus mixed linear model (EMMAX) approach identified a 1.83 Mb locus on ECA5 and a 1.34 Mb locus on ECA13 that reached genome-wide significance (pcorrected = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10− 5, cases: n = 5 and controls: n = 37). A 371 kb run of homozygosity (ROH) on ECA13 was found in 13 of the 14 cases, providing evidence for a recessive mode of inheritance. Haplotype analysis (hapQTL) narrowed the region of association on ECA13 to 163 kb. Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). Functional annotation data supports a tissue-specific regulatory role of this locus. This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10− 13). Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. Conclusions This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. Further functional analysis in relevant tissues from cases and controls will help to clarify the precise role of this deletion in normal and abnormal eyelash development and investigate the hypothesis of incomplete penetrance.

Heritability estimates of distichiasis in Staffordshire bull terriers using pedigrees and genome-wide SNP data

“…The aberrant hairs arise from ectopic hair follicles close to the meibomian glands in the eyelid and mostly emerge from the duct openings of the meibomian glands on the margin of the eyelid as single or multiple hairs [ 2 , 3 ]. The disorder is common in dogs but has also been reported in cats [ 4 ], ferrets [ 5 ], and horses [ 6 ]. It is seen in both purebred and mixed-breed dogs [ 1 , 2 , 7 ].…”

“Adopt-a-Tissue” Initiative Advances Efforts to Identify Tissue-Specific Histone Marks in the Mare

“…While valuable, annotation of regulatory regions based solely on homology with other species is not expected to be sufficient given the evolutionary role of these elements within and among species (Schmidt et al, 2010 ; McLean et al, 2011 ; Shibata et al, 2012 ; Lowdon et al, 2016 ). With the first publication of the equine FAANG data from eight prioritized tissues (Kingsley et al, 2020 ) and the four “adopted” tissues presented in this manuscript, researchers can begin to interrogate the role of regulatory regions in equine traits, such as the recent investigation of a novel 16 KB deletion associated with an ocular disorder known as distichiasis (Hisey et al, 2020 ). Future annotations for the horse will include maps of regulatory states characteristic of healthy tissue, making it a vital resource to compare against disease states.…”

Decoding the Equine Genome: Lessons from ENCODE

“…Using genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) for these four marks in eight prioritized tissues in the two female FAANG horses, Kingsley et al reported over one million putative regulatory sites [69]. The utility of these data were demonstrated when a 16 kB intergenic deletion associated with an ocular condition in horses, namely distichiasis, was discovered and FAANG ChIP-seq data showed that this region harbors a tissue specific active enhancer [70]. Undoubtedly, these data will continue to aid in the understanding of other structural variants causing or associated with disease in the horse as additional tissues are evaluated.…”

“…Just three years after starting the tissue and data collection for the equine FAANG initiative, the community has completed over 400 experiments from more than 50 tissues using a variety of assays targeting different features of the horse regulatory landscape (Table 2). Data are being made available to the public as they are generated and evaluated for passing quality control measures; these data have been and continue to be utilized in unrelated research projects [5,70,115]. Integrated analysis is currently ongoing to provide a systematic annotation of major functional elements in the horse genome available, as a central hub hosted on UCSC genome browser to the research community.…”