全基因组测序鉴定出弗里西亚马的 ECA13 上与双行睫毛有关的 16 千碱基缺失。

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

机构信息

Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA.

Department of Clinical Sciences, Utrecht University, Yalelaan 112-114, NL-3584, CM, Utrecht, The Netherlands.

出版信息

BMC Genomics. 2020 Nov 30;21(1):848. doi: 10.1186/s12864-020-07265-8.

DOI:10.1186/s12864-020-07265-8

PMID:33256610

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7706231/

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 (p = 0.016 and 0.032, respectively). Only the locus on ECA13 withstood replication testing (p = 1.6 × 10, 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). 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.

摘要

背景

双行睫，一种眼部疾病，睫毛从眼睑的麦氏腺开口处长出，已在弗里西亚马中报告。这些错位的睫毛会引起不适、慢性角膜炎和角膜溃疡，如果角膜纤维化，可能会影响视力，或者如果继发感染，可能会导致眼睛丧失。弗里西亚马是报道的大多数马双行睫的病例，由于该品种已知存在遗传性单基因疾病，因此假设这种情况是一种简单的常染色体隐性孟德尔性状。

结果

使用 Axiom 670k 马基因分型阵列（MNEc670k）进行了全基因组关联研究（GWAS），该研究利用 14 例双行睫病例和 38 例对照进行了表型分析。一个加性单基因座混合线性模型（EMMAX）方法确定了 ECA5 上的 1.83Mb 座和 ECA13 上的 1.34Mb 座，达到了全基因组显著水平（分别为 p=0.016 和 0.032）。只有 ECA13 上的座经受住了复制测试（p=1.6×10，病例：n=5，对照：n=37）。在 14 例病例中的 13 例中发现了 ECA13 上的 371kb 纯合性运行（ROH），这为隐性遗传模式提供了证据。单倍型分析（hapQTL）将 ECA13 上的关联区域缩小到 163kb。对 3 例病例和 2 例对照的全基因组测序数据进行分析，确定了 ECA13 相关单倍型内的 16kb 缺失（ECA13：g.178714_195130del）。功能注释数据支持该基因座的组织特异性调节作用。该缺失与双行睫有关，因为 19 例病例中有 18 例为纯合子（p=4.8×10）。在 54 个不同品种的 955 匹马中对该缺失进行基因分型，仅在 11 匹非弗里西亚马中发现了缺失，所有这些马都是携带者，这表明这可能是弗里西亚疾病的原因。