温血马肌纤维病候选基因表达和编码序列变异。
Candidate gene expression and coding sequence variants in Warmblood horses with myofibrillar myopathy.
机构信息
Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA.
Department of Animal Science, University of Nebraska Lincoln, Lincoln, NE, USA.
出版信息
Equine Vet J. 2021 Mar;53(2):306-315. doi: 10.1111/evj.13286. Epub 2020 Jun 25.
BACKGROUND
Myofibrillar myopathy (MFM) of unknown aetiology has recently been identified in Warmblood (WB) horses. In humans, 16 genes have been implicated in various MFM-like disorders.
OBJECTIVES
To identify variants in 16 MFM candidate genes and compare allele frequencies of all variants between MFM WB and non-MFM WB and coding variants with moderate or severe predicted effects in MFM WB with publicly available data of other breeds. To compare differential gene expression and muscle fibre contractile force between MFM and non-MFM WB.
STUDY DESIGN
Case-control.
ANIMALS
8 MFM WB, 8 non-MFM WB, 33 other WB, 32 Thoroughbreds, 80 Quarter Horses and 77 horses of other breeds in public databases.
METHODS
Variants were called within transcripts of 16 candidate genes using gluteal muscle mRNA sequences aligned to EquCab3.0 and allele frequencies compared by Fisher's exact test among MFM WB, non-MFM WB and public sequences across breeds. Candidate gene differential expression was determined between MFM and non-MFM WB by fitting a negative binomial generalised log-linear model per gene (false discovery rate <0.05). The maximal isometric force/cross-sectional area generated by isolated membrane-permeabilised muscle fibres was determined.
RESULTS
None of the 426 variants identified in 16 candidate genes were associated with MFM including 26 missense variants. Breed-specific differences existed in allele frequencies. Candidate gene differential expression and muscle fibre-specific force did not differ between MFM WB (143.1 ± 34.7 kPa) and non-MFM WB (140.2 ± 43.7 kPa) (P = .8).
MAIN LIMITATIONS
RNA-seq-only assays transcripts expressed in skeletal muscle. Other possible candidate genes were not evaluated.
CONCLUSIONS
Evidence for association of variants with a disease is essential because coding sequence variants are common in the equine genome. Variants identified in MFM candidate genes, including two coding variants offered as commercial MFM equine genetic tests, did not associate with the WB MFM phenotype.
背景
最近在温血马中发现了病因不明的肌原纤维肌病（MFM）。在人类中，已有 16 种基因与各种 MFM 样疾病有关。
目的
鉴定 16 种 MFM 候选基因中的变异，并比较 MFM 温血马和非 MFM 温血马之间所有变异的等位基因频率，以及在 MFM 温血马中具有中度或重度预测效应的编码变异与其他品种的公开数据。比较 MFM 和非 MFM 温血马之间的差异基因表达和肌肉纤维收缩力。
研究设计
病例对照。
动物
8 匹 MFM 温血马、8 匹非 MFM 温血马、33 匹其他温血马、32 匹纯血马、80 匹夸特马和 77 匹其他品种马的公共数据库。
方法
使用与 EquCab3.0 对齐的臀肌 mRNA 序列，在 16 个候选基因的转录本内调用变异，并通过 Fisher 精确检验比较 MFM 温血马、非 MFM 温血马和跨品种公共序列中的等位基因频率。通过为每个基因拟合负二项广义对数线性模型（错误发现率<0.05）确定 MFM 和非 MFM 温血马之间的候选基因差异表达。确定分离的膜渗透化肌纤维产生的最大等长力/横截面积。
结果
在 16 个候选基因中鉴定的 426 个变异中，没有一个与 MFM 相关，包括 26 个错义变异。等位基因频率存在品种特异性差异。MFM 温血马（143.1±34.7 kPa）和非 MFM 温血马（140.2±43.7 kPa）之间的候选基因差异表达和肌肉纤维特异性力没有差异（P=0.8）。
主要局限性
RNA-seq 仅检测骨骼肌中表达的转录本。其他可能的候选基因未进行评估。
结论
由于编码序列变异在马基因组中很常见，因此与疾病相关的变异证据至关重要。在 MFM 候选基因中鉴定的变异，包括作为商业 MFM 马遗传测试提供的两个编码变异，与 WB MFM 表型无关。
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