Mitochondrial DNA copy number (mtDNA CN) has been shown to be highly heritable and associated with traits of interest in humans. However, studies are lacking in the literature for livestock species such as beef cattle. In this study, 2,371 individuals from a crossbred beef population comprising the Germplasm Evaluation program from the U.S. Meat Animal Research Center had samples of blood, leucocyte, or semen collected for low-pass sequencing (LPS) that resulted in both nuclear DNA (nuDNA) and mitochondrial DNA (mtDNA) sequence reads. Mitochondrial DNA CN was estimated based on the ratio of mtDNA to nuDNA coverages. Genetic parameters for mtDNA CN were estimated from an animal model based on a genomic relationship matrix (~87K SNP from the nuDNA). Different models were used to test the effects of tissue, sex, age at sample collection, heterosis, and breed composition. Maternal effects, assessed by fitting a maternal additive component and by fitting eleven SNP on the mtDNA, were also obtained. As previously reported, mtDNA haplotypes were used to classify individuals into Taurine haplogroups (T1, T2, T3/T4, and T5). Estimates of heritability when fitting fixed effects in addition to the intercept were moderate, ranging from 0.11 to 0.31 depending on the model. From a model ignoring contemporary group, semen samples had the lowest mtDNA CN, as expected, followed by blood and leucocyte samples (P ≤ 0.001). The effect of sex and the linear and quadratic effects of age were significant (P ≤ 0.02) depending on the model. When significant, females had greater mtDNA CN than males. The effects of heterosis and maternal heterosis were not significant (P ≥ 0.47). The estimates of maternal and mtDNA heritability were near zero (≤0.03). Most of the samples (98%) were classified as haplogroup T3. Variation was observed in the mtDNA within Taurine haplogroups, which enabled the identification of 24 haplotypes. These results suggest that mtDNA CN is under nuclear genetic control and would respond favorably to selection.

中文翻译：

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环境因素和遗传变异对线粒体DNA拷贝数的影响

线粒体 DNA 拷贝数 (mtDNA CN) 已被证明具有高度遗传性，并且与人类感兴趣的特征相关。然而，文献中缺乏对肉牛等牲畜的研究。在这项研究中，来自美国肉类动物研究中心种质资源评估计划的杂交牛肉种群的 2,371 名个体收集了血液、白细胞或精液样本用于低通测序 (LPS)，从而产生核 DNA (nuDNA)和线粒体 DNA (mtDNA) 序列读数。线粒体 DNA CN 是根据 mtDNA 与 nuDNA 覆盖率的比率来估计的。mtDNA CN 的遗传参数是根据基于基因组关系矩阵（来自 nuDNA 的约 87K SNP）的动物模型估算的。使用不同的模型来测试组织、性别、样本采集时的年龄、杂种优势、和品种组成。还获得了母体效应，通过拟合母体附加成分和通过在 mtDNA 上拟合 11 个 SNP 来评估。如前所述，mtDNA 单倍型用于将个体分类为牛磺酸单倍群（T1、T2、T3/T4 和 T5）。除截距外，拟合固定效应时的遗传力估计值适中，范围从 0.11 到 0.31，具体取决于模型。从忽略当代组的模型来看，精液样本的 mtDNA CN 最低，正如预期的那样，其次是血液和白细胞样本 (P ≤ 0.001)。根据模型的不同，性别的影响以及年龄的线性和二次效应是显着的 (P ≤ 0.02)。当显着时，女性的 mtDNA CN 高于男性。杂种优势和母系杂种优势的影响不显着（P≥0.47）。母体和 mtDNA 遗传力的估计值接近于零 (≤0.03)。大多数样本 (98%) 被归类为单倍群 T3。在牛磺酸单倍群内​​的 mtDNA 中观察到变异，这使得能够识别 24 种单倍型。这些结果表明 mtDNA CN 处于核遗传控制之下，并且会对选择做出有利的反应。