Ben Sassi Neila, González-Recio Óscar, de Paz-Del Río Raquel, Rodríguez-Ramilo Silvia T, Fernández Ana I
Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-INIA. Ctra La Coruña km 7.5, 28040 Madrid, Spain.
Departamento Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-INIA. Ctra La Coruña km 7.5, 28040 Madrid, Spain; Departamento Técnico Conafe, Ctra. Andalucía, Km. 23.6, 28340 Valdemoro, Madrid, Spain.
J Dairy Sci. 2016 Aug;99(8):6371-6380. doi: 10.3168/jds.2015-10487. Epub 2016 May 18.
Copy number variants (CNV) are structural variants consisting of duplications or deletions of genomic fragments longer than 1 kb that present variability in the population and are heritable. The objective of this study was to identify CNV regions (CNVR) associated with 7 economically important traits (production, functional, and type traits) in Holstein cattle: fat yield, protein yield, somatic cell count, days open, stature, foot angle, and udder depth. Copy number variants were detected by using deep-sequencing data from 10 sequenced bulls and the Bovine SNP chip array hybridization signals. To reduce the number of false-positive calls, only CNV identified by both sequencing and Bovine SNP chip assays were kept in the final data set. This resulted in 823 CNVR. After filtering by minor allele frequency >0.01, a total of 90 CNVR appeared segregating in the bulls that had phenotypic data. Linear and quadratic CNVR effects were estimated using Bayesian approaches. A total of 15 CNVR were associated with the traits included in the analysis. One CNVR was associated with fat and protein yield, another 1 with fat yield, 3 with stature, 1 with foot angle, 7 with udder depth, and only 1 with days open. Among the genes located within these regions, highlighted were the MTHFSD gene that belongs to the folate metabolism genes, which play critical roles in regulating milk protein synthesis; the SNRPE gene that is related to several morphological pathologies; and the NF1 gene, which is associated with potential effects on fertility traits. The results obtained in the current study revealed that these CNVR segregate in the Holstein population, and therefore some potential exists to increase the frequencies of the favorable alleles in the population after independent validation of results in this study. However, genetic variance explained by the variants reported in this study was small.
拷贝数变异（CNV）是一种结构变异，由长度超过1 kb的基因组片段的重复或缺失组成，在群体中呈现变异性且具有遗传性。本研究的目的是鉴定与荷斯坦奶牛7个经济重要性状（生产、功能和类型性状）相关的CNV区域（CNVR）：产脂量、产蛋白量、体细胞计数、空怀天数、体高、蹄角度和乳房深度。利用来自10头测序公牛的深度测序数据和牛SNP芯片阵列杂交信号检测拷贝数变异。为了减少假阳性检出数量，最终数据集中仅保留通过测序和牛SNP芯片检测均鉴定出的CNV。这产生了823个CNVR。在通过次要等位基因频率>0.01进行过滤后，共有90个CNVR在具有表型数据的公牛中呈现分离状态。使用贝叶斯方法估计线性和二次CNVR效应。共有15个CNVR与分析中包含的性状相关。一个CNVR与产脂量和产蛋白量相关，另一个与产脂量相关，3个与体高相关，1个与蹄角度相关，7个与乳房深度相关，仅一个与空怀天数相关。在这些区域内的基因中，突出的有属于叶酸代谢基因的MTHFSD基因，其在调节乳蛋白合成中起关键作用；与多种形态病理学相关的SNRPE基因；以及与生育性状潜在影响相关的NF1基因。本研究获得的结果表明，这些CNVR在荷斯坦群体中呈现分离状态，因此在本研究结果独立验证后，存在提高群体中有利等位基因频率的潜力。然而，本研究报道的变异所解释的遗传方差较小。
