Descriptive statistics of identified CNVs.

Copy Number Variants (CNV) are modifications affecting the genome sequence of DNA, for instance, they can be duplications or deletions of a considerable number of base pairs (i.e., greater than 1000 bp and up to millions of bp). Their impact on the variation of the phenotypic traits has been widely demonstrated. In addition, CNVs are a class of markers useful to identify the genetic biodiversity among populations related to adaptation to the environment. The aim of this study was to detect CNVs in more than four thousand Holstein cows, using information derived by a genotyping done with the GGP (GeneSeek Genomic Profiler) bovine 100K SNP chip. To detect CNV the SVS 8.9 software was used, then CNV regions (CNVRs) were detected. A total of 123,814 CNVs (4,150 non redundant) were called and aggregated into 1,397 CNVRs. The PCA results obtained using the CNVs information, showed that there is some variability among animals. For many genes annotated within the CNVRs, the role in immune response is well known, as well as their association with important and economic traits object of selection in Holstein, such as milk production and quality, udder conformation and body morphology. Comparison with reference revealed unique CNVRs of the Holstein breed, and others in common with Jersey and Brown. The information regarding CNVs represents a valuable resource to understand how this class of markers may improve the accuracy in prediction of genomic value, nowadays solely based on SNPs markers.拷贝数变异（Copy Number Variants, CNV）是一类可改变基因组DNA序列的遗传变异，具体可表现为大片段碱基对的重复或缺失（长度介于1000 bp至数百万bp之间）。该类变异对表型性状变异的影响已被广泛证实。此外，CNV是一类可用于鉴定种群间遗传多样性的分子标记，有助于解析种群对环境的适应性机制。本研究旨在采用GGP（GeneSeek基因组分型仪）牛100K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片完成基因分型所获得的数据，对4000余头荷斯坦奶牛的CNV进行检测。本研究使用SVS 8.9软件完成CNV检测，并进一步鉴定得到拷贝数变异区域（Copy Number Variant Regions, CNVRs）。最终共检出123814个CNV（其中非冗余CNV共4150个），并将其整合为1397个CNVRs。基于CNV信息的主成分分析（Principal Component Analysis, PCA）结果显示，受试个体间存在一定的遗传变异。在CNVRs所覆盖的众多基因中，其在免疫应答中的功能已得到明确阐释，且这些基因与荷斯坦奶牛选育中的重要经济性状密切相关，包括产奶性能与奶品质、乳房形态以及体躯结构。通过与参考数据集比对，本研究鉴定得到荷斯坦奶牛特有的CNVRs，同时也发现了与泽西牛、褐牛共有的CNVRs。本研究获得的CNV相关数据，可为解析该类标记如何提升当前仅基于SNP标记的基因组育种值预测准确性提供重要参考依据。