Bickhart Derek M, Liu George E
Animal Improvement Programs Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA.
Bovine Functional Genomics Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA.
Front Genet. 2014 Feb 18;5:37. doi: 10.3389/fgene.2014.00037. eCollection 2014.
Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among individuals of each species. Many of these variants have been linked to debilitating diseases in humans, thereby cementing the importance of refining methods for their detection. Despite progress in the field, reliable detection of SVs still remains a problem even for human subjects. Many of the underlying problems that make SVs difficult to detect in humans are amplified in livestock species, whose lower quality genome assemblies and incomplete gene annotation can often give rise to false positive SV discoveries. Regardless of the challenges, SV detection is just as important for livestock researchers as it is for human researchers, given that several productive traits and diseases have been linked to copy number variations (CNVs) in cattle, sheep, and pig. Already, there is evidence that many beneficial SVs have been artificially selected in livestock such as a duplication of the agouti signaling protein gene that causes white coat color in sheep. In this review, we will list current SV and CNV discoveries in livestock and discuss the problems that hinder routine discovery and tracking of these polymorphisms. We will also discuss the impacts of selective breeding on CNV and SV frequencies and mention how SV genotyping could be used in the future to improve genetic selection.
近期对人类和其他模式生物的研究表明，结构变异（SVs）在每个物种的个体变异中占相当大的比例。其中许多变异与人类的衰弱性疾病有关，从而巩固了改进其检测方法的重要性。尽管该领域取得了进展，但即使对于人类受试者，可靠检测SVs仍然是一个问题。许多导致人类中SVs难以检测的潜在问题在牲畜物种中被放大，其质量较低的基因组组装和不完整的基因注释常常会导致假阳性的SV发现。尽管存在挑战，但SV检测对牲畜研究人员和人类研究人员同样重要，因为牛、羊和猪的一些生产性状和疾病已与拷贝数变异（CNVs）相关联。已经有证据表明，许多有益的SVs已在牲畜中被人工选择，例如导致绵羊白色皮毛的刺鼠信号蛋白基因的重复。在本综述中，我们将列出牲畜中当前的SV和CNV发现，并讨论阻碍这些多态性常规发现和追踪的问题。我们还将讨论选择性育种对CNV和SV频率的影响，并提及未来如何使用SV基因分型来改善遗传选择。
