Animal Genomics, AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
PLoS One. 2014 Apr 16;9(4):e93392. doi: 10.1371/journal.pone.0093392. eCollection 2014.
Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.
准确的系谱信息对于动物育种系统至关重要，可确保遗传增益的最大化和近交的管理。大量可用的基因组数据，加上高通量基因分型平台的发展，意味着单核苷酸多态性（SNP）现在是基因组选择研究中首选的 DNA 标记。此外，与微卫星标记相比，SNP 的优越品质允许实验室之间进行标准化；这一特性对于开发用于可追溯性研究的国际标记集至关重要。本研究的目的是开发一种高通量 SNP 测定法，用于新西兰绵羊产业，以实现准确的系谱分配，并减少繁殖者在产羔期间的投入。这需要两个开发阶段——首先，开发一种从耳打孔组织中提取高质量 DNA 的方法，以实现高通量、低成本的效果；其次，开发一种 SNP 测定法，能够对群体交配所产生的后代进行亲子关系鉴定。使用似然法推断亲子关系，即给具有最高 LOD 评分（给定亲子关系的可能性与给定非亲子关系的可能性之比的对数）的父本分配。开发了一个 84 个“亲子 SNP 面板”，可将平均 99%的后代分配给一个父本，在一个有 3000 个后代来自 120 个群体交配父本的问题中，包括许多半同胞父本。在只有 6%的情况下，另一个父本至少有 0.02 的亲子关系概率。此外，没有母本信息（记录的或通过可能的母本基因分型），突出了 SNP 测试适合亲子关系鉴定。该亲子 SNP 测定法的应用将允许在大型商业农场中实施后代测试，从而提高父本分配和遗传评估的准确性，增加绵羊产业的遗传增益。
