Rohrer G A, Freking B A, Nonneman D
USDA, ARS, US Meat Animal Research Center, PO Box 166, Spur 18D, Clay Center, NE 68933-0166, USA.
Anim Genet. 2007 Jun;38(3):253-8. doi: 10.1111/j.1365-2052.2007.01593.x. Epub 2007 Apr 13.
Single nucleotide polymorphisms (SNPs) have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, allele frequencies for public SNP markers in commercial pig populations have not been available. To fulfil this need, SNP markers previously mapped in the USMARC swine reference population were tested in a panel of 155 boars that were representative of US purebred Duroc, Hampshire, Landrace and Yorkshire populations. Multiplex assay groups of 5-7 SNP assays/group were designed and genotypes were determined using Sequenom's massarray system. Of 80 SNPs that were evaluated, 60 SNPs with minor allele frequencies >0.15 were selected for the final panel of markers. Overall identity power across breeds was 4.6 x 10(-23), but within-breed values ranged from 4.3 x 10(-14) (Hampshire) to 2.6 x 10(-22) (Yorkshire). Parentage exclusion probability with only one sampled parent was 0.9974 (all data) and ranged from 0.9594 (Hampshire) to 0.9963 (Yorkshire) within breeds. Sire exclusion probability when the dam's genotype was known was 0.99998 (all data) and ranged from 0.99868 (Hampshire) to 0.99997 (Yorkshire) within breeds. Power of exclusion was compared between the 60 SNP and 10 microsatellite markers. The parental exclusion probabilities for SNP and microsatellite marker panels were similar, but the SNP panel was much more sensitive for individual identification. This panel of SNP markers is theoretically sufficient for individual identification of any pig in the world and is publicly available.
随着能够产生准确基因型的自动化基因分型系统的开发，单核苷酸多态性（SNP）已成为商业诊断和亲子鉴定基因分型应用中的一种重要标记类型。不幸的是，商业猪群中公共SNP标记的等位基因频率尚无可用数据。为满足这一需求，对先前在美国肉类动物研究中心（USMARC）猪参考群体中定位的SNP标记，在一组155头公猪中进行了测试，这些公猪代表了美国纯种杜洛克、汉普夏、长白和约克夏猪群。设计了每组5 - 7个SNP检测的多重检测组，并使用Sequenom的质谱分析系统确定基因型。在评估的80个SNP中，选择了60个次要等位基因频率>0.15的SNP作为最终的标记组。各品种间的总体个体识别能力为4.6×10⁻²³，但品种内的值范围从4.3×10⁻¹⁴（汉普夏）到2.6×10⁻²²（约克夏）。仅对一个采样亲本的亲权排除概率为0.9974（所有数据），品种内范围从0.9594（汉普夏）到0.9963（约克夏）。当母本基因型已知时，父本排除概率为0.99998（所有数据），品种内范围从0.99868（汉普夏）到0.99997（约克夏）。比较了60个SNP标记和10个微卫星标记的排除能力。SNP和微卫星标记组的亲本排除概率相似，但SNP组在个体识别方面更为敏感。这组SNP标记理论上足以对世界上任何一头猪进行个体识别，并且是公开可用的。
