利用微卫星和SNP标记信息进行奶牛亲子鉴定的模拟研究

摘要

The objective of this study was to compare the efficiency of microsatellites and single nucleotide polymorphism (SNP) markers in paternity identification. Microsatellites or SNP geno types of 10000 pseudo-parent-child relationship individuals were randomly simulated, exclusion approach was employed in paternity identification, and this procedure was repeated 100 times.The results showed that exclusion probability was mostly influenced by the polymorphism of markers. To achieve the same exclusion probability, the needed number of low polymorphic markers was greatly higher than that of high polymorphic markers. When the genotypes of the actual mother were available, the efficiency of paternity inference could be greatly improved. No matter to high or low polymorphic markers, more SNPs were required than microsatellites in each inferential scenario, to achieve the same exclusion probability. When the average heterozygosity of SNPs and microsatellites were 0. 484 and 0. 875, the needed number of SNPs was 5～6 times more than that of microsatellites. When the average heterozygosity of SNPs and microsatellites were 0. 363 and 0. 566, the needed number of SNPs was about 2 times more than that of microsatellites. When at least 2 conflicts were required in inference, 0. 45 times more markers were necessary, to achieve the same exclusion probability (＞ 0. 99) , comparing to that required at least 1 conflict, for both two kinds of markers. With the dropping of the genotyping cost, and other characteristics of SNPs, such as lower genotyping error rate, higher repeatability and amenable to high-throughput automated analysis, it is very promising that SNPs would replace microsatellites for dairy paternity identification in the future.%本研究旨在比较微卫星标记和单核苷酸多态(SNP)标记进行奶牛亲子鉴定的效率.研究中随机模拟了10 000对含微卫星或SNP标记信息的非亲子关系的个体,用排除法进行亲子鉴定,该过程重复100次.结果表明,标记的多态性对于排除概率的影响最大.达到同样的排除概率,所需低多态标记数量远高于高多态标记.当真实母亲基因型已知时,个体父亲的推断效率较高.达到同样的排除概率,无论标记多态性高或低,3种鉴定类型所需SNP标记数量均大于微卫星标记.当SNP和微卫星标记的平均杂合度为0.484和0.875时,需要的SNP标记数是微卫星标记的5～6倍;当SNP和微卫星标记的平均杂合度为0.363和0.566时,需要的SNP标记数约是微卫星标记的2倍.在2种标记中,达到同样排除概率(大于0.99),采用至少2个矛盾推断原则推断所需标记数为单个矛盾推断原则的1.45倍.结果表明,由于SNP标记具有误判率低、重复性高和易于高通量自动化检测等特点,随着检测成本降低,SNP标记将来完全有可能取代微卫星标记用于奶牛群体的亲子鉴定.