畜禽群体中基于SNP标记的亲子鉴定及亲本推断方法

发布时间：2019-02-17 18:59

【摘要】：利用双亲高密度SNP标记信息,在畜禽群体中进行亲子鉴定及亲本推断新方法的计算机程序开发,并使用模拟的600 000个SNP标记对该程序进行测试。结果表明:对系谱正确性进行鉴定时,SNP标记数大于100即可达到100%的亲子鉴定准确率;对错误的系谱关系进行潜在亲子关系推断时,SNP标记数大于300可保证100%的推断准确率。标记平均MAF较低会降低亲子推断准确率。在程序运行效率方面,当使用50 000的SNP标记对1 000条错误率为10%的系谱进行亲子鉴定和推断时,共耗时332.87s,且计算耗时与标记数及个体数呈线性变化。本研究基于孟德尔遗传原理,设计并开发了基于双亲及后代基因型的亲子鉴定及亲本推断程序,该方法运行速度快,操作简单,准确性高,值得在畜禽群体基因组相关研究方面进行推广应用。
[Abstract]:Based on the high density SNP marker information of parents, a computer program was developed for paternity test and parental inference in livestock and poultry populations. The program was tested by simulated 600 000 SNP markers. The results showed that when the pedigree was correctly identified, the accuracy of paternity test could be 100% when the number of SNP markers was more than 100%. When the potential parent-child relationship is inferred from the wrong pedigree, the accuracy of the inference is 100% when the number of SNP markers is greater than 300. Low average MAF decreased the accuracy of parent-child inference. In terms of running efficiency of the program, it takes 332.87s to identify and infer 1 000 pedigree with 10% error rate by using 50 000 SNP markers, and the calculation time varies linearly with the number of markers and the number of individuals. Based on Mendelian genetic principle, the program of paternity test and parental inference based on parents and progeny genotypes was designed and developed. The method has the advantages of high speed, simple operation and high accuracy. It is worth popularizing and applying in the research of the genome of livestock and poultry population.
【作者单位】：华南农业大学动物科学学院/广东省农业动物基因组与分子育种重点实验室/国家生猪种业工程中心;
【基金】：国家现代农业(生猪)产业技术体系项目(CARS-36) 科技部科技基础性工作专项(2014FY120800) 国家自然科学基金项目(31200925) 广东省自然科学基金项目(2014A030313453)
【分类号】：S813

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