一种基于高密度遗传标记的亲子鉴定方法及其应用

doi:10.3724/SP.J.1005.2014.0835

遗传 ›› 2014, Vol. 36 ›› Issue (8): 835-841.doi: 10.3724/SP.J.1005.2014.0835

一种基于高密度遗传标记的亲子鉴定方法及其应用

张哲¹, 罗元宇¹, 李晴晴¹, 贺金龙¹, 高宁¹, 张豪¹, 丁向东², 张勤², 李加琪¹

1. 华南农业大学动物科学学院,国家生猪种业工程中心,广东省农业动物基因组与分子育种重点实验室,广州 510642;
2. 中国农业大学动物科学学院,北京 100193

收稿日期:2014-04-29 出版日期:2014-08-20 发布日期:2013-07-19
通讯作者: 李加琪,博士,教授,研究方向：分子数量遗传学与动物育种。E-mail:jqli@scau.edu.cn
作者简介:张哲,博士,讲师,研究方向：分子数量遗传学与动物育种。E-mail:zhezhang@scau.edu.cn
基金资助:
现代农业(生猪)产业技术体系建设专项资金(编号：CARS-36),科技部科技基础性工作专项(编号：2014FY120800),国家自然科学基金项目(编号：31200925)和广东省自然科学基金项目(编号：S2012040007753)资助

Developing and applying of a parentage identification approach based on high density genetic markers

Zhe Zhang¹, Yuanyu Luo¹, Qingqing Li¹, Jinlong He¹, Ning Gao¹, Hao Zhang¹, Xiangdong Ding², Qin Zhang², Jiaqi Li¹

1. National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China;
2. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

Received:2014-04-29 Online:2014-08-20 Published:2013-07-19

摘要/Abstract

摘要： 系谱是人类遗传及动植物育种研究与实践的重要信息来源之一。系谱记录错误是育种生产中普遍存在的一种记录错误,影响基因定位、遗传值及表型值预测等相关研究结果的可靠性。现有的方法软件可以利用遗传标记信息对疑似亲子进行亲子鉴定,但这些软件方法操作复杂,限制标记数量,如Cervus。针对当前高密度SNP标记在人类及动植物研究中广泛应用的现状,文章提出了一种基于全基因组高密度SNP数据的亲子鉴定新方法,命名为EasyPC。对EasyPC及Cervus的运行效率进行了对比,并用中国荷斯坦牛(n=2180)和杜洛克猪(n=191)的全基因组SNP芯片数据对EasyPC进行了验证。结果表明：EasyPC运行效率高于Cervus,牛和猪群体系谱错误率分别为20%和6%,与相关研究报道相符。通过使用全基因组SNP标记对群体孟德尔错误率的经验分布进行分析,该方法不仅可以简单、快速、准确地判别系谱的正确性,而且还可以对错误系谱进行校正。EasyPC为解决全基因组研究中基因型及系谱数据前处理过程中的系谱校正问题提供了一种新的途径。

关键词: 亲子鉴定, 系谱校正, 遗传标记, 孟德尔错误, 动物育种

Abstract: Pedigree is an important information source in the studies on human genetics and animal/plant breeding. Pedigree error is a common data error in breeding practice. It can affect the reliability of results from researches such as gene mapping, genetic or phenotypic value prediction. By using genetic markers, several approaches can identify the suspected pedigrees, but most of them are complex and the allowed number of genetic markers is limited, such as Cervus. Since the wide use of high density single nucleotide polymorphisms (SNPs) in human genetic and animal/plant breeding, a new parentage identification approach (named EasyPC, Easy Pedigree Checking) based on whole genome genetic data was proposed in this study. EasyPC was compared with Cervus on efficiency, and validated with a Chinese Holstein cattle (n=2180) and a Duroc swine (n=191) population. Results showed that EasyPC was much less time demanding than Cervus, and pedigree error rates were 20% for cattle and 6% for swine. Result from the cattle population is in accordance with previous study. By analyzing the empirical distribation of Mendelian error rate calculated in a population using all available SNPs, EasyPC not only can identify the correctness of a pedigree in a simple, fast, and accurate manner, but also can correct the wrong pedigree. EasyPC provides a promising alternative solution to traditional pedigree correction approaches and eases the data analysis of whole genome related studies.

Key words: parentage identification, pedigree correction, genetic marker, Mendelian error, animal breeding

张哲, 罗元宇, 李晴晴, 贺金龙, 高宁, 张豪, 丁向东, 张勤, 李加琪. 一种基于高密度遗传标记的亲子鉴定方法及其应用[J]. 遗传, 2014, 36(8): 835-841.

Zhe Zhang, Yuanyu Luo, Qingqing Li, Jinlong He, Ning Gao, Hao Zhang, Xiangdong Ding, Qin Zhang, Jiaqi Li. Developing and applying of a parentage identification approach based on high density genetic markers[J]. HEREDITAS(Beijing), 2014, 36(8): 835-841.

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一种基于高密度遗传标记的亲子鉴定方法及其应用

Developing and applying of a parentage identification approach based on high density genetic markers

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