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.

参考文献

[1] PM, Woolliams JA, Smith D, Williams JL. Esti-mation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection . J Dairy Sci , 2002, 85(9): 2368-2375.
[2] JI, Feldmesser E, Golik M, Tager-Cohen I, Domoc-hovsky R, Alus O, Ezra E, Ron M. Factors affecting inc-orrect paternity assignment in the Israeli Holstein pop-ulation . J Dairy Sci , 2004, 87(8): 2627-2640.
[3] LG, Madsen P, Petersen J. The influence of incorrect sire identification on the estimates of genetic parameters and breeding values. In: Proceedings of the 2nd World Congress on Genetics Applied to Livestock Prod-uction. Madrid, Spain, 1982: 200-208.
[4] H, Van Arendonk JAM. Estimation of milk pro-tein gene frequencies in crossbred cattle by maximum likelihood . J Dairy Sci , 1991, 74(8): 2728-2736.
[5] JG, Kelly EP. Errors of identification Amongst cattle presented as progeny of some bulls used in the artificial-insemination service in Ireland . Ir Vet J , 1987, 41(10): 348-352.
[6] G, Wiggans GR, Powell RL. Impact of paternity errors in cow identification on genetic evaluations and int-ernational comparisons . J Dairy Sci , 2001, 84(11): 2523- 2529.
[7] 田雨泽, 刘和凤. 应用血型分析技术对奶牛亲子关系正确率的调查初报 . 中国畜牧兽医, 2005, 32(3): 22-23.
[8] 张毅, 孙东晓, 俞英, 王雅春, 张沅. 应用微卫星DNA标记分析荷斯坦母牛系谱可靠性及影响因素 . 畜牧兽医学报, 2011, 42(2): 163-168.
[9] 周磊, 刘林, 李东, 张胜利, 刘剑锋, 丁向东, 张毅, 王雅春, 张勤. 利用 SNP 标记进行北京地区中国荷斯坦牛亲子推断的研究 . 畜牧兽医学报, 2012, 43(1): 44-49.
[10] 张嘉保, 高庆华, 陈庆波. 微卫星DNA在吉戎兔亲子鉴定中的应用研究 . 遗传, 2005, 27(6): 903-907.
[11] K, Bennewitz J, Kalm E. Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population . J Dairy Sci , 2006, 89(1): 315-321.
[12] C. Contribution of blood typing to dairy science progress . J Dairy Sci , 1967, 50(2): 253-260.
[13] 初芹, 王雅春. 单核苷酸多态性标记在牛亲子鉴定中的应用与展望 . 中国畜牧杂志, 2011, 47(7): 73-76.
[14] Y, Lipkin E, Darvasi A, Nave A, Gruenbaum Y, Beckmann JS, Soller M. Parentage identification in the bovine using “deoxyribonucleic acid fingerprints” . J Dairy Sci , 1990, 73(11): 3306-3311.
[15] BS, Anderson AD, Hepler AB. Genetic relatedness analysis: modern data and new challenges . Nat Rev Genet , 2006, 7(10): 771-780.
[16] RL, Hammond HA, Coto I, Caskey CT. Rapid and efficient resolution of parentage by amplification of short tandem repeats . Am J Hum Genet , 1994, 55(1): 190-195.
[17] ML, Gaillard C, Wigger G, Fries R. Microsatellite-based parentage control in cattle . Anim Genet , 1995, 26(1): 7-12.
[18] MP, Harhay GP, Bennett GL, Stone RT, Grosse WM, Casas E, Keele JW, Smith TPL, Chitko-McKown CG, Laegreid WW. Selection and use of SNP markers for animal identification and paternity analysis in US beef cattle . Mamm Genome , 2002, 13(5): 272-281.
[19] EC, Garza JC. The power of single-nucleotide polymorphisms for large-scale parentage inference . Gen - etics , 2006, 172(4): 2567-2582.
[20] JR, Pena SD. Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms . Genet Mol Res , 2010, 9(1): 601-607.
[21] FA, Durstewitz G, Habermann FA, Thaller G, Kramer W, Kollers S, Buitkamp J, Georges M, Brem G, Mosner J, Fries R. Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds . Anim Genet , 2004, 35(1): 44-49.
[22] AG, Ardren WR. Methods of parentage analysis in natural populations . Mol Ecol , 2003, 12(10): 2511-2523.
[23] ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment . Mol Ecol , 2007, 16(5): 1099-1106.
[24] KF, Queller DC. Computer software for performing likelihood tests of pedigree relationship using genetic markers . Mol Ecol , 1999, 8(7): 1231-1234.
[25] Z, Taylor JA. SNPinfo: integrating GWAS and cand-idate gene information into functional SNP selection for genetic association studies . Nucleic Acids Res , 2009, 37(Suppl. 2): W600-W 605.
[26] AC, Li G, Edwards S, Zhu J, Laurie C, Tokiwa G, Lum PY, Wang S, Castellani LW, Lusis AJ, Carlson S, Sa-chs AB, Schadt EE. Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels . Genomics , 2005, 86(5): 505-517.
[27] SH, van der Werf JHJ, Hayes BJ, Goddard ME, Viss-cher PM. Predicting unobserved phenotypes for complex traits from whole-genome SNP data . PLoS Genet , 2008, 4(10): e1000231.
[28] NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM. Pitfalls of predicting complex traits from SNPs . Nat Rev Genet , 2013, 14(7): 507-515.
[29] L, Liu JF, Sun DX, Ma PP, Ding XDQ, Yu Y, Zhang Q. Genome wide association studies for milk production traits in Chinese Holstein population . PLoS ONE , 2010, 5(10): e13661.
[30] X, Zhang Z, Li X, Wang S, Wu X, Sun D, Yu Y, Liu J, Wang Y, Zhang Y, Zhang S, Zhang Y, Zhang Q. Accuracy of genomic prediction for milk production traits in the Chinese Holstein population using a reference population consisting of cows . J Dairy Sci , 2013, 96(8): 5315-5323.
[31] LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, Van Tassell CP. Development and Char-acterization of a High Density SNP Genotyping Assay for Cattle . PLoS ONE , 2009, 4(4): e5350. Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark
[32] Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TPL, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, Groenen MAM. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next genera-tion sequencing technology . PLoS ONE , 2009, 4(8): e6524.
[33] Core Team. R: A language and environment for statis-tical computing . R Foundation for Statistical Computing, Vienna, Austria, 2014.
[34] Wilmer J, Allen PJ, Pomeroy PP, Twiss SD, Amos W. Where have all the fathers gone? An extensive microsatellite analysis of paternity in the grey seal ( Hali - choerus grypus ) . Mol Ecol , 1999, 8(9): 1417-1429.

编辑推荐

Metrics

www.chinagene.cn
备案号：京ICP备09063187号-4
总访问:,今日访问:,当前在线:

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

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	周萌,景军红,毛瑞涵,郭静,王志鹏. 代谢组学在家养动物遗传育种中的应用[J]. 遗传, 2019, 41(2): 111-124.
[2]	谈成, 边成, 杨达, 李宁, 吴珍芳, 胡晓湘, . 基因组选择技术在农业动物育种中的应用[J]. 遗传, 2017, 39(11): 1033-1045.
[3]	张轲, 冯光德, 张宝云, 向伟, 陈龙, 杨芳, 储明星, 王凭青. 表观遗传标记在猪分子育种中的研究与应用前景[J]. 遗传, 2016, 38(7): 634-643.
[4]	杨昭庆，褚嘉祐. 中国人类遗传多样性研究进展[J]. 遗传, 2012, 34(11): 1351-1364.
[5]	李恒德，包振民，孙效文. 基因组选择及其应用[J]. 遗传, 2011, 33(12): 1308-1316.
[6]	侯宁，张研，鲁翠云，李勇，李大宇，季旭，丁雷，孙效文. 微卫星DNA标记分析德国镜鲤的遗传潜力[J]. 遗传, 2007, 29(12): 1509-1518.
[7]	林桂荣，李宝江，魏毓棠. 茄子花色遗传及其对相关性状影响的研究[J]. 遗传, 2006, 28(6): 713-716.
[8]	杨学明，郭亚芬，陈福艳，蒋钦杨，梁万文，蒋和生. 罗氏沼虾不同群体线粒体COI基因的序列差异和遗传标记研究[J]. 遗传, 2006, 28(5): 540-544.
[9]	张正海，康向阳. 植物2n配子发生及其遗传标记研究进展[J]. 遗传, 2006, 28(1): 105-109.
[10]	韩春梅，张嘉保，高庆华，陈庆波. 微卫星DNA在吉戎兔亲子鉴定中的应用研究[J]. 遗传, 2005, 27(6): 903-907.
[11]	聂庆华，张细权，雷明明. 单核苷酸多态性及其在鸡QTL定位上的应用[J]. 遗传, 2003, 25(6): 729-734.
[12]	苏松坤，陈盛禄. 意蜂王浆生产性能形态学遗传标记的研究[J]. 遗传, 2003, 25(6): 677-680.
[13]	张志和，沈富军，孙姗，Victor ADavid，张安居，Stephen JO′Brien. 应用微卫星分型方法进行大熊猫父亲鉴定[J]. 遗传, 2003, 4(5): 504-9.
[14]	俞英，张沅. 畜禽遗传评定方法的研究进展[J]. 遗传, 2003, 25(5): 607-610.
[15]	庞有志，赵淑娟. 鹌鹑羽色遗传的研究及应用[J]. 遗传, 2003, 25(4): 450-454.