基于SNP标记的滩羊亲子鉴定研究

doi:10.11843/j.issn.0366-6964.2022.09.009

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (9): 2912-2919.doi: 10.11843/j.issn.0366-6964.2022.09.009

基于SNP标记的滩羊亲子鉴定研究

李玲^1,2, 李业芳², 梁奔梦², 孙玉江^1,4, 马月辉², 马青³, 蒋琳^2*, 刘书琴^1*

1. 青岛农业大学动物科技学院, 青岛 266109;
2. 中国农业科学院北京畜牧兽医研究所, 北京 100193;
3. 宁夏农林科学院动物科学研究所, 银川 750002;
4. 东营职业学院, 东营 257091

收稿日期:2022-02-23 出版日期:2022-09-23 发布日期:2022-09-23
通讯作者: 蒋琳,主要从事动物种质资源研究,E-mail:jianglin@caas.cn;刘书琴,主要从事马属动物遗传研究,E-mail:sqliu418@163.com
作者简介:李玲(1997-),女,山东莱芜人,硕士,主要从事动物遗传育种与繁殖研究,E-mail:liling184@163.com;李业芳(1994-),女,安徽芜湖人,硕士,主要从事动物种质资源研究,E-mail:yefanglee1994@163.com;梁奔梦(1992-),女,河北邯郸人,女,硕士生,主要从事动物遗传育种研究,E-mail:18812109228@163.com。
基金资助:
宁夏回族自治区农业育种专项-滩羊肉裘兼用品系选育（2018NYYZ0401）；青岛农业大学实验技术研究课题（20210021）

Paternity Identification of Tan Sheep Based on SNP Markers

LI Ling^1,2, LI Yefang², LIANG Benmeng², SUN Yujiang^1,4, MA Yuehui², MA Qing³, JIANG Lin^2*, LIU Shuqin^1*

1. College of Animal Science and Technology, Qingdao Agricultural University, Qindao 266109, China;
2. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
3. Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China;
4. Dongying Vocational Institute, Dongying 257091, China

Received:2022-02-23 Online:2022-09-23 Published:2022-09-23

摘要/Abstract

摘要： 旨在筛选可用于滩羊亲子鉴定的部分SNP标记，对羊群的保种和繁衍具有重要意义。本试验以宁夏盐池地区的159只滩羊为研究对象，利用600K基因芯片进行SNP测定，通过主成分分析了解样本的遗传背景，依据系统进化树划分家系，最后进行亲子鉴定研究。结果显示，大多数滩羊之间遗传背景相近，系统进化树将其划分为5大家系；亲子鉴定筛选到了211个高质量SNPs，单亲累积排除概率超过99.99%，具有很高的准确性和可靠性；父权鉴定结果表明，在95%置信水平下，观测鉴定率为79%，80%置信度下，观测鉴定率达到87%。在有结果的子代中，大部分真实亲本在疑似父本中找到，即非系谱记录的父本，说明场内应加强系谱管理，尽量避免错误的发生。

关键词: 滩羊, SNP标记, 亲子鉴定

Abstract: The purpose of this study was to screen some SNP markers that can be used for paternity identification of Tan sheep, which is of great significance for the conservation and reproduction of sheep. A total of 159 Tan sheep in the Yanchi area of Ningxia was selected as the research object. The 600K gene microarray was used for SNP determination. The genetic background of the sample was explored through principal component analysis. The family lineage was divided according to the phylogenetic tree. A paternity test was conducted. The results showed that most of the Tan sheep had similar genetic backgrounds, and the phylogenetic tree divided them into 5 major lineages; The 211 high-quality SNPs were screened, and the single parent cumulative exclusion probability (CPE) exceeded 99.99%, with high accuracy and reliability. The results of paternity identification show that at the 95% confidence level, the observed identification rate was 79%, and under the 80% confidence level, the observed identification rate reached 87%. In the results, most of the real parents were found in the suspected male parents, that is, the male parents with no pedigree records, indicating that the pedigree management should be strengthened in the field to avoid errors as much as possible.

Key words: Tan sheep, SNP markers, paternity identification

中图分类号:

S826.2

李玲, 李业芳, 梁奔梦, 孙玉江, 马月辉, 马青, 蒋琳, 刘书琴. 基于SNP标记的滩羊亲子鉴定研究[J]. 畜牧兽医学报, 2022, 53(9): 2912-2919.

LI Ling, LI Yefang, LIANG Benmeng, SUN Yujiang, MA Yuehui, MA Qing, JIANG Lin, LIU Shuqin. Paternity Identification of Tan Sheep Based on SNP Markers[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2912-2919.

参考文献 42

[1]	杨秀芳.宁夏盐池滩羊品种资源的保护现状及发展建议[J].中国草食动物, 2006, 26(6):36-37.YANG X F.Conservation status and development suggestions of sheep breed resources in Yanchitan, Ningxia[J].China Herbivore Science, 2006, 26(6):36-37.(in Chinese)
[2]	田黛君, 陈亮, 牛文智.宁夏滩羊发展现状与对策[C]//全国养羊生产与学术研讨会议论文集(2007-2008).榆林:中国畜牧兽医学会养羊学分会, 2008:37-39.TIAN D J, CHEN L, NIU W Z.Ningxia Tan sheep development status and countermeasures[C]//Discussion Papers of the National Sheep Breeding Production and Academic Symposium (2007-2008).Yulin:Sheep Raising Branch of Chinese Society of Animal Husbandry and Veterinary Medicine, 2008:37-39.(in Chinese)
[3]	高彦玲.滩羊种质资源现状及保种研究[J].甘肃畜牧兽医, 2022, 52(5):9-11.GAO Y L.Study on the present situation of Tan sheep germplasm resources and conservation[J].Gansu Animal Husbandry and Veterinary Medicine, 2022, 52(5):9-11.(in Chinese)
[4]	VISSCHER P M, WOOLLIAMS J A, SMITH D, et al.Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection[J].J Dairy Sci, 2002, 85(9):2368-2375.
[5]	O'BRIEN S J, MENOTTI-RAYMOND M, MURPHY W J, et al.The promise of comparative genomics in mammals[J].Science, 1999, 286(5439):458-481.
[6]	FLANAGAN S P, JONES A G.The future of parentage analysis:From microsatellites to SNPs and beyond[J].Mol Ecol, 2019, 28(3):544-567.
[7]	余国春.SSR与SNP标记在动物亲缘关系鉴定中的应用[J].畜禽业, 2020, 31(12):23-25.YU G C.Application of SSP and SNP molecular marker in animal parentage analysis[J].Livestock and Poultry Industry, 2020, 31(12):23-25.(in Chinese)
[8]	HAUSER L, BAIRD M, HILBORN R, et al.An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population[J].Mol Ecol Resour, 2015, 11(Suppl):150-161.
[9]	周磊, 初芹, 刘林, 等.利用微卫星和SNP标记信息进行奶牛亲子鉴定的模拟研究[J].畜牧兽医学报, 2011, 42(2):169-176.ZHOU L, CHU Q, LIU L, et al.Simulation study on paternity identification in dairy cattle with microsatellite and SNP markers[J].Acta Veterinaria et Zootechnica Sinica, 2011, 42(2):169-176.(in Chinese)
[10]	余国春.微卫星与SNP标记技术在猪亲子鉴定中的有效性研究[D].雅安:四川农业大学, 2014.YU G C.The effectiveness of microsatellite and SNP labeling technology in pig paternity testing[D].Ya'an:Sichuan Agricultural University, 2014.(in Chinese)
[11]	ALLEN A R, TAYLOR M, MCKEOWN B, et al.Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the northern Irish cattle population[J].BMC Genet, 2010, 11:5.
[12]	HEATON M P, HARHAY G P, BENNETT G L, et al.Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle[J].Mamm Genome, 2002, 13(5):272-281.
[13]	WERNER F A O, DURSTEWITZ G, HABERMANN F A, et al.Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds[J].Anim Genet, 2004, 35(1):44-49.
[14]	REVERTER A, HUDSON N J, MCWILLIAM S, et al.A low-density SNP genotyping panel for the accurate prediction of cattle breeds[J].J Anim Sci, 2020, 98(11):skaa337.
[15]	YANG T F, MILLER M, FORGACS D, et al.Development of SNP-based genomic tools for the Canadian bison industry:Parentage verification and subspecies composition[J].Front Genet, 2020, 11:585999.
[16]	GEBREHIWOT N Z, STRUCKEN E M, MARSHALL K, et al.SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle[J].Genet Sel Evol, 2021, 53(1):21.
[17]	CLARKE S M, HENRY H M, DODDS K G, et al.A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep[J].PLoS One, 2013, 9(4):e93392.
[18]	HEATON M P, LEYMASTER K A, KALBFLEISCH T S, et al.SNPs for parentage testing and traceability in globally diverse breeds of sheep[J].PLoS One, 2014, 9(4):e94851.
[19]	TORTEREAU F, MORENO C R, TOSSER-KLOPP G, et al.Development of a SNP panel dedicated to parentage assignment in French sheep populations[J].BMC Genet, 2017, 18(1):50.
[20]	马群群.拟穴青蟹SNP和SSR标记开发及系谱认证技术的建立研究[D].上海:上海海洋大学, 2012.MA Q Q.Development of SNP and SSR markers and establishment of parentage analysis technique in Scylla paramamosain[D].Shanghai:Shanghai Ocean University, 2012.(in Chinese)
[21]	葛会争.德国镜鲤与黑龙江野鲤杂交组合的亲子鉴定及鲤鱼免疫功能基因SNP位点研究[D].上海:上海海洋大学, 2012.GE H Z.Parentage identification of Heilongjiang wild carp and the German mirror carp cross combinations on microsatellite DNA markers and carp immune function gene SNP research[D].Shanghai:Shanghai Ocean University, 2012.(in Chinese)
[22]	BEACHAM T D, WALLACE C, MACCONNACHIE C, et al.Population and individual identification of chinook salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms[J].Can J Fish Aquat Sci, 2018, 75(7):1096-1105.
[23]	THONGDA W, ZHAO H G, ZHANG D D, et al.Development of SNP panels as a new tool to assess the genetic diversity, population structure, and parentage analysis of the eastern oyster (Crassostrea virginica)[J].Mar Biotechnol (NY), 2018, 20(3):385-395.
[24]	WENG Z Y, YANG Y, WANG X, et al.Parentage analysis in giant grouper (Epinephelus lanceolatus) using microsatellite and SNP markers from genotyping-by-sequencing data[J].Genes (Basel), 2021, 12(7):1042.
[25]	KALINOWSKI S T, TAPER M L, MARSHALL T C.Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment[J].Mol Ecol, 2007, 16(5):1099-1106.
[26]	李冰.DNA检测用于亲子鉴定的基本原理[J].中国工作犬业, 2006(10):39.LI B.The principle of DNA paternity testing[J].China Working Dog, 2006(10):39.(in Chinese)
[27]	CHANG L, YU H Y, MIAO X Y, et al.Evaluation of a custom SNP panel for identifying and rectifying of misjudged paternity in deficiency cases[J].Front Genet, 2021, 12:602429.
[28]	布蕾楠.法医个体识别多等位基因SNP的筛选及NGS-SNP分型体系的建立[D].石家庄:河北医科大学, 2020.BU L N.Genome-wide screening of multi-allelic SNPs for forensic individual identification and development of NGS-SNP panel[D].Shijiazhuang:Hebei Medical University, 2020.(in Chinese)
[29]	LONG J.Parentage analysis using genome-wide high-density SNP microarray[J].Gene, 2021, 785:145605.
[30]	MO S K, LIU Y C, WANG S Q, et al.Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms[J].Forensic Sci Int Genet, 2016, 22:161-168.
[31]	HU L R, LI D, CHU Q, et al.Selection and implementation of single nucleotide polymorphism markers for parentage analysis in crossbred cattle population[J].Animal, 2021, 15(1):100066.
[32]	MCCLURE M C, MCCARTHY J, FLYNN P, et al.SNP data quality control in a national beef and dairy cattle system and highly accurate SNP based parentage verification and identification[J].Front Genet, 2018, 9:84.
[33]	SERMYAGIN A A, DOTSEV A V, GLADYR E A, et al.Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds[J].Genet Sel Evol, 2018, 50(1):37.
[34]	VAN DER ZWAN H, VISSER C, SCHOONEN M, et al.Development of an SNP-based parentage verification panel for lovebirds[J].Anim Genet, 2019, 50(6):764-767.
[35]	STRUCKEN E M, LEE S H, LEE H K, et al.How many markers are enough?Factors influencing parentage testing in different livestock populations[J].J Anim Breed Genet, 2016, 133(1):13-23.
[36]	王悦, 覃锡忠, 贺三刚, 等.SNP标记用于新疆5个绵羊品种亲子鉴定准确性的研究[J].中国科技论文, 2017, 12(24):2867-2872.WANG Y, QIN X Z, HE S G, et al.Accuracy of parentage identification for 5 sheep breeds in Xinjiang based on SNPs[J].China Sciencepaper, 2017, 12(24):2867-2872.(in Chinese)
[37]	郭刚, 周磊, 刘林, 等.利用SNP标记进行北京地区中国荷斯坦牛亲子推断的研究[J].畜牧兽医学报, 2012, 43(1):44-49.GUO G, ZHOU L, LIU L, et al.Parentage inference with single nucleotide polymorphism markers in the Chinese Holstein in Beijing[J].Acta Veterinaria et Zootechnica Sinica, 2012, 43(1):44-49.(in Chinese)
[38]	殷彬.奶牛分子系谱鉴定的微卫星标记筛选及其与生产性能的关联分析[D].泰安:山东农业大学, 2016.YIN B.Selection of micro-satellite markers for molecular genealogical confirmation and their association with production traits in Holstein dairy cows[D].Tai'an:Shandong Agricultural University, 2016.(in Chinese)
[39]	BOTSTEIN D, WHITE R L, SKOLNICK M, et al.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].Am J Hum Genet, 1980, 32(3):314-331.
[40]	郭立平.利用微卫星和SNP标记对西门塔尔牛进行亲子推断的研究[D].北京:中国农业科学院, 2013.GUO L P.Parentage testing with microsatellite and SNP markers in Simmental[D].Beijing:Chinese Academy of Agricultural Sciences, 2013. (in Chinese)
[41]	ZHANG T L, GUO L P, SHI M Y, et al.Selection and effectiveness of informative SNPs for paternity in Chinese Simmental cattle based on a high-density SNP array[J].Gene, 2018, 673:211-216.
[42]	刘峻宇, 刘均辉, 孔杰, 等.凡纳滨对虾SNP标记开发与家系亲缘关系验证分析[J].渔业科学进展, 2021, 42(1):108-116.LIU J Y, LIU J H, KONG J, et al.Development of SNP markers and verification analysis of relationship on family in Litopenaeus vannamei[J].Progress in Fishery Sciences, 2021, 42(1):108-116.(in Chinese)

基于SNP标记的滩羊亲子鉴定研究

Paternity Identification of Tan Sheep Based on SNP Markers

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