连续性纯合片段在畜禽基因组研究中的应用

doi:10.16288/j.yczz.18-287

遗传 ›› 2019, Vol. 41 ›› Issue (4): 304-317.doi: 10.16288/j.yczz.18-287

连续性纯合片段在畜禽基因组研究中的应用

刘刚,孙飞舟(),朱芳贤(),冯海永,韩旭

全国畜牧总站,北京 100193

收稿日期:2018-10-13 修回日期:2019-02-02 出版日期:2019-04-20 发布日期:2019-03-28
通讯作者: 孙飞舟,朱芳贤 E-mail:fzhsun1968@qq.com;1171277193@qq.com
作者简介:刘刚,博士,畜牧师,研究方向：畜禽遗传资源保护与应用。E-mail: lgang- 2004@126.com
基金资助:
禽种质资源保护项目([2018]45);家养动物平台种质资源项目(2018)

Runs of homozygosity and its application on livestock genome study

Gang Liu,Feizhou Sun(),Fangxian Zhu(),Haiyong Feng,Xu Han

National Animal Husbandry Service, Beijing 100193, China

Received:2018-10-13 Revised:2019-02-02 Online:2019-04-20 Published:2019-03-28
Contact: Sun Feizhou,Zhu Fangxian E-mail:fzhsun1968@qq.com;1171277193@qq.com
Supported by:
the Protection Project of Animal Germplasm Resources([2018]45);the National Infrastructure of Domestic Animal Resources(2018)

摘要/Abstract

摘要：

随着高通量SNP芯片技术的快速发展和测序成本的大幅降低,SNP基因芯片和基因组重测序等技术被广泛地应用于畜禽基因组研究中。在基因组某一段区域内,当一定数量和一定密度的SNPs表现为纯合时,可以判定该区域存在连续性纯合片段(runs of homozygosity, ROH)。目前,连续性纯合片段已经逐渐成为分析畜禽群体近交程度、遗传结构等方面的重要指标之一。但是,ROH计算应用的评价标准还相对匮乏。本文系统介绍了连续性纯合片段的发展历史、原理、鉴定方法以及在畜禽群体结构解析、基因组功能分析和种畜禽品质检测等方面的应用情况,以期为畜禽遗传资源保种区和保种场在遗传多样性等动态监测方面提供参考。

关键词: 高通量测序技术, 连续性纯合片段, 群体结构, 基因组功能, 遗传缺陷

Abstract:

With the rapid development of high-throughput SNP array and significant reduction of sequencing cost, the techniques of genome-resequencing and SNP chip arrays are widely applied in livestock genomic studies. Long runs of homozygosity (ROH) arose when identical haplotypes were inherited from each parent and thus a long tract of genotypes is homozygous. Nowadays, cumulative studies reported that ROH has progressively served as one of the important indexes to estimate the degree of inbreeding and genetic structure of livestock populations. However, the evaluating criteria of ROH in livestock is still inadequate. In this review, we introduce the history, theory and identification methods of ROH analysis. Meanwhile, we also systematically overview the applications and perspectives of ROH in population genetic structure analysis, genome functional assay, quality investigation and dynamic monitoring of livestock genetic resources.

Key words: high-throughput sequencing, runs of homozygosity, population structure, genomic function, genetic defect

刘刚,孙飞舟,朱芳贤,冯海永,韩旭. 连续性纯合片段在畜禽基因组研究中的应用[J]. 遗传, 2019, 41(4): 304-317.

Gang Liu,Feizhou Sun,Fangxian Zhu,Haiyong Feng,Xu Han. Runs of homozygosity and its application on livestock genome study[J]. Hereditas(Beijing), 2019, 41(4): 304-317.

参考文献

[1]	Gibson J, Morton NE, Collins A . Extended tracts of homozygosity in outbred human populations. Hum Mol Genet, 2006,15(5):789-795.
[2]	McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF . Runs of homozygosity in European populations. Am J Hum Genet, 2008,83(3):359-372.
[3]	Johnson EC, Evans LM, Keller MC . Relationships between estimated autozygosity and complex traits in the UK Biobank. PLoS Genet, 2018,14(7):e1007556.
[4]	Ferencaković M, Hamzic E, Gredler B, Curik I, Sölkner J . Runs of homozygosity reveal genome-wide autozygosity in the Austrian Fleckvieh cattle. Agric Conspec Sci, 2011,76:286-293.
[5]	Ferencaković M, Hamzić E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Sölkner J . Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet, 2013,130(4):286-293.
[6]	Keller MC, Visscher PM, Goddard ME . Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics, 2011,189(1):237-249.
[7]	Broman KW, Weber JL . Long homozygous chromosomal segments in reference families from the centre d'Etude du polymorphisme humain. Am J Hum Genet, 1999,65(6):1493-1500.
[8]	Bosse M, Megens HJ, Madsen O, Paudel Y, Frantz LA, Schook LB, Crooijmans RP, Groenen MA . Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLoS Genet, 2012,8(11):e1003100.
[9]	Herrero-Medrano JM, Megens HJ, Groenen MA, Ramis G, Bosse M, Pérez-Enciso M, Crooijmans RP . Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula. BMC Genet, 2013,14:106.
[10]	Purfield DC, Berry DP, McParland S, Bradley DG . Runs of homozygosity and population history in cattle. BMC Genet, 2012,13:70.
[11]	Kim ES, Cole JB, Huson H, Wiggans GR, Van Tassell CP, Crooker BA, Liu G, Da Y, Sonstegard TS . Effect of artificial selection on runs of homozygosity in u.s. Holstein cattle. PLoS One, 2013,8(11):e80813.
[12]	Zhang Q, Guldbrandtsen B, Bosse M, Lund MS, Sahana G . Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics, 2015,16:542.
[13]	Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK . Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA, 2007,104(50):19942-19947.
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连续性纯合片段在畜禽基因组研究中的应用

Runs of homozygosity and its application on livestock genome study

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