牛全基因组拷贝数变异研究进展

doi:10.11843/j.issn.0366-6964.2018.05.001

摘要/Abstract

摘要：

拷贝数变异（Copy number variation，CNV）作为基因组结构变异（Structural variation，SV）的重要组成部分，在物种表型变异、疾病易感性评估、物种演化等方面起着重要作用。目前，高通量、高分辨率的全基因组CNV研究已广泛应用到各种家畜中，并成为全基因组关联性分析（Genome-wide association analysis，GWAS）研究复杂性状的重要分子标记。此外，CNV还为群体遗传结构分析提供新的视角。因此，本文从定义、形成机制、分布特点、检测方法、遗传效应和牛Y染色体CNV等方面对牛全基因组CNV研究进行了较为全面的介绍与阐述，提出全基因组CNV研究所面临的一些问题，并对发展前景做了简单展望，以期为今后牛全基因组CNV的研究提供指导信息。

关键词: 牛, 拷贝数变异, 遗传效应

Abstract:

Copy number variation (CNV), as an important component of genomic structural variation (SV), plays important roles in phenotypic variability, disease susceptibility estimates and species evolution. Currently, a large number of studies have been widely conducted to analyze genome-wide CNV of domestic animals using high throughput and density technologies, which enable CNV as an important molecular marker for complex traits in genome-wide association analysis study (GWAS). In addition, CNV provides a new insight into the analysis of population genetic structure. Therefore, this review comprehensively summarized definition, formation mechanism, distribution characteristics, analyzing methods, genetic effect of CNV in cattle and the CNV on bovine Y chromosome based on previous studies. Meanwhile, we also raised some problems in current CNV studies, and provide a brief outlook of the future for CNV studies, which would supply guidance for cattle genome CNV studies in the future.

Key words: cattle, copy number variation, genetic effect

中图分类号:

S823.2

裴生伟, 王丽, 曹学涛, 李万宏, 李发弟, 乐祥鹏. 牛全基因组拷贝数变异研究进展[J]. 畜牧兽医学报, 2018, 49(5): 871-878.

PEI Sheng-wei, WANG Li, CAO Xue-tao, LI Wan-hong, LI Fa-di, YUE Xiang-peng. Research Progress on Genomic Copy Number Variations in Cattle[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(5): 871-878.

参考文献

[1] REDON R,ISHIKAWA S,FITCH K R,et al.Global variation in copy number in the human genome[J].Nature,2006,444(7118):444-454.
[2] MACDONALD J R,ZIMAN R,YUEN R K,et al.The database of genomic variants:a curated collection of structural variation in the human genome[J].Nucleic Acids Res,2014,42(D1):986-992.
[3] GRICE S J,LIU J L,WEBBER C.Synergistic interactions between Drosophila orthologues of genes spanned by de novo human CNVs support multiple-hit models of Autism[J].PLoS Genet,2015,11(3):e1004998.
[4] MUCHMORE E A.Chimpanzee models for human disease and immunobiology[J].Immunol Rev,2010,183(1):86-93.
[5] HIROI N,TAKAHASHI T,HISHIMOTO A,et al.Copy number variation at 22q11.2:from rare variants to common mechanisms of developmental neuropsychiatric disorders[J].Mol Psychiatry,2013,18(11):1153-1165.
[6] LIU G E,HOU Y L,ZHU B,et al.Analysis of copy number variations among diverse cattle breeds[J].Genome Res,2010,20(5):693-703.
[7] MIELCZAREK M,FRSZCZAK M,GIANNICO R,et al.Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data[J].J Dairy Sci,2017,100(7):5515-5525.
[8] FREEMAN J L,PERRY G H,FEUK L,et al.Copy number variation:new insights in genome diversity[J].Genome Res,2006,16(8):949-961.
[9] SCHERER S W,LEE C,BIRNEY E,et al.Challenges and standards in integrating surveys of structural variation[J].Nat Genet,2007,39:S7-S15.
[10] MILLS R E,WALTER K,STEWART C,et al.Mapping copy number variation by population-scale genome sequencing[J].Nature,2011,470(7332):59-65.
[11] HASTINGS P J,LUPSKI J R,ROSENBERG S M,et al.Mechanisms of change in gene copy number[J].Nat Rev Genet,2009,10(8):551-564.
[12] BAILEY J A,GU Z P,CLARK R A,et al.Recent segmental duplications in the human genome[J].Science,2002,297(5583):1003-1007.
[13] SMITH C E,LLORENTE B,SYMINGTON L S.Template switching during break-induced replication[J].Nature,2007,447(7140):102-105.
[14] BAUTERS M,VAN ESCH H,FRIEZ M J,et al.Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair[J].Genome Res,2008,18(6):847-858.
[15] LIU P F,CARVALHO C M B,HASTINGS P J,et al.Mechanisms for recurrent and complex human genomic rearrangements[J].Curr Opin Genet Dev,2012,22(3):211-220.
[16] ZHANG F,GU W L,HURLES M E,et al.Copy number variation in human health,disease,and evolution[J].Annu Rev Genom Hum Genet,2009,10(1):451-481.
[17] GAO Y H,JIANG J P,YANG S H,et al.CNV discovery for milk composition traits in dairy cattle using whole genome resequencing[J].BMC Genomics,2017,18:265.
[18] 刘欣,王立刚,王立贤.拷贝数变异及其研究进展[J].畜牧兽医学报,2010,41(8):927-931.
LIU X,WANG L G,WANG L X.Current progress in copy number variation study[J].Acta Veterinaria et Zootechnica Sinica,2010,41(8):927-931.(in Chinese)
[19] PIROOZNIA M,GOES F S,ZANDI P P.Whole-genome CNV analysis:advances in computational approaches[J].Front Genet,2015,6:138.
[20] LIU G E,VENTURA M,CELLAMARE A,et al.Analysis of recent segmental duplications in the bovine genome[J].BMC Genomics,2009,10:571.
[21] DA SILVA J M,FERNANDA G P,DA SILVA L O,et al.Genome-wide copy number variation (CGNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits[J].BMC Genomics,2016,17:454.
[22] LIU G E,BROWN T,HEBERT D A,et al.Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes[J].Mamm Genome,2011,22(1-2):111-121.
[23] UPADHYAY M,DA SILVA V H,MEGENS H J,et al.Distribution and functionality of copy number variation across european cattle populations[J].Front Genet,2017,8:108.
[24] MASSAIA A,XUE Y L.Human Y chromosome copy number variation in the next generation sequencing era and beyond[J].Hum Genet,2017,136(5):591-603.
[25] BICKHART D M,HOU Y L,SCHROEDER S G,et al.Copy number variation of individual cattle genomes using next-generation sequencing[J].Genome Res,2012,22(4):778-790.
[26] ZHANG L Z,JIA S G,YANG M J,et al.Detection of copy number variations and their effects in Chinese bulls[J].BMC Genomics,2014,15:480.
[27] SASAKI S,WATANABE T,NISHIMURA S,et al.Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle[J].BMC Genet,2016,17:26.
[28] KARIMI K,ESMAILIZADEH A,WU D D,et al.Mapping of genome-wide copy number variations in the Iranian indigenous cattle using a dense SNP data set[J].Anim Prod Sci,2017.DOI:10.1071/AN16384.
[29] YLSTRA B,VAN DEN IJSSEL P,CARVALHO B,et al.BAC to the future! or oligonucleotides:a perspective for micro array comparative genomic hybridization (array CGH)[J].Nucleic Acids Res,2006,34(2):445-450.
[30] CARTER N P.Methods and strategies for analyzing copy number variation using DNA microarrays[J].Nat Genet,2007,39(7S):S16-S21.
[31] ALKAN C,COE B P,EICHLER E E.Genome structural variation discovery and genotyping[J].Nat Rev Genet,2011,12(5):363-376.
[32] CHEN Y,ZHAO L,WANG Y,et al.SeqCNV:a novel method for identification of copy number variations in targeted next-generation sequencing data[J].BMC Bioinformatics,2017,18:147.
[33] ZHAN B J,FADISTA J,THOMSEN B,et al.Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping[J].BMC Genomics,2011,12:557.
[34] BOUSSAHA M,ESQUERRE D,BARBIERI J,et al.Genome-wide study of structural variants in bovine holstein,montbéliarde and normande dairy breeds[J].PLoS One,2015,10(8):e0135931.
[35] HOU Y L,LIU G E,BICKHART D M,et al.Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle[J].Funct Integr Genomic,2012,12(1):81-92.
[36] SEBAT J,LAKSHMI B,TROGE J,et al.Large-scale copy number polymorphism in the human genome[J].Science,2004,305(5683):525-528.
[37] GONZALEZ E,KULKARNI H,BOLIVAR H,et al.The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility[J].Science,2005,307(5714):1434-1440.
[38] AITMAN T J,DONG R,VYSE T J,et al.Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans[J].Nature,2006,439(7078):851-855.
[39] FELLERMANN K,STANGE D E,SCHAEFFELER E,et al.A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon[J].Am J Hum Genet,2006,79(3):439-448.
[40] ZHANG H,DU Z Q,DONG J Q,et al.Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content[J].BMC Genomics,2014,15:517.
[41] ZHOU L S,LI J,YANG J,et al.Genome-wide mapping of copy number variations in commercial hybrid pigs using a high-density SNP genotyping array[J].Russ J Genet,2016,52(1):85-92.
[42] WANG Y N,TANG Z L,SUN Y Q,et al.Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays[J].PLoS One,2014,9(9):e106780.
[43] JUNG S H,YIM S H,OH H J,et al.De novo copy number variations in cloned dogs from the same nuclear donor[J].BMC Genomics,2013,14:863.
[44] MA Q,LIU X X,PAN J F,et al.Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array[J].Sci Rep,2017,7:912.
[45] FONTANESI L,MARTELLI P L,BERETTI F,et al.An initial comparative map of copy number variations in the goat (Capra hircus) genome[J].BMC Genomics,2010,11:639.
[46] KADER A,LIU X X,DONG K Z,et al.Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array[J].Anim Genet,2016,47(5):560-569.
[47] ZHANG X,WANG K,WANG L Z,et al.Genome-wide patterns of copy number variation in the Chinese yak genome[J].BMC Genomics,2016,17:379.
[48] GIRIRAJAN S,CAMPBELL C D,EICHLER E E.Human copy number variation and complex genetic disease[J].Annu Rev Genet,2011,45(1):203-226.
[49] DURAN A M,ROMÁN PONCE S I,RUIZ LÓPEZ F J,et al.Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers[J].J Anim Breed Genet,2017,134(1):49-59.
[50] HOU Y L,BICKHART D M,CHUNG H,et al.Analysis of copy number variations in Holstein cows identify potential mechanisms contributing to differences in residual feed intake[J].Funct Integr Genomic,2012,12(4):717-723.
[51] STRILLACCI M G,COZZI M C,GORLA E,et al.Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers[J].Animal,2017,11(5):737-745.
[52] XU L Y,HOU Y L,BICKHART D M,et al.Population-genetic properties of differentiated copy number variations in cattle[J].Sci Rep,2016,6:23161.
[53] ZHANG L Z,JIA S G,PLATH M,et al.Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional chinese cattle breeds[J].Genome Biol Evol,2015,7(8):2352-2361.
[54] ROSSE I C,ASSIS J G,OLIVEIRA F S,et al.Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production,disease resistance,and heat tolerance[J].Mamm Genome,2017,28(1-2):66-80.
[55] BICKHART D M,XU L Y,HUTCHISON J L,et al.Diversity and population-genetic properties of copy number variations and multicopy genes in cattle[J].DNA Res,2016,23(3):253-262.
[56] ZHOU J,BERNARDO L,DOPMAN E B,et al.Copy-number variation:the balance between gene dosage and expression indrosophila melanogaster[J].Genome Biol Evol,2011,3:1014-1024.
[57] HAMILTON C K,VERDUZCO-GÓMEZ A R,FAVETTA L A,et al.Testis-specific protein Y-encoded copy number is correlated to its expression and the field fertility of Canadian Holstein bulls[J].Sex Dev,2012,6(5):231-239.
[58] STRANGER B E,FORREST M S,DUNNING M,et al.Relative impact of nucleotide and copy number variation on gene expression phenotypes[J].Science,2007,315(5813):848-853.
[59] HARAKSINGH R R,SNYDER M P.Impacts of variation in the human genome on gene regulation[J].J Mol Biol,2013,425(21):3970-3977.
[60] DOPMAN E B,HARTL D L.A portrait of copy-number polymorphism in Drosophila melanogaster[J].Proc Natl Acad Sci U S A,2007,104(50):19920-19925.
[61] LIU W S,DE LEÓN F A P.Mapping of the bovine Y chromosome[J].Electron J Biol,2007,3:5-12.
[62] LIU W S,CHANG T C.Y chromosome-linked genes implicated in spermatogenesis in cattle[M]//JUENGEL J L,MIYAMOTO A,PRICE C,et al.Reproduction in Domestic Ruminants VⅢ.Leicestershire,England:Context Products Ltd,2014:239-255.
[63] MANDAL A,SHARMA A.Variations in the length of the Y chromosome and the seminal attributes of Karan Fries bulls[J].Vet Res Commun,2003,27(7):567-575.
[64] MUKHERJEE A,DASS G,JAGAN M G,et al.Absolute copy number differences of Y chromosomal genes between crossbred (Bos taurus×Bos indicus) and Indicine bulls[J].J Anim Sci Biotechnol,2013,4:15.
[65] ZHANG G W,GUAN J Q,LUO Z G,et al.A tremendous expansion of TSPY copy number in crossbred bulls (Bos taurus×Bos grunniens)[J].J Anim Sci,2016,94(4):1398-1407.
[66] YUE X P,DECHOW C,CHANG T C,et al.Copy number variations of the extensively amplified Y-linked genes,HSFY and ZNF280BY,in cattle and their association with male reproductive traits in Holstein bulls[J].BMC Genomics,2014,15:113.
[67] YUE X P,CHANG T C,DEJARNETTE J M,et al.Copy number variation of PRAMEY across breeds and its association with male fertility in Holstein sires[J].J Dairy Sci,2013,96(12):8024-8034.
[68] HAMILTON C K,FAVETTA L A,DI MEO G,et al.Copy number variation of testis-specific protein,Y-encoded (TSPY) in 14 different breeds of cattle (Bos taurus)[J].Sex Dev,2009,3(4):205-213.