nav emailalert searchbtn searchbox tablepage yinyongbenwen piczone journalimg journalInfo journalinfonormal searchdiv searchzone qikanlogo popupnotification paper paperNew
2020, 03, v.39 1094-1100
畜禽生产性状主效基因定位技术与方法研究进展
基金项目(Foundation): 国家自然科学基金项目(No.31672393);; 重庆市社会民生类重点研发项目(cstc2017-zdyfX0045);; 重庆市农发资金项目(No.15404)共同资助
邮箱(Email):
DOI: 10.13417/j.gab.039.001094
摘要:

鉴定畜禽重要生产性状形成的关键遗传因子,揭示其产生的分子遗传机制,对动物新品种的培育及特色遗传资源的开发利用具有重要意义。高通量分析技术诞生前,标记数量性状位点(quantitative trait loci,QTL)连锁分析和候选基因分析法作为鉴定畜禽生产性状QTL和主效基因主要方法,但由于其技术局限性,性状因果基因鉴定的效率并不高。人类基因组计划(human genome project, HGP)开启了以大数据为特征的生命科学研究的序幕,在HGP完成后的20余年间,快速发展的高通量分析技术使人们研究生物学问题的思路和方法发生了巨大改变。本综述就近年来被广泛用于畜禽重要性状的候选基因定位的方法与技术进行了较全面的综述,以期为同行提供参考。

Abstract:

Identifying the key genetic factors as well as revealing the molecular genetic mechanism of important economical traits in livestock is of great significance for the cultivation of new animal varieties and the development and utilization of characteristic genetic resources. Before the birth of high-throughput analytic technology,labeled quantitative trait loci(QTL) linkage analysis and candidate gene analysis were used as the main methods for identifying QTL and major genes of production traits in livestock. However, due to their technical limitations,the efficiency for identification of the causative gene is not satisfying. The human genome project(HGP) opened the scene of life science characterized by the Big Data, and great changes have been made in the methods of biological investigations in recent decade since the completion of HGP. In this article, we reviewed the methods and technologies for the candidate gene mapping of important economical traits in livestock in recent years which will provide the valuable reference for peers.

参考文献

Abasht B.,and Lamont S.J.,2007,Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population,Anim.Genet.,38(5):491-498

Al-Mamun H.A.,Kwan P.,Clark S.A.,Ferdosi M.H.,Tellam R.,and Gondro C.,2015,Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight,Genet.Sel.Evol.,47(1):66

Amaral A.J.,Ferretti L.,Megens H.J.,Crooijmans R.P.,Nie H.,Ramos-Onsins S.E.,Perez-Enciso M.,Schook L.B.,and Groenen M.A.,2011,Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA,PLoS One,6(4):e14782

Bastide H.,Betancourt A.,Nolte V.,Tobler R.,Stobe P.,Futschik A.,and Schlotterer C.,2013,A genome-wide,fine-scale map of natural pigmentation variation in Drosophila melanogaster,PLoS Genet.,9(6):e1003534

Broeckx B.J.,Coopman F.,Verhoeven G.E.,Bavegems V.,De Keulenaer S.,De Meester E.,Van Niewerburgh F.,and Deforce D.,2014,Development and performance of a targeted whole exome sequencing enrichment kit for the dog(Canis Familiaris Build 3.1),Sci.Rep.,4:5597

Broeckx B.J.,Coopman F.,Verhoeven G.E.,De Keulenaer S.,De Meester E.,Bavegems V.,Smets P.,Van Ryssen B.,Van Nieuwerburgh F.,and Deforce D.,2016,Toward the most ideal case-control design with related and unrelated dogs in whole-exome sequencing studies,Anim.Genet.,47(2):200-207

Carty C.L.,Johnson N.A.,Hutter C.M.,Reiner A.P.,Peters U.,Tang H.,and Kooperberg C.,2012,Genome-wide association study of body height in African Americans:The women's health initiative SNP health association resource(SHA-Re),Hum.Mol.Genet.,21(3):711-720

Cole J.B.,Wiggans G.R.,Ma L.,Sonstegard T.S.,Lawlor T.J.,Jr Crooker B.A.,Van Tassell C.P.,Yang J.,Wang S.,Matukumalli L.K.,and Da Y.,2011,Genome-wide association analysis of thirty one production,health,reproduction and body conformation traits in contemporary U.S.Holstein cows,BMC Genomics,12(1):408

Demars J.,Fabre S.,Sarry J.,Rossetti R.,Gilbert H.,Persani L.,Tosser-Klopp G.,Mulsant P.,Nowak Z.,Drobik W.,Martyniuk E.,and Bodin L.,2013,Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyperprolificacy phenotype in sheep,PLoSGenet.,9(4):e1003482

Demeure O.,Duclos M.J.,Bacciu N.,Le Mignon G.,Filangi O.,Pitel F.,Boland A.,Lagarrigue S.,Cogburn L.A.,Simon J.,Le Roy P.,and Le Bihan-Duval E.,2013,Genome-wide interval mapping using SNPs identifies new QTL for growth,body composition and several physiological variables in an F2 intercross between fat and lean chicken lines,Genet.Sel.Evol.,45(1):36

Dorshorst B.,Okimoto R.,and Ashwell C.,2010,Genomic regions associated with dermal hyperpigmentation,polydactyly and other morphological traits in the Silkie chicken,J.Hered.,101:339-350

Elvers I.,Turner-Maier J.,Swofford R.,Koltookian M.,Johnson J.,Stewart C.,Zhang C.Z.,Schumacher S.E.,Beroukhim R.,Rosenberg M.,Thomas R.,Mauceli E.,Getz G.,Palma F.D.,Modiano J.F.,Breen M.,Lindblad-Toh K.,and Alfoldi J.,2015,Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background,Genome Res.,25(11):1634-1645

Esteve-Codina A.,Kofler R.,Himmelbauer H.,Ferretti L.,Vivancos A.P.,Groenen M.A.,Folch J.M.,Rodriguez M.C.,and Perez-Enciso M.,2011,Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof,Heredity(Edinb),107(3):256-264

Fairfield H.,Gilbert G.J.,Barter M.,Corrigan R.R.,Curtain M.,Ding Y.,D'Ascenzo M.,Gerhardt D.J.,He C.,Huang W.,Richmond T.,Rowe L.,Probst F.J.,Bergstrom D.E.,Murray S.A.,Bult C.,Richardson J.,Kile B.T.,Gut I.,Hager J.,Sigurdsson S.,Mauceli E.,Di Palma F.,Lindblad-Toh K.,Cunningham M.L.,Cox T.C.,Justice M.J.,Spector M.S.,Lowe S.W.,Albert T.,Donahue L.R.,Jeddeloh J.,Shendure J.,and Reinholdt L.G.,2011,Mutation discovery in mice by whole exome sequencing,Genome Biol.,12(9):R86

Fairfield H.,Srivastava A.,Ananda G.,Liu R.,Kircher M.,Lakshminarayana A.,Harris B.S.,Karst S.Y.,Dionne L.A.,Kane C.C.,Curtain M.,Berry M.L.,Ward-Bailey P.F.,Greenstein I.,Byers C.,Czechanski A.,Sharp J.,Palmer K.,Gudis P.,Martin W.,Tadenev A.,Bogdani L.,Pratt C.H.,Chang B.,Schroeder D.G.,Cox G.A.,Cliften P.,Milbrandt J.,Murray S.,Burgess R.,Bergstrom D.E.,Donahue L.R.,Hamamy H.,Masri A.,Santoni F.A.,Makrythanasis P.,Antonarakis S.E.,Shendure J.,and Reinholdt L.G.,2015,Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders,Genome Res.,25:948-957

Fan B.,Onteru S.K.,Du Z.Q.,Garrick D.J.,Stalder K.J.,and Rothschild M.F.,2011,Genome-wide association study identifies Loci for body composition and structural soundness traits in pigs,PLoS One,6(2):e14726

Fontanesi L.,Schiavo G.,Galimberti G.,Calo D.G.,Scotti E.,Martelli P.L.,Buttazzoni L.,Casadio R.,and Russo V.,2012,A genome wide association study for backfat thickness in italian large white pigs highlights new regions affecting fat deposition including neuronal genes,BMC Genomics,13(1):583

Gholizadeh M.,Rahimi-Mianji G.,Nejati-Javaremi A.,De Koning D.J.,and Jonas E.,2014,Genomewide association study to detect QTL for twinning rate in Baluchi sheep,J.Genet.,93(2):489-493

Gu X.,Feng C.,Ma L.,Song C.,Wang Y.,Da Y.,Li H.,Chen K.,Ye S.,Ge C.,Hu X.,and Li N.,2011,Genome-wide association study of body weight in chicken F2 resource population,PLoS One,6(7):e21872

Hayes B.J.,Bowman P.J.,Chamberlain A.J.,Savin K.,van Tassell C.P.,Sonstegard T.S.,and Goddard M.E.,2009,A validated genome wide association study to breed cattle adapted to an environment altered by climate change,PLoS One,4(8):e6676

Hilton J.M.,Lewis M.A.,Grati M.,Ingham N.,Pearson S.,Laskowski R.A.,Adams D.J.,and Steel K.P.,2011,Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice,Genome Biol.,12(9):R90

Huang W.,Kirkpatrick B.W.,Rosa G.J.,and Khatib H.,2010,Agenome-wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle,Anim.Genet.41(6):570-578

Ionita-Laza I.,Rogers A.J.,Lange C.,Raby B.A.,and Lee C.,2009,Genetic association analysis of copy-number variation(CNV)in human disease pathogenesis,Genomics,93(1):22-26

Kawamura Y.,Otowa T.,Koike A.,Sugaya N.,Yoshida E.,Ya suda S.,Inoue K.,Takei K.,Konishi Y.,Tanii H.,Shimada T.,Tochigi M.,Kakiuchi C.,Umekage T.,Liu X.,Nishida N.,Tokunaga K.,Kuwano R.,Okazak Y.,Kaiya H.,and Sasaki T.,2011,A genome-wide CNV association study on panic disorder in a Japanese population,J.Hum.Genet.,56(12):852-856

Klein R.J.,Zeiss C.,Chew E.Y.,Tsai J.Y.,Sackler R.S.,Haynes C.,Henning A.K.,SanGiovanni J.P.,Mane S.M.,Mayne S.T.,Bracken M.B.,Ferris F.L.,Ott J.,Barnstable C.,and Hoh J.,2005,Complement factor H polymorphism in age-related macular degeneration,Science,308(5720):385-389

Lee J.B.,Jung E.J.,Park H.B.,Jin S.,Seo D.W.,Ko M.S.,Cho I.C.,Lee J.H.,and Lim H.T.,2014,Genome-wide association analysis to identify SNP markers affecting teat numbers in an F2 intercross population between Landrace and Korean native pigs,Mol.Biol.Rep.,41(11):7167-7173

Li D.F.,Lian L.,Qu L.J.,Chen Y.M.,Liu W.B.,Chen S.R.,Zheng J.X.,Xu G.Y.,and Yang N.,2013,A genome-wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease,Anim.Genet.,44(2):217-222

Li M.H.,Tiirikka T.,and Kantanen J.,2014,A genome-wide scan study identifies a single nucleotide substitution in ASIPassociated with white versus non-white coat-colour variation in sheep(Ovis aries),Heredity(Edinb),112(2):122-1231

Lin B.Z.,Kato T.,Kaneda M.,Matsumoto H.,Sasazaki S.,and Mannen H.,2013,Genetic diversity and structure in Asian native goat analyzed by newly developed SNP markers,Anim.Sci.J.,84(8):579-584

Luo C.,Qu H.,Ma J.,Wang J.,Hu X.,Li N.,and Shu D.,2014,A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken,Infect.Genet.Evol.,21(1):351-358

Luo W.,Cheng D.,Chen S.,Wang L.,Li Y.,Ma X.,Song X.,Liu X.,Li W.,Liang J.,Yan H.,Zhao K.,Wang C.,Wang L.,and Zhang L.,2012,Genome-wide association analysis of meat quality traits in a porcine Large White x Minzhu intercross population,Int.J.Biol.Sci.,8(4):580-595

Macciotta N.P.,Gaspa G.,Bomba L.,Vicario D.,Dimauro C.,Cellesi M.,and Ajmone-Marsan P.,2015,Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density(7K)SNP panel,J.Dairy Sci.,98(11):8175-8185

Miller M.R.,Dunham J.P.,Amores A.,Cresko W.A.,and Johnson E.A.,2007,Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA(RAD)markers,Genome Res.,17(2):240-248

Mousel M.R.,Reynolds J.O.,and White S.N.,2015,Genomewide association identifies SLC2A9 and NLN gene regions as associated with entropion in domestic sheep,PLoS One,10(6):e0128909

Mucha S.,Bunger L.,and Conington J.,2015,Genome-wide association study of footrot in Texel sheep,Genet.Sel.Evol.,47(1):35

Nordstrom K.J.,Albani M.C.,James G.V.,Gutjahr C.,Hartwig B.,Turck F.,Paszkowski U.,Coupland G.,and Schneeberger K.,2013,Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers,Nat.Biotechnol.,31(4):325-330

Olsen H.G.,Hayes B.J.,Kent M.P.,Nome T.,Svendsen M.,and Lien S.,2010,A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle,Anim.Genet.,41(3):273-280

Pickering N.K.,Auvray B.,Dodds K.G.,and McEwan J.C.,2015,Genomic prediction and genome-wide association study for dagginess and host internal parasite resistance in New Zealand sheep,BMC Genomics,16(1):958

Raadsma H.W.,Jonas E.,Fleet M.R.,Fullard K.,Gongora J.,Cavanagh C.R.,Tammen I.,and Thomson P.C.,2013,QTLand association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects,Anim.Genet.,44(5):547-559

Ren J.,Mao H.,Zhang Z.,Xiao S.,Ding N.,and Huang L.,2011,A 6-bp deletion in the TYRP1 gene causes the brown colouration phenotype in Chinese indigenous pigs,Heredity(Edinb),106(5):862-868

Robert C.,Fuentes-Utrilla P.,Troup K.,Loecherbach J.,Turner F.,Talbot R.,Archibald A.L.,Mileham A.,Deeb N.,Hume D.A.,and Watson M.,2014,Design and development of exome capture sequencing for the domestic pig(Sus scrofa),BMC Genomics,15(1):550

Rubin C.J.,Zody M.C.,Eriksson J.,Meadows J.R.,Sherwood E.,Webster M.T.,Jiang L.,Ingman M.,Sharp T.,Ka S.,Hallbook F.,Besnier F.,Carlborg O.,Bed'hom B.,TixierBoichard M.,Jensen P.,Siegel P.,Lindblad-Toh K.,and Andersson L.,2010,Whole-genome resequencing reveals loci under selection during chicken domestication,Nature,464:587-591

Salle G.,Jacquiet P.,Gruner L.,Cortet J.,Sauve C.,Prevot F.,Grisez C.,Bergeaud J.P.,Schibler L.,Tircazes A.,Francois D.,Pery C.,Bouvier F.,Thouly J.C.,Brunel J.C.,Legarra A.,Elsen J.M.,Bouix J.,Rupp R.,and Moreno C.R.,2012,Agenome scan for QTL affecting resistance to Haemonchus contortus in sheep,J.Anim.Sci.,90(13):4690-4705

Sanchez M.P.,Tribout T.,Iannuccelli N.,Bouffaud M.,Servin B.,Tenghe A.,Dehais P.,Muller N.,Del Schneider M.P.,Mercat M.J.,Rogel-Gaillard C.,Milan D.,Bidanel J.P.,and Gilbert H.,2014,A genome-wide association study of production traits in a commercial population of Large White pigs:Evidence of haplotypes affecting meat quality,Genet.Sel.Evol.,46(1):12

Sarin S.,Prabhu S.,O'Meara M.M.,Pe'er I.,and Hobert O.,2008,Caenorhabditis elegans mutant allele identification by whole-genome sequencing,Nat.Methods,5(10):865-867

Schlotterer C.,Tobler R.,Kofler R.,and Nolte V.,2014,Sequencing pools of individuals-mining genome-wide polymorphism data without big funding,Nat.Rev.Genet.,15:749-763

Schneeberger K.,2014,Using next-generation sequencing to isolate mutant genes from forward genetic screens,Nat.Rev.Genet.,15:662-676

Sodeland M.,Kent M.P.,Olsen H.G.,Opsal M.A.,Svendsen M.,Sehested E.,Hayes B.J.,and Lien S.,2011,Quantitative trait loci for clinical mastitis on chromosomes 2,6,14 and 20 in Norwegian Red cattle,Anim.Genet.,42(5):457-465

Song S.,Yao N.,Yang M.,Liu X.,Dong K.,Zhao Q.,Pu Y.,He X.,Guan W.,Yang N.,Ma Y.,and Jiang L.,2016,Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat(Capra hircus),BMC Genomics,17(1):122

Spielmann M.,Kakar N.,Tayebi N.,Leettola C.,Nurnberg G.,Sowada N.,Lupianez D.G.,Harabula I.,Flottmann R.,Horn D.,Chan W.L.,Wittler L.,Yilmaz R.,Altmuller J.,Thiele H.,van Bokhoven H.,Schwartz C.E.,Nurnberg P.,Bowie J.U.,Ahmad J.,Kubisch C.,Mundlos S.,and Borck G.,2016,Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice,Genome Res.,26(2):183-191

Stranger B.E.,Forrest M.S.,Dunning M.,Ingle C.E.,Beazley C.,Thorne N.,Redon R.,Bird C.P.,de Grassi A.,Lee C.,Tyler-Smith C.,Carter N.,Scherer S.W.,Tavare S.,Deloukas P.,Hurle M.E.,and Dermitzakis E.T.,2007,Relative impact of nucleotide and copy number variation on gene expression phenotypes,Science,315(5813):848-853

Stratz P.,Wellmann R.,Preuss S.,Wimmers K.,and Bennewitz J.,2014,Genome-wide association analysis for growth,muscularity and meat quality in Pietrain pigs,Anim.Genet.,45(3):350-356

Sun Y.,Zhao G.,Liu R.,Zheng M.,Hu Y.,Wu D.,Zhang L.,Li P.,and Wen J.,2013,The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study,BMC Genomics,14(1):458

Tanisawa K.,Mikami E.,Fuku N.,Honda Y.,Honda S.,Ohsawa I.,Ito M.,Endo S.,Ihara K.,Ohno K.,Kishimoto Y.,Ishigami A.,Maruyama N.,Sawabe M.,Iseki H.,Okazaki Y.,Hasegawa-Ishii S.,Takei S.,Shimada A.,Hosokawa M.,Mori M.,Higuchi K.,Takeda T.,Higuchi M.,and Tanaka M.,2013,Exome sequencing of senescence-accelerated mice(SAM)reveals deleterious mutations in degenerative disease-causing genes,BMC Genomics,14(1):248

Tiezzi F.,Parker-Gaddis K.L.,Cole J.B.,Clay J.S.,and Maltecca C.,2015,A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure,PLoSOne,10(2):e0114919

Wang X.,Ma P.,Liu J.,Zhang Q.,Zhang Y.,Ding X.,Jiang L.,Wang Y.,Zhang Y.,Sun D.,Zhang S.,Su G.,and Yu Y.,2015,Genome-wide association study in Chinese Holstein cows reveal two candidate genes for somatic cell score as an indicator for mastitis susceptibility,BMC Genet.,16:111

Wang Z.,Zhang H.,Yang H.,Wang S.,Rong E.,Pei W.,Li H.,and Wang N.,2014,Genome-wide association study for wool production traits in a Chinese Merino sheep population,PLoS One,9(9):e107101

White S.N.,Mousel M.R.,Herrmann-Hoesing L.M.,Reynolds J.O.,Leymaster K.A.,Neibergs H.L.,Lewis G.S.,and Knowles D.P.,2012,Genome-wide association identifies multiple genomic regions associated with susceptibility to and control of ovine lentivirus,PLoS One,7(10):e47829

Xu X.,Dong G.X.,Hu X.S.,Miao L.,Zhang X.L.,Zhan D.L.,Yang H.D.,Zhang T.Y.,Zou Z.T.,Zhang T.T.,Zhuang Y.,Bhak J.,Cho Y.S.,Dai W.T.,Jiang T.J.,Xie C.,Li R.,and Luo S.J.,2013,The genetic basis of white tigers,Curr.Biol.,23(11):1031-1035

Yano K.,Yamamoto E.,Aya K.,Takeuchi H.,Lo P.C.,Hu L.,Yamasaki M.,Yoshida S.,Kitano H.,Hirano K.,and Matsuoka M.,2016,Genome-wide association study using wholegenome sequencing rapidly identifies new genes influencing agronomic traits in rice,Nat.Genet.,48(8):927-934

Zhang L.,Liu J.,Zhao F.,Ren H.,Xu L.,Lu J.,Zhang S.,Zhang X.,Wei C.,Lu G.,Zheng Y.,and Du L.,2013,Genomewide association studies for growth and meat production traits in sheep,PLoS One,8(6):e66569

Zhao X.,Dittmer K.E.,Blair H.T.,Thompson K.G.,Rothschild M.F.,and Garrick D.J.,2011,A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep,PLoS One,6(7):e21739

基本信息:

DOI:10.13417/j.gab.039.001094

中图分类号:S813

引用信息:

[1]任航行,李杰,王高富,等.畜禽生产性状主效基因定位技术与方法研究进展[J].基因组学与应用生物学,2020,39(03):1094-1100.DOI:10.13417/j.gab.039.001094.

基金信息:

国家自然科学基金项目(No.31672393);; 重庆市社会民生类重点研发项目(cstc2017-zdyfX0045);; 重庆市农发资金项目(No.15404)共同资助

发布时间:

2018-11-22

出版时间:

2018-11-22

网络发布时间:

2018-11-22

检 索 高级检索