高通量测序技术在鉴别影响猪产仔数QTL及候选基因中的应用
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摘要
产仔数是反映猪场生产水平和经济效应的一个重要的指标,作为多基因控制、遗传力低的复杂经济性状,鉴别影响产仔数的基因位点,利用分子选育标记来提高猪的产仔性能倍受重视。随着重测序成本的不断降低,基因组学研究不断深入,以全基因组重测序、简化基因组测序和基于高通量测序技术获得的芯片技术已得到广泛应用。本文综述了通过高通量测序技术以及基于高通量测序的芯片技术研究影响猪产仔数性能的数量性状座位(quantitative trait loci,QTL)及候选基因的研究进展,为后期鉴别影响产仔数变异主效基因提供参考,为生产采用分子育种进行产仔选育提升提供分子标记信息。
Litter size is an important indicator of the level of production and economic efficiency of pig farms. As a complex genetic trait controlled by polygenes and with low heritability,litter size has attracted increasing attention of researchers in identifying its affecting gene loci,and improving its performance with molecular selection markers. With continual reduction of re-sequencing cost,genomics research has been deepened. Chip technology based on genome-wide sequencing,simplified genome sequencing,and high-throughput sequencing technology has been widely used. This paper reviews progress in research on QTLs and candidate genes affecting the sow' s litter size performance through high throughput sequencing technology and chip technology based on the high throughput sequencing. The aim of this review is to provide a reference for later identification of the main genes affecting the variation of litter size and molecular marker information for breeding.
Litter size is an important indicator of the level of production and economic efficiency of pig farms. As a complex genetic trait controlled by polygenes and with low heritability,litter size has attracted increasing attention of researchers in identifying its affecting gene loci,and improving its performance with molecular selection markers. With continual reduction of re-sequencing cost,genomics research has been deepened. Chip technology based on genome-wide sequencing,simplified genome sequencing,and high-throughput sequencing technology has been widely used. This paper reviews progress in research on QTLs and candidate genes affecting the sow' s litter size performance through high throughput sequencing technology and chip technology based on the high throughput sequencing. The aim of this review is to provide a reference for later identification of the main genes affecting the variation of litter size and molecular marker information for breeding.
引文
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[5]胡闪耀,姜佳佳,杨华,等.大白猪ESR基因多态性与繁殖性状能相关性研究[J].猪业科学,2017,34(7):38-40.
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[12]张淑君,熊远著,曾凡同,等.猪八号染色体产仔数微卫星标记的探讨[J].养猪,2001(2):31-33.
[13]李不学,杜军,郭启航,等.OPN基因多态性对长白猪产仔数的影响[J].猪业科学,2013(8):100-101.
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[15]Bosse M,Megens H J,Frantz L A,et al.Genomic analysis reveals selection for Asian genes in European pigs following humanmediated introgression[J].Nat Commun,2014,5:4392.
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[19]Rothschild M,Jacobson C,Vaske D,et al.The estrogen receptor locus is associated with a major gene influencing litter size in pigs[J].Proc Nat Acad Sci USA,1996,93(1):201-205.
[20]Liu C,Ran X,Yu C,et al.Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes[J].Genomics,2018,doi:10.1016/j.ygeno.2018.02.005.
[21]Li W T,Zhang M M,Li Q G,et al.Whole-genome resequencing reveals candidate mutations for pig prolificacy[J].Proc Biol Sci,2017,284(1869).pii:20172437.doi:10.1098/rspb.2017.2437.
[22]Etter P D,Bassham S,Hohenlohe P A,et al.SNP discovery and genotyping for evolutionary genetics using RAD sequencing[J].Methods Mol Biol,2011,772:157-178.
[23]Wang Z,Chen Q,Liao R,et al.Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing[J].Anim Genet,2017,48(1):38-47.
[24]Kim J G,Rohrer G A,Vallet J L,et al.Addition of 14 anchored loci to the porcine chromosome 8 comparative map[J].Anim Genet,2004,35(6):474-476.
[25]Dall’Olio S,Fontanesi L,Tognazzi L,et al.Genetic structure of candidate genes for litter size in Italian Large White pigs[J].Vet Res Commun,2010,34(Suppl 1):S203-S206.
[26]Le T H,Christensen O F,Nielsen B,et al.Genome-wide association study for conformation traits in three Danish pig breeds[J].Genet Sel Evol,2017,49(1):12.
[27]Dunkelberger J R,Ser2o N V,Niederwerder M C,et al.Effect of a major quantitative trait locus for porcine reproductive and respiratory syndrome (PRRS) resistance on response to coinfection with PRRSvirus and porcine circovirus type 2b(PCV2b)in commercial pigs,with or without prior vaccination for PRRS[J].J Anim Sci,2017,95(2):584.
[28]Ramos A M,Crooijmans R P M A,Affara N A,et al.Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology[J].PLoS One,2009,4(8):e6524.
[29]Onteru S K,Fan B,Du Z Q,et al.A whole-genome association study for pig reproductive traits[J].Anim Genet,2012,43(1):18-26.
[30]Onteru S K,Fan B,NikkilM T,et al.Whole-genome association analyses for lifetime reproductive traits in the pig[J].J Anim Sci,2011,89(4):988-995.
[31]Schneider J F,Rempel L A,Snelling W M,et al.Genome-wide association study of swine farrowing traits.PartⅡ:Bayesian analysis of marker data[J].J Anim Sci,2012,90(10):3360-3367.
[32]Goodarzi M O,Maher J F,Cui J,et al.FEM1A and FEM1B:novel candidate genes for polycystic ovary syndrome[J].Hum Reprod,2008,23(12):2842-2849.
[33]Einarsson S,Brandt Y,Lundeheim N,et al.Stress and its influence on reproduction in pigs:a review[J].Acta Veterinaria Scandinavica,2008,50(1):1-8.
[34]Worby C A,Dixon J E.Sorting out the cellular functions of sorting nexins[J].Nat Rev Mol Cell Biol,2002,3(12):919-931.
[35]Tanaka K,Miyamoto N,Shouguchi-Miyata J,et al.HFM1,the human homologue of yeast Mer3,encodes a putative DNA helicase expressed specifically in germ-line cells[J].DNA Seq,2006,17(3):242-246.
[36]Yuan Y,Ida J M,Paczkowski M,et al.Identification of developmental competence-related genes in mature porcine oocytes[J].Mol Reprod Dev,2011,78(8):565-575.
[37]刘小磊,杨松柏,Rothschild M F,等.利用紧缩线性模型和贝叶斯模型对猪总产仔数和产活仔数性状的全基因组关联研究[J].遗传,2012,34(10):1261-1270.
[38]Schneider J F,Nonneman D J,Wiedmann R T,et al.Genomewide association and identification of candidate genes for ovulation rate in swine[J].J Anim Sci,2014,92(9):3792.
[39]Sell-Kubiak E,Duijvesteijn N,Lopes M S,et al.Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population[J].BMC Genomics,2015,16(1):1049.
[40]Bergfelderdrüing S,Grossebrinkhaus C,Lind B,et al.A Genomewide association study in Large White and Landrace Pig populations for number piglets born alive[J].PLoS One,2015,10(3):e0117468.
[41]Guo X,Su G,Christensen O F,et al.Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs[J].BMC Genomics,2016,17(1):1-12.
[42]Trenhaile M D,Petersen J L,Kachman S D,et al.Long-term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes[J].Anim Genet,2016,47(5):534-542.
[43]Wang Y,Ding X,Tan Z,et al.Genome-wide association study for reproductive traits in a Large White pig population[J].Anim Genet,2018,49(2):127-131.
[44]He L C,Li P H,Ma X,et al.Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs[J].Anim Genet,2017,48(1):48-54.
[45]Ma X,Li P H,Zhu M X,et al.Genome-wide association analysis reveals genomic regions on Chromosome 13 affecting litter size and candidate genes for uterine horn length in Erhualian pigs[J].Animal,2018,12(12):2453-2461.
[46]Baker M.Gene data to hit milestone[J].Nature,2012,487(7407):282-283.
[2]Rohrer G A,Ford J J,Wise T H,et al.Identification of quantitative trait loci affecting female reproductive traits in a multigeneration Meishan-White composite swine population[J].J Anim Sci,1999,77(6):1385-1391.
[3]Wilkie P J,Paszek A A,Beattie C W,et al.A genomic scan of porcine reproductive traits reveals possible quantitative trait loci (QTLs) for number of corpora lutea[J].Mammalian Genome,1999,10(6):573-578.
[4]Rothschild M F,Larson R G,Jacobson C,et al.PvuII polymorphisms at the porcine oestrogen receptor locus (ESR)[J].Anim Genet,1991,22(5):448.
[5]胡闪耀,姜佳佳,杨华,等.大白猪ESR基因多态性与繁殖性状能相关性研究[J].猪业科学,2017,34(7):38-40.
[6]赵要风,李宁,陈永福,等.猪FSHβ亚基基因RFLPs研究初报[J].畜牧兽医学报,1998,29(1):23-26.
[7]方宇瑜,马翔,吴艳,等.苏淮猪群体ESR1和FSHβ基因的多态性及其与繁殖性状的关联性研究[J].畜牧与兽医,2017,49(2):1-5.
[8]李小平,施启顺,柳小春,等.催乳素受体基因对大白、长白猪产仔数的影响[J].养猪,2005(6):19-20.
[9]沈永巧,胡九英,孙敬礼,等.PRLR和ITGB1基因多态性对大白猪繁殖性能的影响[J].石河子大学学报(自科版),2017,35(2):146-151.
[10]Rothschild M F,Messer L,Day A,et al.Investigation of the retinolbinding protein 4(RBP4)gene as a candidate gene for increased litter size in pigs[J].Mamm Genome,2000,11(1):75-77.
[11]胡闪耀,陈佳,姜佳佳,等.大白猪FSHβ和RBP4基因多态性与繁殖性状的相关性研究[J].猪业科学,2017,34(7):38-40.
[12]张淑君,熊远著,曾凡同,等.猪八号染色体产仔数微卫星标记的探讨[J].养猪,2001(2):31-33.
[13]李不学,杜军,郭启航,等.OPN基因多态性对长白猪产仔数的影响[J].猪业科学,2013(8):100-101.
[14]林国珊.二花脸猪特异选择位点与猪产仔数的关联性分析[D].南昌:江西农业大学,2013.
[15]Bosse M,Megens H J,Frantz L A,et al.Genomic analysis reveals selection for Asian genes in European pigs following humanmediated introgression[J].Nat Commun,2014,5:4392.
[16]Kim H Y,Caetanoanolles K,Seo M,et al.Prediction of genes related to positive selection using whole-genome resequencing in three commercial pig breeds[J].Genomics Inform,2015,13(4):137-145.
[17]Church P C,Goscinski A,Lefèvre C.EXP-PAC:providing comparative analysis and storage of next generation gene expression data[J].Genomics,2012,100(1):8.
[18]Wang C,Wang H,Zhang Y,et al.Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs[J].Mol Ecol Resour,2014,15(2):414-424.
[19]Rothschild M,Jacobson C,Vaske D,et al.The estrogen receptor locus is associated with a major gene influencing litter size in pigs[J].Proc Nat Acad Sci USA,1996,93(1):201-205.
[20]Liu C,Ran X,Yu C,et al.Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes[J].Genomics,2018,doi:10.1016/j.ygeno.2018.02.005.
[21]Li W T,Zhang M M,Li Q G,et al.Whole-genome resequencing reveals candidate mutations for pig prolificacy[J].Proc Biol Sci,2017,284(1869).pii:20172437.doi:10.1098/rspb.2017.2437.
[22]Etter P D,Bassham S,Hohenlohe P A,et al.SNP discovery and genotyping for evolutionary genetics using RAD sequencing[J].Methods Mol Biol,2011,772:157-178.
[23]Wang Z,Chen Q,Liao R,et al.Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing[J].Anim Genet,2017,48(1):38-47.
[24]Kim J G,Rohrer G A,Vallet J L,et al.Addition of 14 anchored loci to the porcine chromosome 8 comparative map[J].Anim Genet,2004,35(6):474-476.
[25]Dall’Olio S,Fontanesi L,Tognazzi L,et al.Genetic structure of candidate genes for litter size in Italian Large White pigs[J].Vet Res Commun,2010,34(Suppl 1):S203-S206.
[26]Le T H,Christensen O F,Nielsen B,et al.Genome-wide association study for conformation traits in three Danish pig breeds[J].Genet Sel Evol,2017,49(1):12.
[27]Dunkelberger J R,Ser2o N V,Niederwerder M C,et al.Effect of a major quantitative trait locus for porcine reproductive and respiratory syndrome (PRRS) resistance on response to coinfection with PRRSvirus and porcine circovirus type 2b(PCV2b)in commercial pigs,with or without prior vaccination for PRRS[J].J Anim Sci,2017,95(2):584.
[28]Ramos A M,Crooijmans R P M A,Affara N A,et al.Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology[J].PLoS One,2009,4(8):e6524.
[29]Onteru S K,Fan B,Du Z Q,et al.A whole-genome association study for pig reproductive traits[J].Anim Genet,2012,43(1):18-26.
[30]Onteru S K,Fan B,NikkilM T,et al.Whole-genome association analyses for lifetime reproductive traits in the pig[J].J Anim Sci,2011,89(4):988-995.
[31]Schneider J F,Rempel L A,Snelling W M,et al.Genome-wide association study of swine farrowing traits.PartⅡ:Bayesian analysis of marker data[J].J Anim Sci,2012,90(10):3360-3367.
[32]Goodarzi M O,Maher J F,Cui J,et al.FEM1A and FEM1B:novel candidate genes for polycystic ovary syndrome[J].Hum Reprod,2008,23(12):2842-2849.
[33]Einarsson S,Brandt Y,Lundeheim N,et al.Stress and its influence on reproduction in pigs:a review[J].Acta Veterinaria Scandinavica,2008,50(1):1-8.
[34]Worby C A,Dixon J E.Sorting out the cellular functions of sorting nexins[J].Nat Rev Mol Cell Biol,2002,3(12):919-931.
[35]Tanaka K,Miyamoto N,Shouguchi-Miyata J,et al.HFM1,the human homologue of yeast Mer3,encodes a putative DNA helicase expressed specifically in germ-line cells[J].DNA Seq,2006,17(3):242-246.
[36]Yuan Y,Ida J M,Paczkowski M,et al.Identification of developmental competence-related genes in mature porcine oocytes[J].Mol Reprod Dev,2011,78(8):565-575.
[37]刘小磊,杨松柏,Rothschild M F,等.利用紧缩线性模型和贝叶斯模型对猪总产仔数和产活仔数性状的全基因组关联研究[J].遗传,2012,34(10):1261-1270.
[38]Schneider J F,Nonneman D J,Wiedmann R T,et al.Genomewide association and identification of candidate genes for ovulation rate in swine[J].J Anim Sci,2014,92(9):3792.
[39]Sell-Kubiak E,Duijvesteijn N,Lopes M S,et al.Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population[J].BMC Genomics,2015,16(1):1049.
[40]Bergfelderdrüing S,Grossebrinkhaus C,Lind B,et al.A Genomewide association study in Large White and Landrace Pig populations for number piglets born alive[J].PLoS One,2015,10(3):e0117468.
[41]Guo X,Su G,Christensen O F,et al.Genome-wide association analyses using a Bayesian approach for litter size and piglet mortality in Danish Landrace and Yorkshire pigs[J].BMC Genomics,2016,17(1):1-12.
[42]Trenhaile M D,Petersen J L,Kachman S D,et al.Long-term selection for litter size in swine results in shifts in allelic frequency in regions involved in reproductive processes[J].Anim Genet,2016,47(5):534-542.
[43]Wang Y,Ding X,Tan Z,et al.Genome-wide association study for reproductive traits in a Large White pig population[J].Anim Genet,2018,49(2):127-131.
[44]He L C,Li P H,Ma X,et al.Identification of new single nucleotide polymorphisms affecting total number born and candidate genes related to ovulation rate in Chinese Erhualian pigs[J].Anim Genet,2017,48(1):48-54.
[45]Ma X,Li P H,Zhu M X,et al.Genome-wide association analysis reveals genomic regions on Chromosome 13 affecting litter size and candidate genes for uterine horn length in Erhualian pigs[J].Animal,2018,12(12):2453-2461.
[46]Baker M.Gene data to hit milestone[J].Nature,2012,487(7407):282-283.