SNP标记在动物遗传育种及人类疾病动物模型研究中的应用
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摘要
单苷酸多态性(single nucleotide polymorphism,SNP)标记是一种发生在基因组特定位点的单个核苷酸突变的遗传标记,其丰富度高、密度大、易于进行基因分型,广泛应用于动植物育种、抗病性基因标记、优势品种筛选和疾病相关基因的鉴定中。本文首先对SNP遗传标记在动物群体遗传结构、遗传图谱构建、标记辅助选择、亲缘关系鉴定以及杂种优势等方面的应用进行介绍,其次简述了在人类疾病动物模型中SNP位点与某些疾病的关联性,以期为SNP分子标记技术在动物遗传育种及人类疾病动物模型的建立、遗传学分析等方面的应用提供参考。
Single-nucleotide polymorphism(SNP) markers are genetic markers in which a single nucleotide variation occurs at a specific position in the genome.Characterized by their high abundance,density,and easy genotyping,SNP markers have been widely used in animal and plant breeding,as disease resistance markers,and for the screening of heterosis and identification of disease-related genes.In the present paper,we first present the application of SNP arrays for analyzing animal population genetic structure,genetic mapping,and for characterizing marker-assisted selection,kinship,and heterosis.Second,we describe the relationship between SNP loci and animal models of human diseases,which can provide a valuable reference for the improved application of SNP molecular marker technology in animal genetic breeding,and the establishment and genetic analysis of animal models of human diseases.
Single-nucleotide polymorphism(SNP) markers are genetic markers in which a single nucleotide variation occurs at a specific position in the genome.Characterized by their high abundance,density,and easy genotyping,SNP markers have been widely used in animal and plant breeding,as disease resistance markers,and for the screening of heterosis and identification of disease-related genes.In the present paper,we first present the application of SNP arrays for analyzing animal population genetic structure,genetic mapping,and for characterizing marker-assisted selection,kinship,and heterosis.Second,we describe the relationship between SNP loci and animal models of human diseases,which can provide a valuable reference for the improved application of SNP molecular marker technology in animal genetic breeding,and the establishment and genetic analysis of animal models of human diseases.
引文
[1]董志会,王卫,丛喆,等.恒河猴BST-2基因编码区单核苷酸多态性及其对蛋白结构和功能的影响[J].中国比较医学杂志,2015,25(7):20-24.
[2]Gao Y,Li S,Zhan A.Genome-wide single nucleotide polymorphisms(SNPs)for a model invasive ascidian Botryllus schlosseri[J].Genetica,2018,146(2):227-234.
[3]Jiang SY,Xu HY,Shen ZN,et al.Genome-wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken[J].Anim Genet,2018,49(4),337-339.
[4]赵杰,游新勇,徐贞贞,等.SNP检测方法在动物研究中的应用[J].农业工程学报,2018,34(4):299-305.
[5]李银银,王洪,李长龙,等.用45个SNP位点组合对国家啮齿类实验动物种子中心3个封闭群小鼠群体的遗传状况分析[J].实验动物科学,2018,35(1):1-7.
[6]赵紫霞,许建,白庆利,等.国内虹鳟代表性养殖群体的高通量SNP芯片检测及遗传分析[J].中国水产科学,2018,25(3):485-493.
[7]Nicoloso L,Bomba L,Colli L,et al.Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip[J].Genet Sel Evol,2015,47(1):62.
[8]Du ZQ,Ciobanu DC,Onteru SK,et al.A gene-based SNPlinkage map for pacific white shrimp,Litopenaeus vannamei[J].Anim Genet,2009,41(3):286-294.
[9]郑先虎,匡友谊,鲁翠云,等.镜鲤体长、体高、体厚性状QTL定位分析[J].遗传,2011,33(12):1366-1373.
[10]Xie M,Ming Y,Shao F,et al.Restriction site-associated DNAsequencing for SNP discovery and high-density genetic map construction in southern catfish(Silurus meridionalis)[J].RSoc Open Sci,2018,5(5):172054.
[11]梁国明,陈锋剑,赵勤涛,等.猪ZP4基因的SNP鉴定、选择压及其与产仔数的关联分析[J].畜牧兽医学报,2017,48(05):793-801.
[12]陈小明,李佳凯,王志勇,等.基于简化基因组测序的大黄鱼耐高温性状全基因组关联分析[J].水生生物学报,2017,41(04):735-740.
[13]齐传翔,徐奎,牟玉莲,等.猪CBR1基因不同拷贝形式克隆及其多态性分析[J].中国农业科学,2018,51(8):1607-1616.
[14]胡培丽,岳秉飞.小鼠SNP与Car2、Gpi1基因多态性的关联性[J].中国实验动物学报,2013,21(3):61-64.
[15]Tan S,Zhou T,Wang W,et al.GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish[J].Mol Genet Genomics,2018,293(5):1-14.
[16]柴欣,胡晓坤,马徐发,等.团头鲂MHCⅡα基因的SNP位点开发、鉴定及与抗病性状关联分析[J].华中农业大学学报,2017,36(04):76-82.
[17]王文浩,李国辉,王金玉,等.京海黄鸡禽流感抗病性状的全基因组关联分析[J].中国畜牧兽医,2015,42(03):509-515.
[18]Naderi S,Bohlouli M,Yin T,et al.Genomic breeding values,SNP effects and gene identification for disease traits in cow training sets[J].Anim Genet,2018,49(3),178-192.
[19]Kroezen V,Schenkel FS,Miglior F,et al.Candidate gene association analyses for ketosis resistance in Holsteins[J].JDairy Sci,2018,101(6):5240-5249.
[20]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.
[21]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.
[22]Edea Z,Dessie T,Dadi H,et al.Genetic diversity and population structure of Ethiopian sheep populations revealed by high-density SNP markers[J].Front Genet,2017,8:218.
[23]Akanno EC,Abo-Ismail MK,Chen L,et al.Modelling heterotic effects in beef cattle using genome-wide SNP-marker genotypes[J].J Anim Sci,2018,96(3):830-845.
[24]Amuzu-Aweh EN,Bovenhuis H,de Koning DJ,et al.Predicting heterosis for egg production traits in crossbred offspring of individual White Leghorn sires using genome-wide SNP data[J].Genet Sel Evol,2015,47(1):27.
[25]谭芳慧.SNP致病因素在疾病诊断上的应用研究[D].西安:西安电子科技大学,2014.
[26]中华医学会糖尿病学分会.中国2型糖尿病防治指南(2017年版)[J].中华糖尿病杂志,2018,10(1):4-67.
[27]柳明玉,孙飞,蒙裕欢,等.基于人2型糖尿病易感SNP位点筛查食蟹猴2型糖尿病易感SNP标记[J].中国比较医学杂志,2014,24(10):18-26.
[28]Arndt T,Wedekind D,J9rns A,et al.A novel Dock8 gene mutation confers diabetogenic susceptibility in the LEW.1AR1/Ztm-iddm rat,an animal model of human type 1 diabetes[J].Diabetologia,2015,58(12):2800-2809.
[29]Hidayat K,Yang CM,Shi BM.Body fatness at a young age,body fatness gain and risk of breast cancer:systematic review and meta-analysis of cohort studies[J].Obes Rev,2017,19(2):254-268.
[30]Setayesh T,Nersesyan A,Mi2ík M,et al.Impact of obesity and overweight on DNA stability:Few facts and many hypotheses[J].Mutat Res,2018,777:64-91.
[31]Stachowiak M,Szczerbal I,Switonski M.Genetics of adiposity in large animal models for human obesity-studies on pigs and dogs[J].Prog Mol Biol Transl Sci,2016,140:233-270.
[32]Mankowska M,Stachowiak M,Graczyk A,et al.Sequence analysis of three canine adipokine genes revealed an association between TNF polymorphisms and obesity in Labrador dogs[J].Anim Genet,2016,47(2):245-249.
[33]Jang HM,Erf GF,Rowland KC,et al.Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model[J].BMCGenomics,2014,15(1):707.
[34]Gelatt KN,Mackay EO.Prevalence of the breed-related glaucomas in pure-bred dogs in North America[J].Vet Ophthalmol,2004,7(2):97-111.
[35]Kuchtey J,Olson LM,Rinkoski T,et al.Mapping of the disease locus and identification of ADAMTS10 as a candidate gene in a canine model of primary open angle glaucoma[J].Plos Genet,2011,7(2):e1001306.
[36]Lantinga E,Kooistra HS,van Nes JJ.Periodic muscle weakness and cervical ventroflexion caused by hypokalemia in a Burmese cat[J].Tijdschr Diergeneeskd,1998,123(14-15):435-437.
[37]Gandolfi B,Gruffyddjones TJ,Malik R,et al.First WNK4-hypokalemia animal model identified by genome-wide association in burmese cats[J].PLoS One,2012,7(12):e53173.
[38]徐伟,晁天柱,刘丽均,等.小鼠冷冻胚胎和精子SNP遗传鉴定方法的建立[J].中国实验动物学报,2016,24(2):169-174.
[2]Gao Y,Li S,Zhan A.Genome-wide single nucleotide polymorphisms(SNPs)for a model invasive ascidian Botryllus schlosseri[J].Genetica,2018,146(2):227-234.
[3]Jiang SY,Xu HY,Shen ZN,et al.Genome-wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken[J].Anim Genet,2018,49(4),337-339.
[4]赵杰,游新勇,徐贞贞,等.SNP检测方法在动物研究中的应用[J].农业工程学报,2018,34(4):299-305.
[5]李银银,王洪,李长龙,等.用45个SNP位点组合对国家啮齿类实验动物种子中心3个封闭群小鼠群体的遗传状况分析[J].实验动物科学,2018,35(1):1-7.
[6]赵紫霞,许建,白庆利,等.国内虹鳟代表性养殖群体的高通量SNP芯片检测及遗传分析[J].中国水产科学,2018,25(3):485-493.
[7]Nicoloso L,Bomba L,Colli L,et al.Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip[J].Genet Sel Evol,2015,47(1):62.
[8]Du ZQ,Ciobanu DC,Onteru SK,et al.A gene-based SNPlinkage map for pacific white shrimp,Litopenaeus vannamei[J].Anim Genet,2009,41(3):286-294.
[9]郑先虎,匡友谊,鲁翠云,等.镜鲤体长、体高、体厚性状QTL定位分析[J].遗传,2011,33(12):1366-1373.
[10]Xie M,Ming Y,Shao F,et al.Restriction site-associated DNAsequencing for SNP discovery and high-density genetic map construction in southern catfish(Silurus meridionalis)[J].RSoc Open Sci,2018,5(5):172054.
[11]梁国明,陈锋剑,赵勤涛,等.猪ZP4基因的SNP鉴定、选择压及其与产仔数的关联分析[J].畜牧兽医学报,2017,48(05):793-801.
[12]陈小明,李佳凯,王志勇,等.基于简化基因组测序的大黄鱼耐高温性状全基因组关联分析[J].水生生物学报,2017,41(04):735-740.
[13]齐传翔,徐奎,牟玉莲,等.猪CBR1基因不同拷贝形式克隆及其多态性分析[J].中国农业科学,2018,51(8):1607-1616.
[14]胡培丽,岳秉飞.小鼠SNP与Car2、Gpi1基因多态性的关联性[J].中国实验动物学报,2013,21(3):61-64.
[15]Tan S,Zhou T,Wang W,et al.GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish[J].Mol Genet Genomics,2018,293(5):1-14.
[16]柴欣,胡晓坤,马徐发,等.团头鲂MHCⅡα基因的SNP位点开发、鉴定及与抗病性状关联分析[J].华中农业大学学报,2017,36(04):76-82.
[17]王文浩,李国辉,王金玉,等.京海黄鸡禽流感抗病性状的全基因组关联分析[J].中国畜牧兽医,2015,42(03):509-515.
[18]Naderi S,Bohlouli M,Yin T,et al.Genomic breeding values,SNP effects and gene identification for disease traits in cow training sets[J].Anim Genet,2018,49(3),178-192.
[19]Kroezen V,Schenkel FS,Miglior F,et al.Candidate gene association analyses for ketosis resistance in Holsteins[J].JDairy Sci,2018,101(6):5240-5249.
[20]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.
[21]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.
[22]Edea Z,Dessie T,Dadi H,et al.Genetic diversity and population structure of Ethiopian sheep populations revealed by high-density SNP markers[J].Front Genet,2017,8:218.
[23]Akanno EC,Abo-Ismail MK,Chen L,et al.Modelling heterotic effects in beef cattle using genome-wide SNP-marker genotypes[J].J Anim Sci,2018,96(3):830-845.
[24]Amuzu-Aweh EN,Bovenhuis H,de Koning DJ,et al.Predicting heterosis for egg production traits in crossbred offspring of individual White Leghorn sires using genome-wide SNP data[J].Genet Sel Evol,2015,47(1):27.
[25]谭芳慧.SNP致病因素在疾病诊断上的应用研究[D].西安:西安电子科技大学,2014.
[26]中华医学会糖尿病学分会.中国2型糖尿病防治指南(2017年版)[J].中华糖尿病杂志,2018,10(1):4-67.
[27]柳明玉,孙飞,蒙裕欢,等.基于人2型糖尿病易感SNP位点筛查食蟹猴2型糖尿病易感SNP标记[J].中国比较医学杂志,2014,24(10):18-26.
[28]Arndt T,Wedekind D,J9rns A,et al.A novel Dock8 gene mutation confers diabetogenic susceptibility in the LEW.1AR1/Ztm-iddm rat,an animal model of human type 1 diabetes[J].Diabetologia,2015,58(12):2800-2809.
[29]Hidayat K,Yang CM,Shi BM.Body fatness at a young age,body fatness gain and risk of breast cancer:systematic review and meta-analysis of cohort studies[J].Obes Rev,2017,19(2):254-268.
[30]Setayesh T,Nersesyan A,Mi2ík M,et al.Impact of obesity and overweight on DNA stability:Few facts and many hypotheses[J].Mutat Res,2018,777:64-91.
[31]Stachowiak M,Szczerbal I,Switonski M.Genetics of adiposity in large animal models for human obesity-studies on pigs and dogs[J].Prog Mol Biol Transl Sci,2016,140:233-270.
[32]Mankowska M,Stachowiak M,Graczyk A,et al.Sequence analysis of three canine adipokine genes revealed an association between TNF polymorphisms and obesity in Labrador dogs[J].Anim Genet,2016,47(2):245-249.
[33]Jang HM,Erf GF,Rowland KC,et al.Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model[J].BMCGenomics,2014,15(1):707.
[34]Gelatt KN,Mackay EO.Prevalence of the breed-related glaucomas in pure-bred dogs in North America[J].Vet Ophthalmol,2004,7(2):97-111.
[35]Kuchtey J,Olson LM,Rinkoski T,et al.Mapping of the disease locus and identification of ADAMTS10 as a candidate gene in a canine model of primary open angle glaucoma[J].Plos Genet,2011,7(2):e1001306.
[36]Lantinga E,Kooistra HS,van Nes JJ.Periodic muscle weakness and cervical ventroflexion caused by hypokalemia in a Burmese cat[J].Tijdschr Diergeneeskd,1998,123(14-15):435-437.
[37]Gandolfi B,Gruffyddjones TJ,Malik R,et al.First WNK4-hypokalemia animal model identified by genome-wide association in burmese cats[J].PLoS One,2012,7(12):e53173.
[38]徐伟,晁天柱,刘丽均,等.小鼠冷冻胚胎和精子SNP遗传鉴定方法的建立[J].中国实验动物学报,2016,24(2):169-174.