团头鲂低氧耐受相关SNPs标记的开发
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摘要
为寻找耐低氧相关SNPs分子标记辅助团头鲂优良品种选育,利用团头鲂低氧耐受和敏感群体的转录组数据,进行SNPs位点的开发和鉴定,获得52 623个可能的SNPs位点,其中碱基转换和颠换型位点分别占57.4%(30 192个)和31.9%(16 802个);同义SNPs占编码区总SNPs的99.7%,非同义SNPs仅有32～35个;使用PCR-RFLP技术对筛选出的5个非同义的多态性SNPs进行耐低氧性状关联分析。结果显示,Plin2-A1157G和Hif-3α-A2917G位点的SNPs在团头鲂亲本群体中与低氧耐受性状显著相关,但在子代群体中却与低氧耐受性状无显著相关性。这说明亲代中筛选出的分子标记并不一定适用于子代群体,在利用分子标记辅助育种时需要考虑标记在子代中的有效性。
In order to obtain SNP markers associated with hypoxia tolerance trait for applying in molecular marker-assisted breeding of Megalobrama amblycephala,in the present study,based on the constructed transcriptome data in hypoxia tolerant and sensitive M.amblycephala,52 623 potential SNPs including transition type of 30 192(57.4%)and transversion type of 16 802(31.9%)were found.Synonymous SNPs accounted for 99.7% of total SNPs located in the coding region,while only 32～35(0.3%)nonsynonymous SNPs were found.Five nonsynonymous and polymorphic SNPs were obtained using PCR-RFLP method.Analysis showed that two SNPs,Plin2-A1157 Gand Hif-3α-A2917 G,were significantly associated with hypoxia tolerance trait in the parental populations.But further analysis revealed that no significant association existed between the two SNPs and hypoxia tolerance trait in the offspring populations.It is indicated that molecular markers isolated in the parent populations may be inappropriate in their offspring,therefore,the effectiveness of markers in offspring needs to be considered in molecular marker assisted breeding.
In order to obtain SNP markers associated with hypoxia tolerance trait for applying in molecular marker-assisted breeding of Megalobrama amblycephala,in the present study,based on the constructed transcriptome data in hypoxia tolerant and sensitive M.amblycephala,52 623 potential SNPs including transition type of 30 192(57.4%)and transversion type of 16 802(31.9%)were found.Synonymous SNPs accounted for 99.7% of total SNPs located in the coding region,while only 32～35(0.3%)nonsynonymous SNPs were found.Five nonsynonymous and polymorphic SNPs were obtained using PCR-RFLP method.Analysis showed that two SNPs,Plin2-A1157 Gand Hif-3α-A2917 G,were significantly associated with hypoxia tolerance trait in the parental populations.But further analysis revealed that no significant association existed between the two SNPs and hypoxia tolerance trait in the offspring populations.It is indicated that molecular markers isolated in the parent populations may be inappropriate in their offspring,therefore,the effectiveness of markers in offspring needs to be considered in molecular marker assisted breeding.
引文
[1]陈秀华,于丽娟,罗黎明,等.玉米分子标记辅助育种及标记开发研究进展[J].中国农业科技导报,2016,18(1):26-31.
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[3]孙永建,田永宏,余华强,等.利用分子标记辅助选择改良水稻恢复系R997对稻瘟病的抗性[J].湖北农业科学,2016,55(1):20-23.
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[6]黄智慧.大菱鲆耐高温性状选育及遗传机理研究[D].青岛:中国海洋大学,2014.
[7]陈松林,邵长伟,徐鹏.水产生物技术发展战略研究[J].中国工程科学,2016,18(3):49-56.
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[10]WANG X,LIU S,JIANG C,et al.Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish[J].Mol Genet Genomics,2017,292(1):63-76.
[11]ZHANG B,CHEN N,HUANG C H,et al,Molecular response and association analysis of Megalobrama amblycephala fih-1with hypoxia[J],Mol Genet Genomics,2016,291(4):1615-1624.
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[13]陈汝丽.团头鲂养殖产业现状与发展趋势[J].科学养鱼,2015(2):4-5.
[14]CHEN N,HUANG C H,CHEN B X,et al.Alternative splicing transcription of Megalobrama amblycephala HIF prolyl hydroxylase PHD3and up-regulation of PHD3by HIF-1α[J].Biochem Biophys Res Commun,2016,469(3):737-742.
[15]CHEN N,HUANG C X,HUANG C H,et al.The molecular characterization,expression pattern and alternative initiation of Megalobrama amblycephala Hif prolyl hydroxylase Phd1[J].Gene,2018,678:219-225.
[16]LIU Z,ZHAO X,JIANG X,et al.Transcription of blunt snout bream(Megalobrama amblycephala)HIF3αand its localization in the nucleus under both normoxic and hypoxic conditions[J].Biochem Biophys Res Commun,2018,500(2):443-449.
[17]SHEN R J,JIANG X Y,PU J W,et al.HIF-1alpha and-2alpha genes in a hypoxia-sensitive teleost species Megalobramaamblycephala:cDNA cloning,expression and different responses to hypoxia[J].Comp Biochem Physiol B Biochem Mol Biol,2010,157(3):273-280.
[18]SUN Y,GUO H H,GUO D D,et al.Divergence of genes encoding CITED1and CITED2in blunt snout bream(Megalobrama amblycephala)and their transcriptional responses to hypoxia[J].Front Physiol,2018,9:186.
[19]WANG H,HUANG C,CHEN N,et al.Molecular characterization and mRNA expression of HIF-prolyl hydroxylase-2(phd2)in hypoxia-sensing pathways from Megalobrama amblycephala[J].Comp Biochem Physiol B Biochem Mol Biol,2015,186:28-35.
[20]CHEN B X,YI S K,WANG W F,et al.Transcriptome comparison reveals insights into muscle response to hypoxia in blunt snout bream(Megalobrama amblycephala)[J].Gene,2017,624:6-13.
[21]周华,张新,刘腾云,等.高通量转录组测序的数据分析与基因发掘[J].江西科学,2012,30(5):607-611.
[22]李纪勤.栉孔扇贝(Chlamys farreri)EST-SNP的开发及其应用[D].青岛:中国海洋大学,2012.
[23]逄锦菲.“黄海2号”中国对虾高通量SNP筛选及其与抗WSSV性状的关联分析[D].上海:上海海洋大学,2013.
[24]王婷.基于高通量转录组数据的大菱鲆SNP标记筛选及相关功能基因的研究[D].大连:大连海洋大学,2014.
[25]张建勇.中国对虾(Fenneropenaeus chinensis)基因组SNP标记的开发与应用[D].青岛:中国海洋大学,2011.
[26]李素红,张天时,孔杰,等.中国对虾抗病性状遗传标记筛选及遗传多样性分析[J].渔业科学进展,2009,30(2):54-59.
[27]李三磊,徐冬冬,楼宝,等.褐牙鲆耐热相关分子标记筛选及遗传多样性分析[J].上海海洋大学学报,2012,21(4):516-523.
[28]WRIGHT S.Evolution and the genetics of populations:variability within and among natural populations[M].Chicago:U-niversity of Chicago Press,1978:24.
[29]XIAO W.The hypoxia signaling pathway and hypoxic adaptation in fishes[J].Sci China Life Sci,2015,58(2):148-155.
[30]鹿辉,尹强,王荣,等.低氧诱导因子-3α的研究进展[J].中国药理学通报,2014,30(3):318-321.
[31]HARA S,HAMADA J,KOBAYASHI C,et al.Expression and characterization of hypoxia-inducible factor(HIF)-3αin human kidney:suppression of HIF-mediated gene expression by HIF-3α[J].Biochem Biophys Res Commun,2001,287(4):808-813.
[32]ZHANG P,YAO Q,LU L,et al.Hypoxia-inducible factor 3is an oxygen-dependent transcription activator and regulates a distinct transcriptional response to hypoxia[J].Cell Rep,2014,6(6):1110-1121.
[33]胡濒月,黄英,杨明华,等.PLIN2对脂类代谢的调控研究[J].中国医药科学,2018,8(15):40-43.
[34]BILDIRICI I,SCHAIFF W T,CHEN B,et al.PLIN2is essential for trophoblastic lipid droplet accumulation and cell survival during hypoxia[J].Endocrinology,2018,doi:10.1210/en.2018-00752.
[35]卢钟磊,池信才,王义权,等.褐牙鲆耐热性状相关的微卫星分子标记筛选[J].厦门大学学报(自然科学版),2007,46(3):396-402.
[2]鲁绍雄,吴常信.动物遗传标记辅助选择研究及其应用[J].遗传,2002,24(3):359-362.
[3]孙永建,田永宏,余华强,等.利用分子标记辅助选择改良水稻恢复系R997对稻瘟病的抗性[J].湖北农业科学,2016,55(1):20-23.
[4]FUJI K,HASEGAWA O,HONDA K,et al.Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder(Paralichthys olivaceus)[J].Aquaculture,2007,272:291-295.
[5]WANG D,MAO H L,CHEN H X,et al.Isolation of Y-and X-linked SCAR markers in yellow catfish and application in the production of all-male populations[J].Anim Genet,2009,40:978-981.
[6]黄智慧.大菱鲆耐高温性状选育及遗传机理研究[D].青岛:中国海洋大学,2014.
[7]陈松林,邵长伟,徐鹏.水产生物技术发展战略研究[J].中国工程科学,2016,18(3):49-56.
[8]LI H L,GU X H,LI B J,et al.Genome-wide QTL analysis identified significant associations between hypoxia tolerance and mutations in the GPR132and ABCG4genes in Nile tilapia[J].Mar Biotechnol(NY),2017,19(5):441-453.
[9]ZHONG X,WANG X,ZHOU T,et al.Genome-wide association study reveals multiple novel QTL associated with low oxygen tolerance in hybrid catfish[J].Mar Biotechnol(NY),2017,19(4):379-390.
[10]WANG X,LIU S,JIANG C,et al.Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish[J].Mol Genet Genomics,2017,292(1):63-76.
[11]ZHANG B,CHEN N,HUANG C H,et al,Molecular response and association analysis of Megalobrama amblycephala fih-1with hypoxia[J],Mol Genet Genomics,2016,291(4):1615-1624.
[12]王卫民.团头鲂养殖产业现状[J].科学养鱼,2009(4):49-50.
[13]陈汝丽.团头鲂养殖产业现状与发展趋势[J].科学养鱼,2015(2):4-5.
[14]CHEN N,HUANG C H,CHEN B X,et al.Alternative splicing transcription of Megalobrama amblycephala HIF prolyl hydroxylase PHD3and up-regulation of PHD3by HIF-1α[J].Biochem Biophys Res Commun,2016,469(3):737-742.
[15]CHEN N,HUANG C X,HUANG C H,et al.The molecular characterization,expression pattern and alternative initiation of Megalobrama amblycephala Hif prolyl hydroxylase Phd1[J].Gene,2018,678:219-225.
[16]LIU Z,ZHAO X,JIANG X,et al.Transcription of blunt snout bream(Megalobrama amblycephala)HIF3αand its localization in the nucleus under both normoxic and hypoxic conditions[J].Biochem Biophys Res Commun,2018,500(2):443-449.
[17]SHEN R J,JIANG X Y,PU J W,et al.HIF-1alpha and-2alpha genes in a hypoxia-sensitive teleost species Megalobramaamblycephala:cDNA cloning,expression and different responses to hypoxia[J].Comp Biochem Physiol B Biochem Mol Biol,2010,157(3):273-280.
[18]SUN Y,GUO H H,GUO D D,et al.Divergence of genes encoding CITED1and CITED2in blunt snout bream(Megalobrama amblycephala)and their transcriptional responses to hypoxia[J].Front Physiol,2018,9:186.
[19]WANG H,HUANG C,CHEN N,et al.Molecular characterization and mRNA expression of HIF-prolyl hydroxylase-2(phd2)in hypoxia-sensing pathways from Megalobrama amblycephala[J].Comp Biochem Physiol B Biochem Mol Biol,2015,186:28-35.
[20]CHEN B X,YI S K,WANG W F,et al.Transcriptome comparison reveals insights into muscle response to hypoxia in blunt snout bream(Megalobrama amblycephala)[J].Gene,2017,624:6-13.
[21]周华,张新,刘腾云,等.高通量转录组测序的数据分析与基因发掘[J].江西科学,2012,30(5):607-611.
[22]李纪勤.栉孔扇贝(Chlamys farreri)EST-SNP的开发及其应用[D].青岛:中国海洋大学,2012.
[23]逄锦菲.“黄海2号”中国对虾高通量SNP筛选及其与抗WSSV性状的关联分析[D].上海:上海海洋大学,2013.
[24]王婷.基于高通量转录组数据的大菱鲆SNP标记筛选及相关功能基因的研究[D].大连:大连海洋大学,2014.
[25]张建勇.中国对虾(Fenneropenaeus chinensis)基因组SNP标记的开发与应用[D].青岛:中国海洋大学,2011.
[26]李素红,张天时,孔杰,等.中国对虾抗病性状遗传标记筛选及遗传多样性分析[J].渔业科学进展,2009,30(2):54-59.
[27]李三磊,徐冬冬,楼宝,等.褐牙鲆耐热相关分子标记筛选及遗传多样性分析[J].上海海洋大学学报,2012,21(4):516-523.
[28]WRIGHT S.Evolution and the genetics of populations:variability within and among natural populations[M].Chicago:U-niversity of Chicago Press,1978:24.
[29]XIAO W.The hypoxia signaling pathway and hypoxic adaptation in fishes[J].Sci China Life Sci,2015,58(2):148-155.
[30]鹿辉,尹强,王荣,等.低氧诱导因子-3α的研究进展[J].中国药理学通报,2014,30(3):318-321.
[31]HARA S,HAMADA J,KOBAYASHI C,et al.Expression and characterization of hypoxia-inducible factor(HIF)-3αin human kidney:suppression of HIF-mediated gene expression by HIF-3α[J].Biochem Biophys Res Commun,2001,287(4):808-813.
[32]ZHANG P,YAO Q,LU L,et al.Hypoxia-inducible factor 3is an oxygen-dependent transcription activator and regulates a distinct transcriptional response to hypoxia[J].Cell Rep,2014,6(6):1110-1121.
[33]胡濒月,黄英,杨明华,等.PLIN2对脂类代谢的调控研究[J].中国医药科学,2018,8(15):40-43.
[34]BILDIRICI I,SCHAIFF W T,CHEN B,et al.PLIN2is essential for trophoblastic lipid droplet accumulation and cell survival during hypoxia[J].Endocrinology,2018,doi:10.1210/en.2018-00752.
[35]卢钟磊,池信才,王义权,等.褐牙鲆耐热性状相关的微卫星分子标记筛选[J].厦门大学学报(自然科学版),2007,46(3):396-402.