5种类型鲤鱼线粒体DNA D-loop及邻近区段的遗传多样性分析
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摘要
采用PCR技术对乌克兰鳞鲤、德国镜鲤、框鳞镜鲤、红镜鲤和州河鲤共97尾个体的线粒体DNA D-loop及邻近区段进行了扩增,经测序后获得碱基顺序排列清晰的DNA片段,长度分别为1342、1343、1344 bp。共得到8种单倍型(GenBank序列号为MG786481～MG786483,MG786485～MG786487,KC292935,KC292936)。使用Mega 6.0软件计算出5个群体的组内及组间遗传距离,并构建邻接系统树。线粒体DNA D-loop及邻近区段、单独D-loop区段的碱基序列分析结果表明,单倍型Ⅰ至Ⅳ为欧洲血统,碱基差异位点数较多,变异程度较高;单倍型Ⅴ至Ⅷ为亚洲血统,碱基差异位点数较少,变异程度较低。在线粒体DNA D-loop及邻近区段内,德国镜鲤组内平均遗传距离为0.00462,核苷酸多样性指数为0.00458,平均核苷酸差异性为6.150,遗传多样性最大;州河鲤组内的平均遗传距离为0.00065,核苷酸多样性指数为0.00065,平均核苷酸差异性为0.870,遗传多样性最低。
In this study, the mitochondrial DNA(mtDNA) D-loop and its adjacent region were amplified in 97 samples including of Zhouhe carp, mirror carp, Germany mirror carp, red mirror carp and Ukraine scale carp by PCR. The DNA fragment lengths were found to be 1342 bp, 1343 bp and 1344 bp. The sequences of 8 haplotypes had submitted to GenBank, and the sequence numbers were MG786481—MG786483, MG786485—MG786487, KC292935 and KC292936. The genetic distance and neighbor-joining(NJ) phylogenetic tree analysis were performed by Mega 6.0 software. Through the analysis of base sequence in mtDNA D-loop and its adjacent region or D-loop region, the results showed that the haplotypesⅠ to Ⅳ were European descent, and that there were many points of base difference, with low variation extent. The haplotypes Ⅴ to Ⅷ were Asian descent, and that there was little point of base difference, with high variation extent. In mtDNA D-loop and its adjacent region, the average genetic distance within the Germany mirror carp group was 0.00462, with nucleotide diversity of 0.00458, average nucleotide differences of 6.150, and the maximal genetic diversity, the average genetic distance within the Zhouhe carp group of 0.00065, nucleotide diversity of 0.00065, with average nucleotide differences number of 0.870, the minimal genetic diversity among the five types of common carp.
In this study, the mitochondrial DNA(mtDNA) D-loop and its adjacent region were amplified in 97 samples including of Zhouhe carp, mirror carp, Germany mirror carp, red mirror carp and Ukraine scale carp by PCR. The DNA fragment lengths were found to be 1342 bp, 1343 bp and 1344 bp. The sequences of 8 haplotypes had submitted to GenBank, and the sequence numbers were MG786481—MG786483, MG786485—MG786487, KC292935 and KC292936. The genetic distance and neighbor-joining(NJ) phylogenetic tree analysis were performed by Mega 6.0 software. Through the analysis of base sequence in mtDNA D-loop and its adjacent region or D-loop region, the results showed that the haplotypesⅠ to Ⅳ were European descent, and that there were many points of base difference, with low variation extent. The haplotypes Ⅴ to Ⅷ were Asian descent, and that there was little point of base difference, with high variation extent. In mtDNA D-loop and its adjacent region, the average genetic distance within the Germany mirror carp group was 0.00462, with nucleotide diversity of 0.00458, average nucleotide differences of 6.150, and the maximal genetic diversity, the average genetic distance within the Zhouhe carp group of 0.00065, nucleotide diversity of 0.00065, with average nucleotide differences number of 0.870, the minimal genetic diversity among the five types of common carp.
引文
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[6] 白晓慧,杨华,孟一耕,等.大鳞副泥鳅群体线粒体DNA D-loop序列遗传变异分析[J].水产科学,2018,37(5):658-664.
[7] 郭健康,安苗,周其椿,等.喀斯特山区大眼鳜线粒体COⅠ基因序列分析[J].水产科学,2016,35(6):649-657.
[8] 郑文娟,来育洪,尤昕煜,等.舟山小黄鱼线粒体DNA D-loop区序列变异的遗传多样性分析[J].动物学研究,2012,33(3):329-336.
[9] 袁振兴,代应贵,刘伟,等.都柳江鲤、鲫和草鱼种群mtDNA控制区及遗传多样性分析[J].基因组学与应用生物学,2017,36(5):1926-1934.
[10] 董新培,穆淑梅,周楠,等.不同地理群体乌鳢线粒体DNA控制区结构分析及遗传多样性[J].水产学报,2014,38(9):1277-1285.
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[13] 胡雪松,李池陶,马波,等.3个德国镜鲤养殖群体遗传变异的微卫星分析[J].水产学报,2007,31(5):575-580.
[14] 汪根成.德国镜鲤的引种养殖[J].宁夏农林科技1991,4(15):47-48.
[15] 张秋亮,艾明艳,卢黄华,等.基于框鳞镜鲤形体和营养特征的分类研究[J].食品科学,2011,32(5):249-253.
[16] 成凤莲,王珊.水库网箱养殖框镜鲤的试验[J].内蒙古农业科技,2005(7):294-295.
[17] 杨建利,滕淑芹.土著鱼州河鲤保护现状与前景分析[J].中国水产,2017(2):80-82.
[18] 姜巨峰,韩现芹,傅志茹,等.雌雄州河鲤肌肉营养成分分析[J].江苏农业科学,2011,39(5):405-407.
[19] 杨建利,滕淑芹,赵士海,等.增殖放流对恢复州河鲤种质性状的影响[J].中国水产,2017(8):91-93.
[20] Perez-Enriquze R,Taniguchi N.Genetic structure of red seabream(Pagrus major) population of Japan and the Southwest Pacific,using microsatellite DNA markers[J].Fisheries Science,1999,65(1):23-30.
[21] Iguchi K,Tanimura Y,Nishida M.Sequence divergence in the mtDNA control region of amphidromous and landlocked forms of ayu[J].Fisheries Science,1997,63(6):901-905.
[22] Takahashi Y,Kobayashi T,Ueda T.Genetical variation of the D-loop region in mitochondrial DNA using PCR method in metropolitan bitterling[J].Fish Genetics and Breeding Science,1994(20):39-45.
[23] 王淞,曹晓霞,谷口顺彦,等.4个群体鲢mtDNA D-loop的PCR-RFLP分析[J].淡水渔业,2010,40(4):3-15.
[24] 张方,米志勇,毛钟荣,等.草鱼(Ctenopharyngodon idellus)线粒体DNA控制区及其两侧tRNA基因的克隆与结构分析[J].中国生物化学与分子生物学报,1999,15(3):417-422.
[25] Broughton R E,Milam J E,Roe B A.The complete sequence of the zebrafish(Danio rerio)mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA[J].Genome Resource,2001,11(11):1958-1967.
[26] Mabuchi K.Complete mitochondrial genomes of five introduced strains of common carp (Cyprinus carpio) in Japan with 29 diagnostic SNPs distinguishable by restriction enzyme analysis[J].Mitochondrial DNA Part B Resources,2016,1(1):261-263.
[27] Mabuchi K,Senou H,Nishida M.Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp (Cyprinus carpio) in Japan[J].Molecular Ecology,2008,17(3):796-809.
[28] 梁宏伟,邹桂伟,罗相忠,等.3种中国鲤mtDNA D-loop序列的多态性与系统进化研究[J].西北农林科技大学学报:自然科学版,2009,37(3):55-65.
[29] Zhou J F,Wu Q J,Ye Y Z,et al.Genetic divergence between Cyprinus carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis,with emphasis on origin of European domestic carp[J].Genetica,2003,119(1):93-97.
[30] 杨正玲,赵世海,龚疏影,等.州河鲤、建鲤和框鳞镜鲤的mtDNA D-loop的RFLP分析[J].淡水渔业,2008,38(3):40-45.
[2] 全国水产技术推广总站.2016水产新品种推广指南[M].北京:中国农业出版社,2016:170-181.
[3] 向燕,朱玲,胡世然,等.清水江鲤鱼线粒体COⅠ基因序列变异及遗传多样性[J].贵州农业科学,2013,41(6):17-19.
[4] 邹芝英,杨弘,罗永巨,等.长鳍鲤mtDNA D-loop区序列结构和多态性分析[J].江苏农业科学,2013,41(8):27-30.
[5] 郝君,杨蔷,鲍迪,等.6种鱼mtDNA D-loop及其邻近区段的序列比较分析[J].大连海洋大学学报,2013,28(2):160-165.
[6] 白晓慧,杨华,孟一耕,等.大鳞副泥鳅群体线粒体DNA D-loop序列遗传变异分析[J].水产科学,2018,37(5):658-664.
[7] 郭健康,安苗,周其椿,等.喀斯特山区大眼鳜线粒体COⅠ基因序列分析[J].水产科学,2016,35(6):649-657.
[8] 郑文娟,来育洪,尤昕煜,等.舟山小黄鱼线粒体DNA D-loop区序列变异的遗传多样性分析[J].动物学研究,2012,33(3):329-336.
[9] 袁振兴,代应贵,刘伟,等.都柳江鲤、鲫和草鱼种群mtDNA控制区及遗传多样性分析[J].基因组学与应用生物学,2017,36(5):1926-1934.
[10] 董新培,穆淑梅,周楠,等.不同地理群体乌鳢线粒体DNA控制区结构分析及遗传多样性[J].水产学报,2014,38(9):1277-1285.
[11] 天津市水产技术推广总站.2010 年天津市渔业主导品种[J].中国水产,2010(2):28-29.
[12] 刘明华,白庆利,沈俊宝.德国镜鲤选育及生产应用研究[J].黑龙江水产,1995(3):4-10.
[13] 胡雪松,李池陶,马波,等.3个德国镜鲤养殖群体遗传变异的微卫星分析[J].水产学报,2007,31(5):575-580.
[14] 汪根成.德国镜鲤的引种养殖[J].宁夏农林科技1991,4(15):47-48.
[15] 张秋亮,艾明艳,卢黄华,等.基于框鳞镜鲤形体和营养特征的分类研究[J].食品科学,2011,32(5):249-253.
[16] 成凤莲,王珊.水库网箱养殖框镜鲤的试验[J].内蒙古农业科技,2005(7):294-295.
[17] 杨建利,滕淑芹.土著鱼州河鲤保护现状与前景分析[J].中国水产,2017(2):80-82.
[18] 姜巨峰,韩现芹,傅志茹,等.雌雄州河鲤肌肉营养成分分析[J].江苏农业科学,2011,39(5):405-407.
[19] 杨建利,滕淑芹,赵士海,等.增殖放流对恢复州河鲤种质性状的影响[J].中国水产,2017(8):91-93.
[20] Perez-Enriquze R,Taniguchi N.Genetic structure of red seabream(Pagrus major) population of Japan and the Southwest Pacific,using microsatellite DNA markers[J].Fisheries Science,1999,65(1):23-30.
[21] Iguchi K,Tanimura Y,Nishida M.Sequence divergence in the mtDNA control region of amphidromous and landlocked forms of ayu[J].Fisheries Science,1997,63(6):901-905.
[22] Takahashi Y,Kobayashi T,Ueda T.Genetical variation of the D-loop region in mitochondrial DNA using PCR method in metropolitan bitterling[J].Fish Genetics and Breeding Science,1994(20):39-45.
[23] 王淞,曹晓霞,谷口顺彦,等.4个群体鲢mtDNA D-loop的PCR-RFLP分析[J].淡水渔业,2010,40(4):3-15.
[24] 张方,米志勇,毛钟荣,等.草鱼(Ctenopharyngodon idellus)线粒体DNA控制区及其两侧tRNA基因的克隆与结构分析[J].中国生物化学与分子生物学报,1999,15(3):417-422.
[25] Broughton R E,Milam J E,Roe B A.The complete sequence of the zebrafish(Danio rerio)mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA[J].Genome Resource,2001,11(11):1958-1967.
[26] Mabuchi K.Complete mitochondrial genomes of five introduced strains of common carp (Cyprinus carpio) in Japan with 29 diagnostic SNPs distinguishable by restriction enzyme analysis[J].Mitochondrial DNA Part B Resources,2016,1(1):261-263.
[27] Mabuchi K,Senou H,Nishida M.Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp (Cyprinus carpio) in Japan[J].Molecular Ecology,2008,17(3):796-809.
[28] 梁宏伟,邹桂伟,罗相忠,等.3种中国鲤mtDNA D-loop序列的多态性与系统进化研究[J].西北农林科技大学学报:自然科学版,2009,37(3):55-65.
[29] Zhou J F,Wu Q J,Ye Y Z,et al.Genetic divergence between Cyprinus carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis,with emphasis on origin of European domestic carp[J].Genetica,2003,119(1):93-97.
[30] 杨正玲,赵世海,龚疏影,等.州河鲤、建鲤和框鳞镜鲤的mtDNA D-loop的RFLP分析[J].淡水渔业,2008,38(3):40-45.