基于线粒体COI基因序列的5种鲤养殖品种遗传多样性研究
|
摘要
本研究通过对5个鲤养殖品种即高寒鲤(Cyprinus carpio Frigid carp)、松浦鲤(Cyprinus carpio Songpu carp)、蓝鳞鲤(Cyprinus carpio blue var)、松浦镜鲤(Cyprinus carpio Songpu mirror carp)和红镜鲤(Cyprinus carpio Red mirror carp)的线粒体COI基因部分序列的测定,比较并分析了其遗传多样性和系统进化关系。在5个鲤品种共100个样本的线粒体COI序列中检测到8种单倍型,其中5个单倍型(H1、H2、H4、H5、H6)涵盖样本较多,占总样本数的94.06%。蓝鳞鲤的单倍型数最少,仅有1个,红镜鲤单倍型数为2个,其余3个品种的单倍型数均为5个。5个品种单倍型多样性(Hd)在0.160±0.070~0.811±0.055,其中,遗传多样性最高的为高寒鲤。AMOVA结果表明,品种间变异(50.28%)略高于品种内变异(49.72%),各品种间的FST值在0.711 4~0.831 2,其中蓝鳞鲤与其他群体之间差异最大。用MEGA4.0软件构建的基于遗传距离的进化树表明,5个养殖品种中,高寒鲤和红镜鲤的遗传距离最近(D=0.31),聚为一支;松浦镜鲤和松浦鲤的遗传距离较近(D=0.33),聚为一支;蓝鳞鲤与其他品种存在较大遗传差异,单独形成一个分支。除蓝鳞鲤外,其余4个养殖品种间均存在共享的单倍型(H2、H4、H5、H6),可能是由于其在选育过程中亲本的遗传背景存在交叉,同时也证明DNA条码在分析种内品种间遗传关系时具有可行性但具有一定的局限性。
The mitochondrial COI gene of five cyprinoid aquaculture varieties were sequenced and their genetic diversity and cluster analysis were compared. Eight haplotypes were detected from 100 individuals, of which 94.06 % belonged to five haplotypes(H1, H2, H4, H5, H6). Cyprinus carpio blue var has only one haplotype, C. c.Red mirror carp has two haplotypes, and the other varieties including Cyprinus carpio Frigid carp, C. c. Songpu carp and C. c. Songpu mirror carp had five. Haplotype diversity(Hd) was 0.160±0.070 ~ 0.811±0.055, the highest Hd frequency was observed in Frigid carp. The AMOVA and cluster analysis revealed that genetic distance between varieties(50.28%) was a little higher than that within varieties(49.72%), and the FST ranged from 0.7114 0.831 2. Compared with the others varieties, Cyprinus carpio blue var exhibited the biggest differences. According to the evolutionary tree based on genetic distance, five varieties could be divided into three groups, the first group included Frigid carp and Red mirror carp, the second included Songpu mirror carp and Songpu carp,and the last included Cyprinus carpio blue var. With the exception of Cyprinus carpio blue var, all varieties shared the same haplotypes(H2, H4, H5, H6), which may be due to cross breeding. This study also indicated that DNA barcoding is a practical tool for analyzing the hereditary of different varieties. However, some limitations still exist.
The mitochondrial COI gene of five cyprinoid aquaculture varieties were sequenced and their genetic diversity and cluster analysis were compared. Eight haplotypes were detected from 100 individuals, of which 94.06 % belonged to five haplotypes(H1, H2, H4, H5, H6). Cyprinus carpio blue var has only one haplotype, C. c.Red mirror carp has two haplotypes, and the other varieties including Cyprinus carpio Frigid carp, C. c. Songpu carp and C. c. Songpu mirror carp had five. Haplotype diversity(Hd) was 0.160±0.070 ~ 0.811±0.055, the highest Hd frequency was observed in Frigid carp. The AMOVA and cluster analysis revealed that genetic distance between varieties(50.28%) was a little higher than that within varieties(49.72%), and the FST ranged from 0.7114 0.831 2. Compared with the others varieties, Cyprinus carpio blue var exhibited the biggest differences. According to the evolutionary tree based on genetic distance, five varieties could be divided into three groups, the first group included Frigid carp and Red mirror carp, the second included Songpu mirror carp and Songpu carp,and the last included Cyprinus carpio blue var. With the exception of Cyprinus carpio blue var, all varieties shared the same haplotypes(H2, H4, H5, H6), which may be due to cross breeding. This study also indicated that DNA barcoding is a practical tool for analyzing the hereditary of different varieties. However, some limitations still exist.
引文
[1]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(3):55-59.
[2]Hebert P D N,Cywinska A,Ball S L,et al.Biological identifications through DNA barcodes[J].Proc Royal Soc London B:Biol Sci,2003,270(1512):313-321.
[3]Hebert P D N,Penton E H,Burns J M,et al.Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator[J].Proc Natl Acad Sci,2004,101(41):14812-14817.
[4]Pfenninger M,Nowak C,Kley C,et al.Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus(Diptera)species[J].Mol Ecol,2007,16(9):1957-1968.
[5]杜启艳,常重杰.DNA条形码在鉴定物种中的应用[J].生物学教学,2010,12(35):60-61.
[6]程希婷,王爱民,顾志峰,等.DNA条形码研究进展[J].基因组学与应用生物学,2011,30(6):748-758.
[7]律迎春,左淘,唐庆娟,等.海参DNA条形码的构建及应用[J].中国水产科学,2011,18(4):782-789.
[8]郭昱嵩,王中铎,贾菠,等.南海常见7种石斑鱼的DNA条码构建与亲缘关系分析[J].现代农业科学,2009,16(5):201-205.
[9]姚雪,于丹,王绪敏,等.大型海洋藻类DNA条形码技术的开发与应用[J].应用技术,2011,1(2):161-162.
[10]王中铎,郭昱嵩,陈荣玲,等.南海常见硬骨鱼类COI条码序列[J].海洋与湖沼,2009,40(5):608-614.
[11]王中铎,郭昱嵩,李路,等.笛鲷属鱼类DNA分子条码、系统进化和成种机制[J].中国科学,2010,40(6):516-521.
[12]白庆利,刘明华,尹洪滨,等.高寒鲤染色体核型分析[J].水产学杂志,1999,12(1):47-49.
[13]贾智英,李飞,李池陶,等.松浦鲤保护群体遗传结构研究[J].华北农学报,2011(1):29-34.
[14]沈俊宝,刘明华.蓝色鳞鲤品系的起源、筛选和培育[J].淡水渔业,1988(4):3-6.
[15]刘明华,沈俊宝,王强,等.松浦镜鲤(散鳞镜鲤/德国镜鲤)Fl主要经济性状及遗传特性[J].水产学杂志,1993,6(1):19-25.
[16]长江水产研究所育种室.鲤新品种-红镜鲤选育简报[J].淡水渔业科技杂志,1977(4):25.
[17]卢圣栋.现代分子生物学实验技术[M].第2版.北京:中国协和医科大学出版社,1999.
[18]Ward R D,Zemlak T S,Innes B H,et al.DNA barcoding Australia’s fish species[J].Philosoph Trans Royal Soc,2005,360(1462)B:1847-1857.
[19]何继满.分支系统学的外群分析方法中外群性状状态确定的探讨[J].动物学报,43(l):108-109,1997.
[20]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Oxford J Bioinform,2009,25(1):1451-1452.
[21]Tamura K,Dudley J,Nei M,et al.MEGA4:Molecular evolutionary genetics analysis(MEGA)software version-4.0[J].Mol Biol Evol,2007,24(8):1596-1599.
[22]Srivathsan A,Meier R.On the inappropriate use of Kimura-2-parameter(K2P)divergences in the DNA-barcoding literature[J].Cladistics,2012,28(2):190-194.
[23]Excoffier L,Laval G,Schneider S.Arlequin(version-3.0):An integrated software package for population genetics data analysis[J].Evol Bioinform,2005,1:47-50.
[24]Saitou N,Nei M.The neighbor-joining method:A new method for reconstructing phylogenetic trees[J].Mol Biol Evol,1987,4(4):406-425.
[25]欧阳小艳,莫帮辉,余华丽,等.DNA条形码识别一DNA条形码与DNA芯片识别蚊媒准确性的比较[J].中国国境卫生检疫杂志,2007,30(6):349-352.
[26]伍献文.中国理科鱼类志[M].上海:上海科学技术出版社,1982:12.
[27]童金苟,吴清江.三个鲤品种线粒体基因片段序列保守性[J].水生生物学报,2001,25(1):54-60.
[28]Fedorov A,Saxonov S,Gilbert W.Regularities of contextdependent codon bias in eukaryotic genes[J].Nucl Acids Res,2002,30(5):1192-1197.
[29]黄原.分子系统学一原理,方法和应用[M].北京:中国农业出版社,1998:70-76.
[30]陈念,赵树进.入侵种的DNA条形码鉴定[J].生物技术通讯,2009,20(1):135-137.
[31]韦嫔媛,彭金霞,房振峰,等.卵形鲳鲹线粒体COI基因全长序列的克隆与分析[J].西南农业学报,2011,24(4):1552-1557.
[32]Hebert P D N,Ratnasingham S,Jeremy R W.Bareodinganimal life:cytochrome coxidase subunitl divergences among closely related species[J].Proc Royal Soc London B:Biol Sci,2003,270(1):96-99.
[2]Hebert P D N,Cywinska A,Ball S L,et al.Biological identifications through DNA barcodes[J].Proc Royal Soc London B:Biol Sci,2003,270(1512):313-321.
[3]Hebert P D N,Penton E H,Burns J M,et al.Ten species in one:DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator[J].Proc Natl Acad Sci,2004,101(41):14812-14817.
[4]Pfenninger M,Nowak C,Kley C,et al.Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus(Diptera)species[J].Mol Ecol,2007,16(9):1957-1968.
[5]杜启艳,常重杰.DNA条形码在鉴定物种中的应用[J].生物学教学,2010,12(35):60-61.
[6]程希婷,王爱民,顾志峰,等.DNA条形码研究进展[J].基因组学与应用生物学,2011,30(6):748-758.
[7]律迎春,左淘,唐庆娟,等.海参DNA条形码的构建及应用[J].中国水产科学,2011,18(4):782-789.
[8]郭昱嵩,王中铎,贾菠,等.南海常见7种石斑鱼的DNA条码构建与亲缘关系分析[J].现代农业科学,2009,16(5):201-205.
[9]姚雪,于丹,王绪敏,等.大型海洋藻类DNA条形码技术的开发与应用[J].应用技术,2011,1(2):161-162.
[10]王中铎,郭昱嵩,陈荣玲,等.南海常见硬骨鱼类COI条码序列[J].海洋与湖沼,2009,40(5):608-614.
[11]王中铎,郭昱嵩,李路,等.笛鲷属鱼类DNA分子条码、系统进化和成种机制[J].中国科学,2010,40(6):516-521.
[12]白庆利,刘明华,尹洪滨,等.高寒鲤染色体核型分析[J].水产学杂志,1999,12(1):47-49.
[13]贾智英,李飞,李池陶,等.松浦鲤保护群体遗传结构研究[J].华北农学报,2011(1):29-34.
[14]沈俊宝,刘明华.蓝色鳞鲤品系的起源、筛选和培育[J].淡水渔业,1988(4):3-6.
[15]刘明华,沈俊宝,王强,等.松浦镜鲤(散鳞镜鲤/德国镜鲤)Fl主要经济性状及遗传特性[J].水产学杂志,1993,6(1):19-25.
[16]长江水产研究所育种室.鲤新品种-红镜鲤选育简报[J].淡水渔业科技杂志,1977(4):25.
[17]卢圣栋.现代分子生物学实验技术[M].第2版.北京:中国协和医科大学出版社,1999.
[18]Ward R D,Zemlak T S,Innes B H,et al.DNA barcoding Australia’s fish species[J].Philosoph Trans Royal Soc,2005,360(1462)B:1847-1857.
[19]何继满.分支系统学的外群分析方法中外群性状状态确定的探讨[J].动物学报,43(l):108-109,1997.
[20]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Oxford J Bioinform,2009,25(1):1451-1452.
[21]Tamura K,Dudley J,Nei M,et al.MEGA4:Molecular evolutionary genetics analysis(MEGA)software version-4.0[J].Mol Biol Evol,2007,24(8):1596-1599.
[22]Srivathsan A,Meier R.On the inappropriate use of Kimura-2-parameter(K2P)divergences in the DNA-barcoding literature[J].Cladistics,2012,28(2):190-194.
[23]Excoffier L,Laval G,Schneider S.Arlequin(version-3.0):An integrated software package for population genetics data analysis[J].Evol Bioinform,2005,1:47-50.
[24]Saitou N,Nei M.The neighbor-joining method:A new method for reconstructing phylogenetic trees[J].Mol Biol Evol,1987,4(4):406-425.
[25]欧阳小艳,莫帮辉,余华丽,等.DNA条形码识别一DNA条形码与DNA芯片识别蚊媒准确性的比较[J].中国国境卫生检疫杂志,2007,30(6):349-352.
[26]伍献文.中国理科鱼类志[M].上海:上海科学技术出版社,1982:12.
[27]童金苟,吴清江.三个鲤品种线粒体基因片段序列保守性[J].水生生物学报,2001,25(1):54-60.
[28]Fedorov A,Saxonov S,Gilbert W.Regularities of contextdependent codon bias in eukaryotic genes[J].Nucl Acids Res,2002,30(5):1192-1197.
[29]黄原.分子系统学一原理,方法和应用[M].北京:中国农业出版社,1998:70-76.
[30]陈念,赵树进.入侵种的DNA条形码鉴定[J].生物技术通讯,2009,20(1):135-137.
[31]韦嫔媛,彭金霞,房振峰,等.卵形鲳鲹线粒体COI基因全长序列的克隆与分析[J].西南农业学报,2011,24(4):1552-1557.
[32]Hebert P D N,Ratnasingham S,Jeremy R W.Bareodinganimal life:cytochrome coxidase subunitl divergences among closely related species[J].Proc Royal Soc London B:Biol Sci,2003,270(1):96-99.