基于COI序列的长江中上游鲢6个地理群体遗传多样性分析
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摘要
为了对长江中上游鲢(Hypophthalmichthys molitrix)种质资源现状进行监测和评价,本研究利用线粒体细胞色素C氧化酶I(cytochrome c oxidase subunit I)基因(COI)对长江中上游宜宾、忠县、万州、石首、监利、湘江6个鲢群体进行了遗传多样性分析。结果表明,在648 bp的COI序列中共检测到42个变异位点,其中单变异位点14个,简约信息位点28个。6个群体123个个体共定义了26个单倍型,单倍型多样性为0.0476~0.0945,核苷酸多样性为0.00196~0.00982。6个鲢群体总体遗传多样性丰富,万州群体单倍型多样性和核苷酸多样性均最高,忠县群体单倍型多样性最低,核苷酸多样性最低的为石首群体。遗传变异主要来自群体内个体间,单倍型网络图和系统进化树显示各群体的单倍型没有形成明显的地理格局。此外,上游宜宾群体和万州群体与中游的石首、监利和湘江群体具有明显的遗传分化,中游的监利群体与石首群体和湘江群体也有一定的遗传分化,上游群体和中游群体应该分属于长江水系两个不同的种群。
The silver carp(Hypophthalmichthys molitrix), one of the four major Chinese carps, is widely distributed in the Yangtze, Pearl, and Heilongjiang River Basins of China. The wild silver carp populations in the Yangtze River, with an excellent production performance, is an important germplasm resource for artificial farming and breeding. Because of overfishing, habitat fragmentation, and water pollution, the natural carp populations have been continuously declining in recent years. The basic genetic background analysis of the silver carp would be theoretically and practically important for the conservation of germplasm resources and genetic improvement. In this study, mitochondrial cytochrome C oxidase subunit I gene(COI) was sequenced to determine the genetic diversity and variation of six geographical silver carp populations: Yibin, Zhongxian, Wanzhou, Shishou, Jianli, and Xiangjiang. The amplified fragment was 648 bp in length, and a total of 26 haplotypes were defined among 123 sequences of COI from the six silver carp populations. The haplotype and nucleotide diversity index of the six populations ranged from 0.0476 to 0.0945, and from 0.00196 to 0.00982, respectively. The six groups exhibited a high genetic diversity, of which the Wanzhou population showed the highest haplotype and nucleotide diversities; the lowest haplotype and nucleotide diversities were observed in the Zhongxian and Shishou populations, respectively. The molecular variance(AMOVA) analysis showed that the variation within populations(accounting for 88.72%) was the main source of variation, and only 11.28% of the variation was found among the groups. The haplotype network was radial, centering on the main haplotype. The neighbor-joining phylogenetic tree of haplotypes based on genetic distances were inconsistent with their geographical distances. According to the differentiation index(Fst) between populations of H. molitrix, there were high differences between the Yinbin, Wanzhou, and 3 populations from the middle reach(P < 0.05); meanwhile, the Jianli population showed a significant differentiation from the Shishou and Xiangjiang populations(P < 0.01). The results revealed that the upper-and middle-reach populations should have originated from different populations in the Yangtze River. This study could provide useful basic data for the scientific protection, and reasonable and sustainable utilization of this germplasm resource in the Yangtze River Basin.
The silver carp(Hypophthalmichthys molitrix), one of the four major Chinese carps, is widely distributed in the Yangtze, Pearl, and Heilongjiang River Basins of China. The wild silver carp populations in the Yangtze River, with an excellent production performance, is an important germplasm resource for artificial farming and breeding. Because of overfishing, habitat fragmentation, and water pollution, the natural carp populations have been continuously declining in recent years. The basic genetic background analysis of the silver carp would be theoretically and practically important for the conservation of germplasm resources and genetic improvement. In this study, mitochondrial cytochrome C oxidase subunit I gene(COI) was sequenced to determine the genetic diversity and variation of six geographical silver carp populations: Yibin, Zhongxian, Wanzhou, Shishou, Jianli, and Xiangjiang. The amplified fragment was 648 bp in length, and a total of 26 haplotypes were defined among 123 sequences of COI from the six silver carp populations. The haplotype and nucleotide diversity index of the six populations ranged from 0.0476 to 0.0945, and from 0.00196 to 0.00982, respectively. The six groups exhibited a high genetic diversity, of which the Wanzhou population showed the highest haplotype and nucleotide diversities; the lowest haplotype and nucleotide diversities were observed in the Zhongxian and Shishou populations, respectively. The molecular variance(AMOVA) analysis showed that the variation within populations(accounting for 88.72%) was the main source of variation, and only 11.28% of the variation was found among the groups. The haplotype network was radial, centering on the main haplotype. The neighbor-joining phylogenetic tree of haplotypes based on genetic distances were inconsistent with their geographical distances. According to the differentiation index(Fst) between populations of H. molitrix, there were high differences between the Yinbin, Wanzhou, and 3 populations from the middle reach(P < 0.05); meanwhile, the Jianli population showed a significant differentiation from the Shishou and Xiangjiang populations(P < 0.01). The results revealed that the upper-and middle-reach populations should have originated from different populations in the Yangtze River. This study could provide useful basic data for the scientific protection, and reasonable and sustainable utilization of this germplasm resource in the Yangtze River Basin.
引文
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[2]Li Z,Liang H W,Luo X Z,et al.A consecutive self-proliferate silver carp(Hypophthalmichthys molitrix)variety created through artificial meiotic gynogenesis[J].Aquaculture,2015,437:21-29.
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[8]Wang C Z,Liang H W,Zou G W,et al.Genetic variation analysis of two silver carp populations in the middle and upper Yangtze River by microsatellite[J].Hereditas,2008,30(10):1341-1348.[王长忠,梁宏伟,邹桂伟,等.长江中上游两个鲢群体遗传变异的微卫星分析[J].遗传,2008,30(10):1341-1348.]
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[12]Wang D,Chen Q W,Yang Z Y,et al.Preliminary analysis on the mt DNA COI genetic diversity of Culter spp.(Cyprinidae)in the Three Gorges Reservoir[J].Acta Hydrobiologica Sinica,2015,39(5):1054-1058.[王丹,程庆武,杨镇宇,等.三峡库区鲌属鱼类线粒体COI基因遗传多样性的初步分析[J].水生生物学报,2015,39(5):1054-1058.]
[13]Hu Y T,Jiang H,Pan T S,et al.Genetic differentiation of Monopterus albus population from Anhui Province in Yangtze River basin based on mitochondrial COI barcode sequence[J].Journal of Northeast Agricultural University,2016,47(2):74-80.[胡玉婷,江河,潘庭双,等.基于线粒体COI序列探讨安徽长江流域黄鳝群体遗传分化[J].东北农业大学学报,2016,47(2):74-80.]
[14]Chen W,Zhang F Y,Wang J,et al.Genetic diversity of wild and cultured populations of Larimichthys crocea in the East China Sea and Yellow Sea based on CO I sequence[J].Journal of Fishery Sciences of China,2016,23(6):1255-1267.[谌微,张凤英,王景,等.基于CO I基因序列的东、黄海区野生与养殖大黄鱼遗传多样性分析[J].中国水产科学,2016,23(6):1255-1267.]
[15]Hu J,Hou X Y,Yin S W,et al.Genetic diversity and divergence of Cheilinus undulatus of different geographic populations of the south china sea revealed by COI and Cyt b gene analyses[J].Acta Hydrobiologica Sinica,2014,38(6):1008-1016.[胡静,侯新远,尹绍武,等.基于mt DNA COI和Cyt b基因序列对南中国海不同海域波纹唇鱼群体遗传多样性的研究[J].水生生物学报,2014,38(6):1008-1016.]
[16]Aljanabi S M,Martinez I.Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques[J].Nucleic Acids Research,1997,25(22):4692-4693.
[17]Thompson J D,Gibson T J,Plewniak F,et al.The Clustal X windows interface:Flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25:4876-4882.
[18]Librado P,Rozas J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25:1451-1452.
[19]Saitoun,Nei M.The neighbor-joining method:A new method for reconstructing phylogenetic trees[J].Molecular Biology and Evolution,1987,4:406-425.
[20]Excoffier L,Lischer H E L.Arlequin suite ver3.5:A new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10:564-567.
[21]Dupanloup I,Schneider S,Excoffier L.A simulated annealing approach to define the genetic structure of populations[J].Molecular Ecology,2002,11(12):2571-2581.
[22]Ni S S,Yang Y,Liu S F,et al.Population-genetics analysis of the Japanese scallop Patinopecten yessoensis based on mitochondrial Cyt b gene[J].Journal of Fishery Sciences of China,2017,24(3):432-439.[倪守胜,杨钰,柳淑芳,等.基于线粒体Cyt b基因的虾夷扇贝群体遗传结构分析[J].中国水产科学,2017,24(3):432-439.]
[23]Grant W,Bowen B.Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89:415-426.
[24]Wang S T,Zhang M,Dang Y F,et al.Genetic variation of mitochondrial DNA d-loop region in wild and breeding populations of grass carp[J].Acta Hydrobiologica Sinica,2017,41(5):947-955.[王沈同,张猛,党云飞,等.草鱼野生与选育群体线粒体DNA控制区D-loop遗传变异分析[J].水生生物学报,2017,41(5):947-955.]
[25]Yang Z Y,Wang D Q,Chen D Q,et al.Genetic structure analysis based on the mitochondrial DNA of Mylopharyngodon piceus[J].Freshwater Fisheries,2015(2):3-7.[杨宗英,汪登强,陈大庆,等.基于mt DNA序列分析青鱼群体遗传结构[J].淡水渔业,2015(2):3-7.]
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