结合线粒体D-loop序列和SSR标记对宝石鲈养殖群体遗传多样性的分析
|
摘要
采用线粒体D-loop序列及SSR标记分析广东4个宝石鲈(Scortum barcoo)养殖群体的遗传多样性。D-loop序列分析显示,长度为598 bp的D-loop片段上有14个多态性位点,共定义8个单倍型。4个群体单倍型多样性指数、核苷酸多样性指数分别为0.000 0～0.543 5、0.000 00～0.001 76,表明4个群体遗传多样性水平均较低。利用11个SSR位点分析显示,4个群体期望杂合度(H_e)=0.396～0.516、PIC=0.320～0.420,说明各群体遗传多样性处于中低水平。虽然二种方法获得的遗传分化指数F_(ST)上存在差异,分别为0.403 5(D-loop)和0.044 5(SSR),但二种分析结果均显示4个广东群体的遗传多样性较低、亲缘关系较近,因此有必要引进原种以丰富国内养殖群体的遗传多样性。
Mitochondrial D-loop sequences and simple sequence repeat(SSR) markers were used in this study to analyze the genetic diversity in 4 different reared Scortum barcoo populations in Guangdong. D-loop sequences analysis showed that the 598 bp long D-loop fragment contained 14 polymorphic loci and a total of 8 defined haplotypes. The haplotype diversity index and nucleotide diversity index of the 4 populations were ranged from 0.000 0 to 0.543 5 and from 0.000 00 to 0.001 76, respectively, which showed that the genetic diversity levels of the 4 populations were low. Analysis of 11 SSR loci showed that the expected heterozygosity(H_e) of the 4 different populations were ranged from 0.396 to 0.516 and polymorphism information content(PIC) were ranged from 0.320 to 0.420, which suggested that the genetic diversity between the various populations were at moderate to low level. Although there were differences in the genetic differentiation coefficient(F_(ST)) obtained via the two different methods(0.403 5 for D-loop and 0.044 5 for SSR), the results of these 2 methods showed that the 4 Guangdong populations had low genetic diversity and close phylogenetic relationships. Therefore, there is a need to introduce the original species to enrich the genetic diversity of the reared populations in China.
Mitochondrial D-loop sequences and simple sequence repeat(SSR) markers were used in this study to analyze the genetic diversity in 4 different reared Scortum barcoo populations in Guangdong. D-loop sequences analysis showed that the 598 bp long D-loop fragment contained 14 polymorphic loci and a total of 8 defined haplotypes. The haplotype diversity index and nucleotide diversity index of the 4 populations were ranged from 0.000 0 to 0.543 5 and from 0.000 00 to 0.001 76, respectively, which showed that the genetic diversity levels of the 4 populations were low. Analysis of 11 SSR loci showed that the expected heterozygosity(H_e) of the 4 different populations were ranged from 0.396 to 0.516 and polymorphism information content(PIC) were ranged from 0.320 to 0.420, which suggested that the genetic diversity between the various populations were at moderate to low level. Although there were differences in the genetic differentiation coefficient(F_(ST)) obtained via the two different methods(0.403 5 for D-loop and 0.044 5 for SSR), the results of these 2 methods showed that the 4 Guangdong populations had low genetic diversity and close phylogenetic relationships. Therefore, there is a need to introduce the original species to enrich the genetic diversity of the reared populations in China.
引文
[1]张娜,罗国芝,谭洪新,等.温度对宝石鲈生长及血液生化免疫指标的影响[J].中国水产科学,2010,17(6):1236-1242.
[2]褚嘉祐,李绍武,张亚平.努力推动中国的遗传多样性研究[J].遗传,2012,34(11):1349-1350.
[3]陈会娟,刘明典,汪登强,等.长江中上游4个鲢群体遗传多样性分析[J].淡水渔业,2018,48(1):20-25.
[4]乔慧,吴滟,傅洪拓,等.应用SSR和SRAP标记构建青虾遗传连锁图谱[J].中国水产科学,2012,19(2):202-210.
[5]Hou L,Lv H L,Zou X Y,et al.Genetic characterizations of Mactra veneriformis,(Bivalve) along the Chinese coast using ISSR-PCR markers [J].Aquaculture,2006,261(3):865-871.
[6]李大命,张彤晴,关浩勇,等.基于线粒体Cytb基因和D-loop区序列的高邮湖湖鲚(Coilia nasus)遗传多样性分析[J].淡水渔业,2017,47(6):3-8.
[7]Presti F T,Wasko A P.A review of microsatellite markers and their application on genetic diversity studies in parrots [J].Ojgen,2014,4(2):69-77.
[8]Bornman D M,Hester M E,Schuetter J M,et al.Short-read,high-throughput sequencing technology for STR genotyping [J].Biotech Rapid Dispatches,2015,21(1):1-6.
[9]Davis C,Peters D,Warshauer D,et al.Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing:Enhanced data acquisition for DNA samples encountered in forensic testing [J].Legal Med,2015,17(2):123-127.
[10]Bektas Y,Turan D,Aksu I,et al.Molecular phylogeny of the genus Capoeta(Teleostei:Cyprinidae) in Anatolia,Turkey [J].Biochem Syst Ecol,2017,70:80-94.
[11]Moreira D A,Buckup P A,Furtado C,et al.Reducing the information gapon Loricarioidei(Siluriformes) mitochondrial genomics [J].Bmc Genomics,2017,18(1):345-357.
[12]Barman A S,Singh M,Pandey P K.DNA barcoding and genetic diversity analyses of fishes of Kaladan River of Indo-Myanmar biodiversity hotspot [J].Mitochondrial DNA A,2017,29(3):1-12.
[13]Behera B K,Kunal S P,Baisvar V S,et al.Genetic variation in wild and hatchery population of Catlacatla(Hamilton,1822) analyzed through mtDNA cytochrome b region [J].Mitochondrial DNA A,2018,29(1):126-131.
[14]Zhang J B,Hanner R.DNA barcoding is a useful tool for the identification of marine fishes from Japan [J].Biochem Syst Ecol,2011,39(1):31-42.
[15]Maltsev A N,Stakheev V V,Bogdanov A S,et al.Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus:Analysis of variability of the control region(D-loop) of mitochondrial DNA [J].Dokl Biol Sci,2015,465(1):285-288.
[16]Liu C,Li K,Wang Q,et al.The complete mitochondrial genome of jade perch,Scortumbarcoo(Perciformes:Terapontidae:Scortum) [J].Mitochondrial DNA A,2016,27(5):3346-3347.
[17]Wright S.Evolution and the genetics of populations.A treatise in four volumes.Volume 4.Variability within and among natural populations [J].J Biosoc Sci,1972,4(2):253-256.
[18]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.
[19]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.
[20]Shete S,Tiwari H,Elston R C.On estimating the heterozygosity and polymorphism information content value[J].Theor Popul Biol,2000,57(3):265-271.
[21]Botstein D,White R L,Skolnick M,et al.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].Am J Hum Genet,1980,32(3):314-331.
[22]Qin Y,Shi G,Sun Y.Evaluation of genetic diversity in Pampus argenteus using SSR markers[J].Genet Mol Res,2013,12(4):5833-5841.
[23]Hamrick J L,Godt M J W,Sherman B S L.Gene flow among plant populations:evidence from genetic markers [M].// Hoch P C,Stephenson A G.Exp Mol Approaches Plant Biosyst,Missouri:Missouri Botanical,1995:215-232.
[24]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data[J].Genetics,2000,7(4):574-578.
[25]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software structure:a simulation study [J].Mol Ecol,2005,14(8):2611-2620.
[26]傅建军,徐如卫,薛婷,等.3种泥鳅微卫星标记和D-Loop部分序列遗传变异分析[J].水产学报,2015,39(4):465-474.
[27]Nilsson J.mtDNA and microsatellite variation in Baltic Atlantic salmon [J].Ices J Mar Sci,1997,54(6):173-1176.
[2]褚嘉祐,李绍武,张亚平.努力推动中国的遗传多样性研究[J].遗传,2012,34(11):1349-1350.
[3]陈会娟,刘明典,汪登强,等.长江中上游4个鲢群体遗传多样性分析[J].淡水渔业,2018,48(1):20-25.
[4]乔慧,吴滟,傅洪拓,等.应用SSR和SRAP标记构建青虾遗传连锁图谱[J].中国水产科学,2012,19(2):202-210.
[5]Hou L,Lv H L,Zou X Y,et al.Genetic characterizations of Mactra veneriformis,(Bivalve) along the Chinese coast using ISSR-PCR markers [J].Aquaculture,2006,261(3):865-871.
[6]李大命,张彤晴,关浩勇,等.基于线粒体Cytb基因和D-loop区序列的高邮湖湖鲚(Coilia nasus)遗传多样性分析[J].淡水渔业,2017,47(6):3-8.
[7]Presti F T,Wasko A P.A review of microsatellite markers and their application on genetic diversity studies in parrots [J].Ojgen,2014,4(2):69-77.
[8]Bornman D M,Hester M E,Schuetter J M,et al.Short-read,high-throughput sequencing technology for STR genotyping [J].Biotech Rapid Dispatches,2015,21(1):1-6.
[9]Davis C,Peters D,Warshauer D,et al.Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing:Enhanced data acquisition for DNA samples encountered in forensic testing [J].Legal Med,2015,17(2):123-127.
[10]Bektas Y,Turan D,Aksu I,et al.Molecular phylogeny of the genus Capoeta(Teleostei:Cyprinidae) in Anatolia,Turkey [J].Biochem Syst Ecol,2017,70:80-94.
[11]Moreira D A,Buckup P A,Furtado C,et al.Reducing the information gapon Loricarioidei(Siluriformes) mitochondrial genomics [J].Bmc Genomics,2017,18(1):345-357.
[12]Barman A S,Singh M,Pandey P K.DNA barcoding and genetic diversity analyses of fishes of Kaladan River of Indo-Myanmar biodiversity hotspot [J].Mitochondrial DNA A,2017,29(3):1-12.
[13]Behera B K,Kunal S P,Baisvar V S,et al.Genetic variation in wild and hatchery population of Catlacatla(Hamilton,1822) analyzed through mtDNA cytochrome b region [J].Mitochondrial DNA A,2018,29(1):126-131.
[14]Zhang J B,Hanner R.DNA barcoding is a useful tool for the identification of marine fishes from Japan [J].Biochem Syst Ecol,2011,39(1):31-42.
[15]Maltsev A N,Stakheev V V,Bogdanov A S,et al.Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus:Analysis of variability of the control region(D-loop) of mitochondrial DNA [J].Dokl Biol Sci,2015,465(1):285-288.
[16]Liu C,Li K,Wang Q,et al.The complete mitochondrial genome of jade perch,Scortumbarcoo(Perciformes:Terapontidae:Scortum) [J].Mitochondrial DNA A,2016,27(5):3346-3347.
[17]Wright S.Evolution and the genetics of populations.A treatise in four volumes.Volume 4.Variability within and among natural populations [J].J Biosoc Sci,1972,4(2):253-256.
[18]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.
[19]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.
[20]Shete S,Tiwari H,Elston R C.On estimating the heterozygosity and polymorphism information content value[J].Theor Popul Biol,2000,57(3):265-271.
[21]Botstein D,White R L,Skolnick M,et al.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].Am J Hum Genet,1980,32(3):314-331.
[22]Qin Y,Shi G,Sun Y.Evaluation of genetic diversity in Pampus argenteus using SSR markers[J].Genet Mol Res,2013,12(4):5833-5841.
[23]Hamrick J L,Godt M J W,Sherman B S L.Gene flow among plant populations:evidence from genetic markers [M].// Hoch P C,Stephenson A G.Exp Mol Approaches Plant Biosyst,Missouri:Missouri Botanical,1995:215-232.
[24]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data[J].Genetics,2000,7(4):574-578.
[25]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software structure:a simulation study [J].Mol Ecol,2005,14(8):2611-2620.
[26]傅建军,徐如卫,薛婷,等.3种泥鳅微卫星标记和D-Loop部分序列遗传变异分析[J].水产学报,2015,39(4):465-474.
[27]Nilsson J.mtDNA and microsatellite variation in Baltic Atlantic salmon [J].Ices J Mar Sci,1997,54(6):173-1176.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |