Preliminary analysis of population genetic diversity of cultivated <Emphasis Type="Italic">Laminaria japonica</Emphasis> sporophyte via AFLP technique

The amplified fragment length polymorphic DNA (AFLP) technique was adopted to estimate the population genetic polymorphism among 30 sporophytes of Laminaria japonica collected from a cultivating farm in Rongcheng, China. Three methods were used for genomic DNA extraction from Laminaria japonica sporophyte and only the products obtained using the improved genomic DNA extraction kit method proved qualified for AFLP analysis. The parameters of the method were optimized. Samples of forty milligrams and the cell lysis time of 120 min were suggested to replace the parameters recommended by the manufacturer. Thirty individuals of Laminaria japonica from the same cultivating site were investigated using one pair of selective primers. A total of 21 loci were obtained and 17 of them were polymorphic. The mean percent age of polymorphic loci of this population was 80.95%. The Nei’s gene diversity (H) within this population was 0.3028 and the average Shannon’s Information index (I) was 0.4498. A genetic distance matrix among different individuals was constructed as well. Through this study, an applicable AFLP genetic analysis working system for Laminaria japonica sporophyte was established. The results of this research also revealed a high level of genetic diversity within the studied population.     

Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%, 50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH, QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands, average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations, while the LZ population was the lowest among the wild populations. Compared with the wild populations, the hatchery population showed a low genetic viability.     

胡子鲇3个养殖群体遗传结构的AFLP分析

应用AFLP方法,从64对引物中筛选出5对用于分析胡子鲇(Claris fuscus)厦门(XM)、江门(JM)、玉林(YL)等3个养殖群体共90个个体群体内、群体间遗传多样性。扩增共得到289条清晰谱带,引物多态性介于47.8%～63.8%,平均多态性比率为56.4%。胡子鲇群体总遗传杂合度(Ht)、遗传分化系数(Hs)、遗传分化度(Gst)和基因流(Nm)分别为0.161 1、0.153 6、0.051 1和8.501 8,表明胡子鲇多态性处于中等偏下水平,群体内部遗传分化系数较高,三个群体间无较大分化,群体间基因流动较好。其中,JM群体多态性比率、有效等位基因数Ne、Nei’s指数和Shannon指数都较XM群体和YL群体高,种内分化程度较好。对群体进行两两比较发现,XM群体和YL群体间分化程度最大,XM群体和JM群体次之,JM群体和YL群体最小。基于杂交优势,推断XM和YL群体繁殖所产生的后代将具有比亲代更为优良的性状。     

Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

Amplified fragment length polymorphisms(AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye(Scyphozoa,Rhizostomatidae).One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations.The polymorphic ratio,Shannon’s diversity index and average heterozygosity were 70.3%,0.346 and 0.228 for the white hatchery population,74.3%,0.313,and 0.201 for the red hatchery population,79.3%,0.349,and 0.224 for the Jiangsu wild population,and 74.9%,0.328 and 0.210 for the Penglai wild population,respectively.Thus,all populations had a relatively high level of genetic diversity.A specific band was identified that could separate the white from the red hatchery population.There was 84.85% genetic differentiation within populations.Individual cluster analysis using unweighted pair-group method with arithmetic mean(UPGMA) suggested that hatchery populations and wild populations could be divided.For the hatchery populations,the white and red populations clustered separately;however,for the wild populations,Penglai and Jiangsu populations clustered together.The genetic diversity at the clone level was also determined.Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations,which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing.These findings will benefit the artificial seeding and conservation of the germplasm resources.     

蜂巢石斑鱼随机扩增多态性DNA的初步研究

采用RAPD技术分析了湛江沿海野生蜂巢石斑鱼的遗传多样性 ,从 6个系列 1 2 0个引物筛选出1 6个引物 ,对 1 0尾蜂巢石斑鱼进行RAPD分析 ,1 6个引物共检测到 1 5 4个位点 ,其中 ,多态位点比例 (P)为 6 5 5 8% ,平均个体间遗传相似系数 (S)为 0 7887,平均个体间遗传距离 (D)为 0 2 1 1 3,遗传多样性指数 (H)为 0 1 776。研究结果表明 ,湛江沿海的野生蜂巢石斑鱼的遗传多样性较高。     

紫红笛鲷随机扩增多态性DNA及遗传多样性分析

采用RAPD技术分析了湛江近海紫红笛鲷 (LutjanusargentimaculatusForsk l)的遗传多样性。从 12 0个随机引物中筛选出了 14个引物。 14个引物共检测到 173个位点 ,其中多态位点比例 (P)为 6 8.79%,遗传距离 (D)为 0 .2 2 2 8,遗传多样性指数 (H)为 0 .190 4。结果表明 ,目前湛江近海的紫红笛鲷自然群体的遗传多样性仍然维持在良好水平 ,捕捞尚未对其造成明显影响。     

长江下游鳊鱼遗传多样性的RAPD分析

应用RAPD技术对长江下游鳊鱼群体的遗传多样性进行分析,从40个随机引物中筛选出28个引物对鳊鱼24个个体的基因组DNA进行扩增,共检测到178个位点,分子片段在0.2～2.0kb之间,其中多态位点83个,占46.63%;个体间最大的遗传距离为0.1326,最小的遗传距离为0.0476,平均遗传距离为0.0885;群体的Nei基因多样性指数为0.2593,Shannon多样性指值为0.0986。与其他鱼类的遗传多样性研究结果相比,长江下游鳊鱼群体的遗传多样性处于中等水平。     

AFLP analysis of genetic variation among three natural populations of horseshoe crab Tachypleus tridentatus along Chinese coast

The AFLP(amplified fragment length polymorphism) technique was used to analyze and compare the genetic diversity of Tachypleus tridentatus from three south-eastern coastal sites of China(Pingtan,Hong Kong and Beihai).Eight pairs of primers generated 361 loci,including 285 polymorphic loci.The ratio of polymorphic loci was 96.97%.Nei's genetic diversity index was 0.420 8 and the Shannon information index was 0.607 5,both of which were higher than that reported for many other arthropods.These results show tha...     

军曹鱼群体遗传结构的AFLP分析

筛选出10对扩增片段长度多态分析技术(Amplified fragment length polymorphism,AFLP)的选择性扩增引物(E-aga/M-cgt、E-aga/M-cga、E-agc/M-cga、E-agg/M-cga、E-act/M-cgc、E-aag/M-cgc、E-aca/M-cga、E-aac/M-cgc、E-aac/M-cac和E-aac/M-cat),分析了4个军曹鱼(Rachycentron canadum)全人工繁育群体海南1(HN1)、海南2(HN2)、湛江(ZJ)和流沙湾(LS)的遗传结构。结果表明:总体多态位点比例(83.9%)、分化指数(0.427 8)和Shannon信息指数(0.614 9)均处于较高水平,遗传多样性丰富;主坐标分析和邻位连接树中LS-HN2支与ZJ-HN1支明显分离,各群体内多样性水平存在差异(遗传多样性大小依次为HN1、HN2、LS、ZJ),但总体基因流仍然较大(Nm=10.327),分子方差分析(AMOVA)获得的群内方差(53%)也略大于群间(47%)。     

Genetic Variation and Differentiation in Wide Ranging Populations of Razor Clam （Sinonovacula constricta） Inferred from AFLP Markers

The genetic variation and differentiation of the razor clam Sinonovacula constricts distributed along the coast of China were studied through amplified fragment length polymorphism(AFLP)analysis. Six primer combinations generated 193 fragments. The He values varied from 0. 322 to 0. 463 and the percentage of polymorphic loci ranged from 74. 1% to 98. 4%, which indicates a high level of genetic diversity. Cluster analysis by Nei's pairwise distance grouped all specimens by geographical origins. AMOVA consistently showed that genetic variation among populations was 8. 71%, and most of the variation came from the genetic variation within populations(91.29%). Genetic differentiation among the six populations was moderate; pairwise FST ranged from 0. 0282 to0. 1480, which indicated that S. Constricts populations along the coast of China are genetically connected. Among all the six populations, the Beihai population is the mostly differentiated from the others, suggesting that Hainan Island and Leizhou Peninsula act as barriers to gene flow. All populations abide isolation by distance model as indicated by Mantel test, except for ZS(Zhoushan)and YQ(Yueqing)populations. Information obtained in this study will provide guidelines for conservation and fishery management of this species in the future.     

Genetic analysis of floating Enteromorpha prolifera in the Yellow Sea with AFLP marker

Extremely large accumulation of green algae Enteromorpha prolifera floated along China’coastal region of the Yellow Sea ever since the summer of 2008.Amplified Fragment Length Polymorphism (AFLP) analysis was applied to assess the genetic diversity and relationships among E. prolifera samples collected from 9 affected areas of the Yellow Sea.Two hundred reproducible fragments were generated with 8 AFLP primer combinations,of which 194 (97%) were polymorphic. The average Nei’s genetic diversity, the coefficiency of genetic differentiation (Gst), and the average gene flow estimated from Gst in the 9 populations were 0.4018, 0.6404 and 0.2807 respectively. Cluster analysis based on the unweighed pair group method with arithmetic averages (UPGMA) showed that the genetic relationships within one population or among different populations were all related to their collecting locations and sampling time. Large genetic differentiation was detected among the populations.The E. prolifera originated from different areas and were undergoing a course of mixing.     

The comparison between allozyme and RAPD makers for the population genetic structure analysis of scallop Chlamys farreri

1INTRODUCTION Since the first use in human genetic research in1966,allozyme has become the most popular genetic marker for population genetics studies for almost all groups of animals and plants(Lewontin and Hubby,1966;Murphy et al.,1996).In the past seve…     

The loss of genetic diversity during captive breeding of the endangered sculpin, Trachidermus fasciatus, based on ISSR markers: implications for its conservation

Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured and wild populations of Trachidermus fasciatus, an endangered catadromous fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals, and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of polymorphic loci PPL = 73.80%, Nei’s gene diversity h = 0.178 2, Shannon information index ...     

Genome-wide mining,characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats(SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class(44.08%), followed by mononucleotides(29.67%), trinucleotides(18.96%), tetranucleotides(5.66%), hexanucleotides(1.07%), and pentanucleotides(0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci(90.0%) were successfully amplified with specific products and 24(80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17(with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.     

Genome-wide mining,characterization, and development of microsatellite markers in <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis> by genome survey sequencing

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.     

Genetic differentiation of Japanese sardinella (Sardinella zunasi) populations in the Northwest Pacific revealed by ISSR analysis

Knowledge of population genetic structure plays an important role in fisheries management.In this research,In-ter-Simple-Sequence-Repeat(ISSR)markers were employed to evaluate the genetic structure of Japanese sardinella(Sardinella zun-asi)populations in the Northwest Pacific.Eighty seven individuals from 5 locations were screened using 4 highly polymorphic prim-ers.A total of 173 polymorphic loci were detected out of 191 loci amplified.Small but significant genetic differentiation was de-tected between the Chinese and Japanese populations by both AMOVA and pairwise FST analyses,which was further supported by cluster analysis.We consider that climate change during glaciations should be responsible for the genetic differentiation.Isolation by geographic distance among populations was observed,indicating that the distance might also lead to the genetic differentiation.However,no genetic structure was found within the populations off both the Chinese and Japanese coasts,indicating a high-level along-coast gene flow,which might result from ocean current transport and common ground for over-wintering.     

Genetic Variation Among White Croaker Populations

To investigate the genetic structures and differentiation of different wild populations of white croaker （Pennahia argentara）, horizontal starch gel electrophoresis was performed on 133 individuals collected from five different locations in China and Japan. The eleven enzyme systems revealed 15 loci, of which eleven were polymorphic. The percentage ofpolymorphic loci of white croaker populations varied from 6.67% to 53.3.3%; the mean observed and expected heterozygosity ranged from 0.0033 to 0.0133 and 0.0032 to 0.0191, respectively. The expected heterozygosity revealed a low genetic variability for white croaker in comparison with other marine fishes. The genetic distances between populations ranged from 0.00005 to 0.00026. A weak differentiation was observed within each clade and between clades; and no significant differences in gene frequencies among populations were observed in white croaker. Among the five populations, three Chinese populations showed more genetic diversity than that in Japanese populations.     

两种体色画眉笛雕的遗传多样性及分子标记

根据体侧纵带颜色差异,暂将画眉笛鲷(Lutjanus vitta)分为黄带画眉笛鲷和褐带画眉笛鲷,应用RAPD技术,选用22个引物对黄带画眉笛鲷与褐带画眉笛鲷进行遗传多样性及分子标记研究。结果表明,黄带画眉笛鲷与褐带画眉笛鲷的遗传距离为0.832 9,其多态位点比例(P)分别为66.99%和85.28%,遗传多样性指数(H)分别为0.161 7和0.289 3,种内遗传距离(D)分别为0.243 5和0.431 9,表明褐带画眉笛鲷的遗传多样性比黄带画眉笛鲷丰富。共得到OPP14-629bp和OPP14-674bp等11个特异性分子标记,可用于两种笛鲷的鉴定。     

红鳍笛鲷微卫星DNA标记的开发与遗传多样性分析

以三亚外海的红鳍笛鲷(Lutjanus erythropterus)自然群体为研究对象,利用磁珠富集法开发19个适用于红鳍笛鲷的微卫星DNA标记,其中16个为多态性标记,等位基因数为2～11,期望杂合度为0.242～0.896,观测杂合度为0.156～1.000,Ler 14、Ler 29、Ler 49等3个位点偏离哈迪-温伯格平衡(P<0.0031),Ler9-Ler18、Ler12-Ler19、Ler46-Ler47、Ler46-Ler49、Ler18-Ler50、Ler14-Ler51等6对位点间检测到明显的连锁(P<0.05),Ler29、Ler13、Ler49、Ler19、Ler24、Ler25、Ler14、Ler51、Ler18、Ler9等10个位点属于高度多态位点[多态信息含量(PIC)>0.5],Ler47、Ler12、Ler15、Ler46等4个为中度多态位点(0.25>PIC>0.5)。