Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.     

Phosphoglucomutase-1 subtypes: polymorphic occurrence of PGM1*7+ and geographical variation in Japan

The distribution of gene frequencies in the phosphoglucomutase-1 (PGM1) system was investigated in two Japanese populations from Yamaguchi (Western Japan) and Okinawa (Southern Japan) using an improved isoelectric focusing method permitting the successful detection of the most anodal variant PGM1 3+. PGM1*7+ occurred with a polymorphic frequency of 0.012-0.021. A difference in the gene frequency was observed between the two populations. In comparison with neighboring populations, the Yamaguchi population was similar to Mongolians and Koreans in North China, and Okinawa to Zhuang in South China.     

Microsatellite profiles reveal an unexpected genetic relationship between Asian populations

Allelic frequencies for up to five short tandem repeat systems (HumTH01, HumVWA, HumF13B, HumCD4, HumD21S11) were analyzed in seven population samples from Asia using the polymerase chain reaction and gel electrophoresis. No deviations from Hardy-Weinberg equilibrium were observed. Two new alleles of the CD4 and TH01 loci were detected, and sequenced and their molecular structure is presented. A phylogenetic tree based on Thai, Han Chinese (from the northeast of China), Japanese, German and Ovambo allelic frequencies was constructed and demonstrates the close relationship of the Asian populations. Additionally, allelic frequency data for the VWA and TH01 systems were determined for the south Chinese minorities Bai, Dai and Qiang and for Koreans and compared with the above data. The Bai and Dai populations were clear outliers of the cluster of all other Asians, indicating an unexpected pattern of genetic heterogeneity of the Chinese nation. Two clusters of Asian populations could be established: the Koreans and Japanese together with the Han and Qiang Chinese, and, forming a separate cluster, the Bai and Dai populations. Received: 10 June 1997 / Accepted: 15 March 1998     

花鲈群体的遗传变异

采用水平淀粉凝胶电泳技术对花鲈群体的遗传结构进行了研究 ,共检测了中国沿海花鲈 14 6尾和 40尾日本东京湾花鲈。其群体的多态位点比例为 0 2 667— 0 53 3 3 ,观测杂合度和预期杂合度分别为 0 0 2 11— 0 0 515和0 0 3 98— 0 0 797。中日花鲈在LDH ,GPI 1 ,GPI 2 基因位点上的等位基因接近完全置换。中国花鲈各群体之间的根井遗传距离为 0 0 0 0 4— 0 0 0 11,平均值约为 0 0 0 80 ;而中日花鲈间的根井遗传距离为 0 1870— 0 1954,平均值为 0 192 6。以上结果表明中国花鲈群体间遗传变异很小 ,中日花鲈间遗传变异远大于中国花鲈群体间的遗传距离。     

德宏水牛微卫星标记分析的群体遗传变异

德宏水牛是云南省地方水牛的优良品种之一,为了进一步阐明其群体遗传变异和遗传结构,筛选了分别位于水牛14条染色体上的15对微卫星引物,对德宏水牛81个个体进行了检测分析.共检测到62个等位基因,每个座位等位基因数目从2到6个不等,平均等位基因数为4.13,该水牛群体期望杂合度和多态信息含量分别为0.6520±0.1526和0.5863±0.1789,各座位的遗传分化系数在0～0.0919之间,平均值为0.0202.每个座位的基因流较大,平均12.1502.研究结果表明德宏水牛群体遗传多样性较丰富,亚群间的遗传分化程度低,基因流较大,且很少发生近交.     

Restriction Polymorphism of Mitochondrial DNA in Koreans and Mongolians

Using the data on mitochondrial DNA (mtDNA) restriction polymorphism, the gene pools of Koreans (N = 164) and Mongolians (N = 48) were characterized. It was demonstrated that the gene pools were represented by the common set of mtDNA haplogroups of East Asian origin (M*, M7, M8a, M10, C, D4, G*, G2, A, B*, B5, F1, and N*). In addition to this set, mtDNA haplogroups D5 and Y were identified in Koreans while Mongolians possessed haplogroup Z. Only in Mongolians, a European component with the frequency of 10.4% and represented by the mtDNA types belonging to haplogroups K, U4, and N1, was identified. Phylogenetic and statistical analyses of the data on mtDNA variation in the populations of South Siberia, Central, and East Asia suggested the existence of interpopulation differentiation within these regions, the main role in which was played by the geographical and linguistic factors. Analysis of the pairwise F _ST distances demonstrated close genetic similarity of Koreans to Northern Chinese, which in turn, were clearly different from Southern Chinese populations. Mongolians occupied an intermediate position between the ethnic groups of South Siberia and Central/East Asia.     

Population genetic studies in three Chinese minorities

Three minority ethnic groups from China (Mongolians, Koreans, Zhuang) were examined with respect to the genetic markers GLO, GPT, ACP, ESD, 6-PGD, PGM₁ subtypes, C3, and TF. Significant variations were noted for the gene frequencies of GLO, GPT, ESD, sub PGM₁ between Zhuang and Mongolians; for GPT, ACP, ESD, sub PGM₁ between Zhuang and Koreans; and for GLO between Mongolians and Koreans.     

Isolation and characterization of 16 novel microsatellite loci in two inbred strains of the Chinese hamster (Cricetulus griseus)

The Shanyi inbred A and E strains of the Chinese hamster are widely used in biomedical research, but detailed genetic characterization has been lacking. We developed microsatellite markers that could be used for genetic diversity analysis and linkage map construction. We isolated and characterized 16 novel microsatellite loci from a microsatellite-enriched genomic DNA library. These loci were genotyped in 48 animals from the two strains, and the polymorphic information content was determined. In the Shanyi A and E populations, 14 and 15 loci were found to be polymorphic, respectively, with polymorphic information content ranging from 0.1393 to 0.8082 and from 0.1109 to 0.7397, respectively. A total of 115 alleles were found for the 16 microsatellite loci in the two populations; the mean observed heterozygosity (H(O)) was 0.5191 and 0.4333 for the A and E populations, respectively, indicating marked genetic variation within the two populations. Correspondingly, the F(ST) values ranged from 0.002 to 0.9253, with an overall mean of 0.1935, indicating significant genetic difference between the two strains. The population differentiation levels were substantiated by Nei's genetic distance and full Bayesian analyses computed with STRUCTURE. Despite the genetic diversity and differentiation within and between the two inbred populations, the 48 individuals were correctly allocated into their original populations with high statistical confidence based on these 16 microsatellite loci. These novel microsatellite loci should be useful genetic markers for these two Chinese hamster inbred strains.     

Human Population Genetic Studies Using Hypervariable Loci. I. Analysis of Assamese, Australian, Cambodian, Caucasian, Chinese and Melanesian Populations

Population genetic studies, in Australian, Assamese, Cambodian, Chinese, Caucasian and Melanesian populations, were performed with several highly polymorphic DNA loci. Results showed that the Caucasian and Chinese had the highest level of heterozygosity. The size range of the majority of the polymorphic DNA fragments of a locus was the same in the different populations. The distinguishing feature of each ethnic group was the relative frequency of a particular set or group of alleles. For example, alleles greater than 9.0 kb in size, in D14S13, or from 4.5 to 4.7 kb, in D18S27, were less than half as frequent in Caucasians than in the other populations. Overall, there were groups of alleles, at one or more loci, whose frequencies were different among some of the ethnic groups and therefore could be used to differentiate one group from the other.     

中国主要地方品种猪血液蛋白遗传多样性研究

实验采用水平板淀粉凝胶电泳技术,对中国地方猪五大类型９个品种,１个引入品种共２０１个个体进行了遗传多样性分析。共分析遗传座痊３０个,其中只有ＭＤＨ、ＰＥＰＢ、Ａ从位具有多在记民生。中国主要地方猪品种的多态座位百分比Ｐ＝０．２００,平均杂２合度Ｈ＝０．０６５,平均等位基因数Ａ＝１．３００。根据基因频率采用ＰＨＹＬＩＰ３．５ｃ民计算Ｎｅｉ氏遗传距离,然后用“ＮＥＩＧＨＢＯＲ”程序分别构建Ｎｅｉｇｈｂｏ     

Molecular genetic analysis of remains of a 2,000-year-old human population in China-and its relevance for the origin of the modern Japanese population.

We extracted DNA from the human remains excavated from the Yixi site ( approximately 2,000 years before the present) in the Shandong peninsula of China and, through PCR amplification, determined nucleotide sequences of their mitochondrial D-loop regions. Nucleotide diversity of the ancient Yixi people was similar to those of modern populations. Modern humans in Asia and the circum-Pacific region are divided into six radiation groups, on the basis of the phylogenetic network constructed by means of 414 mtDNA types from 1, 298 individuals. We compared the ancient Yixi people with the modern Asian and the circum-Pacific populations, using two indices: frequency distribution of the radiation groups and genetic distances among populations. Both revealed that the closest genetic relatedness is between the ancient Yixi people and the modern Taiwan Han Chinese. The Yixi people show closer genetic affinity with Mongolians, mainland Japanese, and Koreans than with Ainu and Ryukyu Japanese and less genetic resemblance with Jomon people and Yayoi people, their predecessors and contemporaries, respectively, in ancient Japan.     

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in Inhabitants of Astana,the Capital City of Kazakhstan

Background

Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations.

Methodology/Principal Findings

A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians.

Conclusions/Significance

The HLA-DRB1, -DQA1and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.     

广西区西南桦天然居群遗传多样性的研究

 以采自广西区11个西南桦(Betula alnoides)天然居群的种子培育出的幼苗为材料,取其嫩叶开展21种酶系统的水平切片淀粉凝胶电泳实验,运用作者改进的Tris-马来酸提取缓冲液 (含30%PVP 40 000和1%2-巯基乙醇),筛选出AMP(氨基肽酶Aminopeptidase)、FBA(果糖二磷酸酶Fructose-bisphosphate aldolase)、GDH(谷氨酸脱氢酶Glutamate dehydrogenase)、G6PD(6-磷酸葡萄糖脱氢酶Glucose-6-phosphate dehydrogenase)、IDH(异柠檬酸脱氢酶Isocitrate dehydrogenase)、MDH(苹果酸脱氢酶Malate dehydrogenase)、PGD(6-磷酸葡萄糖酸脱氢酶Phosphogluconate dehydrogenase)、PGI(磷酸葡萄糖异构酶Phosphoglucoisomerase)、PGM(磷酸葡萄糖变位酶Phosphoglucomutase)和SKD(莽草酸脱氢酶Shikimate dehydrogenase)等10种酶,获得了清晰且可重复的酶谱。通过谱带遗传分析确定了15个位点,其中有6个单态位点,9个多态位点 (0.95标准),具40个等位基因。在居群水平上,西南桦的多态位点百分数 (P) 为55.2%,平均每个位点的等位基因数 (A) 为2.00,平均预期杂合度 (He) 为0.204。均超过Hamrick (1992)等提出的远交风媒木本植物的平均值(53.0%,184%和0154),表明西南桦的遗传变异水平高。在11个西南桦居群内,实际杂合度 (Ho)均高于预期杂合度,出现杂合子过量,可能存在利于杂合子的自然选择。西南桦遗传多样性与地理位置相关不显著。居群2 (靖西地州)、5 (平果海城)、9 (田林者苗) 包含绝大部分的等位基因,而且具较高的遗传多样性,应加以保护和管理,作为其基因资源就地保存的基地。本研究解决了以西南桦嫩叶为材料进行等位酶分析的关键技术,为进一步开展西南桦乃至桦木属树种的遗传结构和遗传多样性等提供了技术基础;同时掌握了西南桦天然居群的遗传多样性现状,为其有效保护和合理经营以及西南桦的遗传改良提供了理论依据。     

Polymorphic microsatellite loci for Japanese Spanish mackerel (Scomberomorus niphonius)

We isolated and characterized 21 polymorphic microsatellite loci in Japanese Spanish mackerel (Scomberomorus niphonius) using a (GT)(13)-enriched genomic library. Forty individuals were collected from Qingdao, China. We found 3 to 24 alleles per locus, with a mean of 8.8. The observed and expected heterozygosities ranged from 0.263 to 0.975 and from 0.385 to 0.946, with means of 0.655 and 0.685, respectively. Deviation from Hardy-Weinberg proportions was detected at three loci. Two loci showed evidence for null alleles. These microsatellite markers will be useful for population genetic analysis of Japanese Spanish mackerel.     

药用植物天麻（Gastrodia elata Bl.）的等位酶遗传变异及其变型间的遗传关系

采用超薄平板聚丙烯酰胺等电聚焦电泳,对湖北西部药用植物天麻（Gastrodia elata Bl.）的4种变型进行了等位酶遗传变异的初步分析。在6个酶系统共检测到17个清晰位点和37个等位基因,其中多态位点11个,位点最大等位基因数为4,位点Acp-4和Prx-2的等位基因表现出变型特异性。遗传多样性分析结果表明：天麻在物种水平维持着较高遗传多样性,平均多态位点比率P=56.3%,每位点平均等位基因数A=2.1,平均预期杂合度He=0.222;但其变型水平遗传多样性较低（P=42.2%,A=1.7,He=0.146）,其中乌天麻遗传多样性最高,药天麻最低。天麻变型间遗传分化系数（GST）达0.3595,平均基因流（Nm）仅为0.4450,说明天麻变型间遗传分化较大,缺乏基因交流。聚类分析结果表明,天麻居群以变型为单元优先聚类而非地域优先聚类,揭示各天麻变型在遗传上是相对独立的进化显著单元,支持天麻种内变型的划分。红天麻与乌天麻两变型最为近缘,火天麻与药天麻两类群有着较近的遗传关系。     

不同生境三裂叶豚草种群的遗传结构

采用水平切片淀粉凝胶电泳测定了东北地区分布的不同生态环境条件下7个三裂叶豚草种群的遗传结构。统计分析了10个酶系统的10个位点,结果表明:三裂叶豚草种群内存在着丰富的遗传变异。多态位点百分率为80.00%,等位基因平均数为1.80,期望杂合度为0.375,遗传一致度和遗传距离为0.959和0.042。     

中国东北汉族群体3个MiniSTR基因座的遗传多态性研究

我们使用D10S1248、D14S1434和D22S1045三个miniSTR基因座对东北汉族群体的141名随机个体样本进行遗传多态性研究, 通过荧光标记多重PCR扩增, 310遗传分析仪电泳, 确定个体的基因型, 获得相应的群体遗传数据。对所得数据进行统计学分析。共检出25个等位基因, 56种基因型。3个基因座在所检测群体内均符合哈迪温伯格平衡, 具有较高的杂合度、个体识别率和非父排除率。累积个体识别率为0.99876, 累计非父排除率为0.89819。3个基因座在东北汉族均具有高度的遗传多态性,在群体遗传学和法医学研究中有一定的应用价值。     

Genetic diversity of wild emmer wheat in Israel and Turkey

Summary Allozyme variation in the tetraploid wild emmer wheat, Triticum dicoccoides, the progenitor of all cultivated wheats, was studied for the proteins encoded by 42 gene loci in 1815 plants representing 37 populations - 33 from Israel and 4 from Turkey - sampled in 33 localities from 1979 to 1987. The results showed that: (a) 6 loci (14%) were monomorphic in all populations, 15 loci (36%) were locally polymorphic, and 21 loci (50%) were regionally polymorphic. These results are similar to those obtained earlier on 12 Israeli populations. All polymorphic loci (except 4) displayed high local levels of polymorphism (>/ 10%). (b) The mean number of alleles per locus, A, was 1.252 (range: 1.050–1.634); the proportion of polymorphic loci per population averaged 0.220 (range: 0.050–0.415); genic diversity, He, averaged 0.059 (range: 0.002–0.119). (c) Altogether there were 119 alleles at the 42 putative loci tested, 114 of these in Israel, (d) Genetic differentiation was primarily regional and local, not clinal; 70% of the variant alleles were common (>/ 10%) and not widespread, but rather localized or sporadic, displaying an archipelago population genetics and ecology structure. The coefficients of genetic distance between populations were high and averaged D = 0.134; range: 0.018–0.297, an indication of sharp genetic differentiation over short distances, (e) Discriminant analyses differentiated Israeli from Turkish populations, and within Israel, between central and 3 marginal regions, as well as between different soil-type populations, (f) Allozymic variation comprised 40% within and 60% between populations, (g) Gametic phase disequilibria were abundant, their number being positively correlated (r_s = 0.60, P<0.01) with the humidity, (h) Multilocus organization was substantive, also positively correlated with humidity, (i) Allozyme diversity, overall and at single loci, was significantly correlated with, and partly predictable by, climatic and edaphic factors, (j) The distrubition of the significant positive and negative values and the absence of autocorrelations in the correlogram revealed no similar geographic patterns across loci, eliminating migration as a prime factor of population genetic differentiation. These results suggest: (I) during the evolutionary history of wild emmer, diversifying natural selection, through climatic and edaphic factors, was a major agent of genetic structure and differentiation at both the single and multilocus levels; (II) wild emmer harbors large amounts of genetic diversity exploitable as genetic markers in sampling and abundant genetic resources utilizable for wheat improvement.     

Low genetic differentiation among widely separated populations of the pearl oyster Pinctada fucata as revealed by AFLP

Genetic variation within and among five populations of the pearl oyster Pinctada fucata, from China (Daya Bay, Sanya Bay and Beibu Bay), Japan (Mie Prefecture) and Australia (Port Stephens) was studied using AFLP. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic diversity of 0.38 among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise G_ST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese, Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and G_ST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow.     

猕猴桃野生居群的SSR分析初报

采用SSR分子标记技术对我国猕猴桃的2个商业栽培物种——中华猕猴桃和美味猕猴桃的9个天然居群(共221个样)的遗传多样性进行了初步分析。通过对14对猕猴桃引物的筛选,8对重现性好的引物扩增结果表现出良好的多态性。在8个多态性位点上共获得222个等位基因。居群等位基因平均数A=17．3,多态位点百分率P-100,多态信息指数PIC为0．87～0．96,显示出我国的猕猴桃野生居群具有极高的遗传多样性。中华猕猴桃和美味猕猴桃野生居群拥有高比例的共同等位基因,反映出二者的亲缘关系极近。