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 in the Pantaneiro horse breed assessed using microsatellite DNA markers

The genetic variability for a sample of 227 animals from three populations of Pantaneiro horses was estimated using data from 10 microsatellite loci. The number of alleles and the proportion of heterozygosity indicated high variability. A total of 91 alleles were found, with a significantly high mean number of alleles. The mean polymorphic information content was 0.7 and the paternity exclusion probability was 99.3%. The inbreeding coefficient (F(IS)) was low for the three populations: Ipiranga (F(IS) = 0.147), Nova Esperan?a (F(IS) = 0.094) and Promiss?o (F(IS) = 0.108). Genetic differentiation among all three populations was low (F(ST) = 0.008 to 0.064). Three methods were used to test for a recent bottleneck effect. The graphical method and the Wilcoxon test using the stepwise mutation model showed no bottleneck pattern for any of the populations. The test by two-phase mutation model showed genetic signatures of bottleneck for Ipiranga and Promiss?o. When we consider standard deviation value for Nova Esperan?a, the M-statistic detected a bottleneck pattern, but this result could be explained by a sample size effect. Therefore, there is no immediate cause for concern regarding loss of variation within the breed.     

Genetic variation of new 21 autosomal short tandem repeat loci in a Chinese Salar ethnic group

In the present study, we reported the allele frequencies for new 21 autosomal short tandem repeat (STR) loci, including D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435 and D5S2500 loci. Forensic statistical parameters were estimated from a sample set of 120 unrelated healthy individuals from the Salar ethnic group in Xunhua Salar Autonomous County of Qinghai province, China. A total of 151 alleles were observed at 21 STR loci in the population, and their allele frequencies were in the range of 0.004–0.554. All STR loci showed a high degree of genetic polymorphisms, and the combined probability of exclusion, combined power of discrimination and combined probability of matching for all 21 STR loci were 0.9999993134, 0.99999999999999999991739 and 8.2607 × 10⁻²⁰, respectively. For all the 21 STR loci in the Salar ethnic group, the observed genotypic data showed no significant deviation from those expected under the Hardy-Weinberg equilibrium. The allele frequency distributions for the 21 autosomal STR loci were compared between the Salar group and its neighboring populations and significant differences were detected among these populations at D1S1677, D2S441, D3S4529, D4S2408, D6S1017, D11S4463, D12ATA63, D14S14343, D18S853, D19S433 and D22S1045 loci.     

Low genetic structure in an epiphytic Orchidaceae (Oncidium hookeri) in the Atlantic rainforest of South-eastern Brazil

BACKGROUND AND AIMS: Oncidium hookeri is a neotropical species of epiphytic Orchidaceae found in the Brazilian Atlantic rainforest at the top of the Mantiqueira Range of mountains. The genetic variation of O. hookeri was studied to assess the distribution of genetic variability within and among six populations localized in Atlantic rainforest remnants. Gene flow among populations and the occurrence of recent bottlenecks were investigated in order to infer the degree of isolation of these populations. METHODS: Thirteen polymorphic loci were used for allozyme electrophoresis. The data were analysed by means of standard statistical approaches, to estimate gene diversity and the genetic structure of the populations. KEY RESULTS: The mean gene diversity and allelic richness were H(e) = 0.099 and A = 1.75, respectively. F-statistics revealed high heterozygote deficiencies in all populations (F(IS) = 0.43-0.82). Several rare alleles were found in all the populations, and three populations presented private alleles. Low genetic differentiation among O. hookeri populations was detected (F(ST) = 0.029); natural selection may be involved in PGM locus differentiation among populations. The genetic differentiation between paired populations was low, bearing no correlation with geographic distance (Mantel test: r = -0.34, P = 0.72). Only two populations showed signs of recent bottlenecks. CONCLUSIONS: The heterozygote deficiency found seems to be caused by pollinator behaviour; the low frequencies of several alleles of different loci can be maintained due to clonal propagation. Despite the stochastic nature of the wind-dispersal of seeds to long distances, this process may promote an effective gene flow among populations, thus avoiding genetic differentiation.     

Psorophora columbiae and Psorophora toltecum (Diptera: Culicidae) Colombian populations cannot be differentiated by isoenzymes

Two populations of the mosquito Psorophora columbiae from the central Andean area of Colombia and one population of Ps. toltecum from the Atlantic coast of Colombia were analyzed for 11 isoenzyme markers. Psorophora columbiae and Ps. toltecum are two of the main vectors of Venezuelan equine encephalitis. We found no conspicuous genetic differences between the two species. The relatively high gene flow levels among these populations indicate that these are not two different species or that there has been recent divergence between these taxa. In addition, no global differential selection among the loci was detected, although the alpha-GDH locus showed significantly less genetic heterogeneity than the remaining loci, which could mean that homogenizing natural selection acts at this locus. No isolation by distance was detected among the populations, and a spatial population analysis showed opposite spatial trends among the 31 alleles analyzed. Multiregression analyses showed that both expected heterozygosity and the average number of alleles per locus were totally determined by three variables: altitude, temperature and size of the human population at the locality. Individually, the expected heterozygosity is more related to these three variables than to the average number of alleles.     

Microsatellite identification of individual sockeye salmon in Barkley Sound, British Columbia

Population structure of sockeye salmon Oncorhynchus nerka in Barkley Sound, British Columbia, Canada was examined by analysis of microsatellite variation at 14 loci in three populations sampled in each of 3 years. The mean F _ST over all 14 loci was 0·063. Differences among populations accounted for 12 times the variation observed among years within populations. The number of alleles present at a locus was related to the power of the locus to provide accurate identification of individuals to population. The more alleles that were present at a locus, the greater was the power of the locus for individual identification. Individuals were correctly classified to one of three lakes of origin at a rate of 89%, and to one of two river drainages at a rate of 96%.     

菲律宾蛤仔EST-SSRs标记开发及不同地理群体遗传多样性

利用13对微卫星引物对大连、莆田、青岛3个地理群体蛤仔遗传多样性进行了检测。结果表明:13个基因座共检测到154个等位基因,每个座位检测到的等位基因数在2-7个之间,平均有效等位基因数为2.7657;3个群体平均观测杂合度分别为0.4387、0.4194、0.2383,平均期望杂合度分别为0.6488、0.6484、0.5526;群体间的遗传多样性差异不显著(P＞0.05)。NJ聚类结果显示大连和莆田群体的蛤仔亲缘关系较近,二者与青岛群体关系较远。3个群体均有不同程度的偏离Hardy-Weinberg平衡现象,表明各群体基因频率和基因型频率的稳定性相对较低。本研究所获得的微卫星标记的多态信息含量(PIC)>0.5,说明这些微卫星位点的多样性较高,可为下一步遗传图谱构建研究提供参考。     

Biochemical polymorphisms in feral and inbred mice (Mus musculus)

Examination of the frequencies of several loci controlling isozymes in three geographically distinct feral populations of mice showed the average animal to be heterozygous at 10.3% of his loci. There was no evidence for interaction between loci, nor any evidence for inbreeding in the populations. Thirty-nine inbred strains, including four newly derived ones, were also characterized for their alleles for as many as 16 polymorphic loci. Among these strains, variability is at least as great as in any single feral population, but probably less than that found among all feral populations of the species.This work was supported by NIH Research Grants GM-9966 and GM-07249 from the Division of General Medical Science, and by contracts AT(30-1)-1979 and AT(30-1)-3671 with the U.S. Atomic Energy Commission.     

Temporal and Microgeographic Variation in Allozyme Frequencies in a Natural Population of DROSOPHILA BUZZATII

Temporal variation in allozyme frequencies at six loci was studied by making monthly collections over 4 yr in one population of the cactophilic species Drosophila buzzatii. Ten sites were defined within the study locality, and for all temporal samples, separate collections were made at each of these sites. Population structure over microgeographic space and changes in population structure over time were analyzed using F-statistic estimators, and multivariate analyses of allele and genotype frequencies with environmental variables were carried out. Allele frequencies showed significant variation over time, although there were no clear cyclical or seasonal patterns. A biplot analysis of allele frequencies over seasons within years and over years showed clear discrimination among years by alleles at four loci. During the 4 yr, three alleles showed directional changes which were associated with directional changes in environmental variables. Significant associations with one or more environmental variables were found for allele frequencies at every locus and for both expected and observed heterozygosities (except those for Est-1 and Est-2). Thus, variation in allele frequencies over time cannot be attributed solely to drift. Significant linkage disequilibria were detected among three loci (Est-2, Hex and Aldox), but there was no evidence for spatial or temporal patterns. The F-statistic analyses showed significant differentiation among months within years for all loci, but the statistic used (coancestry) was heterogeneous among loci. Estimates of F (inbreeding) for all loci were significantly different from zero, with the loci in four groups, Adh-1 (negative), Pgm(small positive), Est-2 and Hex (intermediate) and Est-1 and Aldox (high positive). The correlation of genes within individuals within populations (f) for each locus in each month by site sample differed among loci, as did the (f) for each locus in each month by site sample differed among loci, as did the patterns of change in f over time (seasons). Heterogeneity in the F-statistic estimates indicates that natural selection is directly or indirectly affecting allele and genotype frequencies at some loci. However, the F-statistic analyses showed essentially no microgeographic structure (i.e., among sites), although there was significant heterogeneity in allele frequencies among flies emerging from individual rots. Thus, microspatial heterogeneity probably is most important at the level of individual rots, and coupled with habitat selection, it could be a major factor promoting diversifying selection and the maintenance of polymorphism.(ABSTRACT TRUNCATED AT 400 WORDS)     

Isolation and characterization of 15 nuclear microsatellite markers for Baillonella toxisperma Pierre (Sapotaceae), a low-density tree species of Central Africa

Baillonella toxisperma is a scattered endemic species of the Guineo-Congolian forest. We developed 15 nuclear microsatellite markers specifically for B. toxisperma to analyse the genetic diversity of 188 individuals distributed in two natural populations in Gabon. On average, 8.3 alleles per locus were identified; observed heterozygosity ranged from 0.056 to 0.872 and expected heterozygosity from 0.282 to 0.823 among populations. Only three loci showed a significant departure to Hardy-Weinberg equilibrium, but no linkage disequilibrium was observed for any pair of loci.     

Association of CTLA-4 variation with type I diabetes in Filipinos

The role of non-HLA single nucleotide polymorphisms from a panel of candidate genes in genetic susceptibility to type I diabetes (TID) among Filipinos was examined by PCR/SSOP typing of 90 patients and 94 controls, previously typed for the HLA class I and class II loci. We report the association of CTLA-4 A49G variation (cytotoxic T-lymphocyte associated-4) to TID among Filipinos, consistent with some but not all previous reports in other ethnic groups. The G allele frequency (0.61 versus 0.45, P=0.003) and GG genotype frequency (0.42 versus 0.22, P=0.004) were each increased in patients compared to controls, respectively. Among Filipinos, the CTLA-4 genotypes are associated with disease only in the presence of the predisposing DR3, 4, and 9 haplotypes (P=0.012). Compared to the AA genotype, the increased risk of diabetes predisposition is greatest in genotype GG bearing the DR susceptible alleles (DR3, 4, and 9) (odds ratio=4.6, P=0.001), demonstrating that non- HLA loci, acting in concert with HLA, can play potent roles in modifying susceptibility to TID.     

Microsatellite loci in eelgrass Zostera marina reveal marked polymorphism within and among populations

Using an enriched genomic library, we developed seven (CT)n/(GA)n microsatellite loci for eelgrass Zostera marina L. Enrichment is described and highly recommended for genomes in which microsatellites are rare, such as in many plants. A test for polymorphism was performed on individuals from three geographically separated populations (N = 15/population) and revealed considerable genetic variation. The number of alleles per locus varied between five and 11 and the observed heterozygosities for single loci ranged from 0.16 to 0.81 within populations. Mean allele lengths were markedly different among populations, indicating that the identified loci will be useful in studying population structure in Z. marina. As the frequency of the most abundant multilocus genotype within populations was always < 1%, these loci have sufficient resolving power to address clone size in predominantly vegetatively reproducing populations.     

应用15个STRs揭示广西4个少数民族的遗传关系

为研究广西仫佬、毛南、苗和瑶族的15个短串联重复序列（STR）基因座的遗传多态性,探讨这4个民族群体的遗传差异和进化关系。通过PCR-STR及测序仪,检测了广西4个民族766例无关个体的15个STR位点基因频率的分布并比较各民族间的差异,计算遗传学参数、遗传距离和构建系统进化树。结果显示：仫佬、毛南、苗和瑶族的15个STR位点分别共检出135,134,148,145种等位基因和424,432,445,436种基因型;各民族的平均Ho〉0.7,累积DP,EPP和PIC均在0.99999以上;毛南族和苗族,瑶族和其他民族间在多数位点的基因频率分布上存在显著差异,而仫佬族和毛南族或苗族间在多数位点上不存在差异;4个民族在进化树上被分为两组,仫佬族和毛南族聚成一组,苗族和瑶族聚成另一组。说明广西仫佬、毛南、苗和瑶族的15个STR基因座具有高度的遗传多态性,实用价值较高,是一组可用于人类群体遗传学、法医学个体识别和亲子鉴定等研究的有力工具;4个民族STR的遗传差异性和遗传关系与他们的语言文化和民族历史基本一致。     

Genetic variation among four Mexican populations (Huichol, Purepecha, Tarahumara, and Mestizo) revealed by two VNTRs and four STRs

Allele distributions of two polymorphisms with variable number of tandem repeats (VNTR), D1S80 and APOB, and four polymorphisms with short tandem repeats (STR), VWA, TH01, CSF1PO, and HPRTB, were analyzed in three Mexican ethnic groups: Huichol, Purepecha, and Tarahumara. Genotype distribution was in agreement with Hardy-Weinberg expectations for each locus and ethnic group. Heterozygosity (H), power of discrimination, and probability of exclusion were estimated. The three groups presented some distinctive genetic features: (1) a diminished genetic diversity (H = 66.8% to 73.4%) and mean number of alleles by locus (5.8 to 6.3) in comparison with Mexican mestizos (H = 78.3%, 10.5 alleles/locus), and (2) uneven allele distributions as evidenced by "distinctive alleles" with high frequencies, especially in the Tarahumara and the Huichol. Genetic relatedness analysis included data from a previously typed mestizo population, the largest and most widely distributed population in Mexico. Allele distribution differentiation was observed among all four groups, except between mestizo and Purepecha (p > 0.05), which was interpreted as indicating a larger Spanish component in the Purepecha as a result of gene flow effects. Although intrapopulation inbreeding (FIS) was not significant, heterozygote deficiency in the total population (FIT) and divergence among populations (FST) were significant (p < 0.05). Genetic distances displayed a closer relationship among mestizos, Purepechas, and Huichols in relation to Tarahumaras. Correlation between the observed genetic features and the geographic isolation level points to genetic drift as the main cause of differentiation among these Mexican populations.     

Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.)

Genetic interpretation and diversity of 9 isozyme loci have been estimated in 7 improved varieties and 19 landraces from Sweden by means of starch gel electrophoresis. The isozyme systems were ACO, DIA, GPI, MDH, PGD and PGM. For the statistic analysis we used the following measures: average number of alleles per locus, percentage of polymorphic loci, average heterozygosity direct count and average heterozygosity Hardy-Weinberg expected unbiased estimate. The measures were made on species and population levels. The distribution of the total genetic diversity among populations was also calculated. To illustrate the genetic relationships among populations, genetic distances were measured and principal component analysis performed. As expected in a cross-pollinated crop we found high genetic diversity and a larger variation within than among the populations. Somewhat unexpectedly, however, we found that the currently used varieties have the same high level of heterozygosity as the landraces but in the dendrogram the two groups are separated. The dendrogram showed three main clusters. The large cluster included 21 populations and the two small clusters were clearly distinguishable from the rest. The landrace spring-type could not be separated from the landraces winter-type, but we did detect a difference between different spring types. A few populations had unique alleles for certain loci.     

Genetic polymorphism and forensic parameters of nine short tandem repeat loci in Ngöbé and Emberá Amerindians of Panama

Nine STR loci (CSF1PO, TPOX, TH01, F13A01, FESFPS, VWA, D16S539, D7S820, and D13S317) were analyzed in unrelated Ng?bé and Emberá Amerindians of Panama. The chi-square test demonstrated statistically significant differences (P < 0.001) in the allele frequencies for all markers except one (D16S539; P < 0.01). Both populations shared their alleles with the highest frequencies in seven loci. However, there were also noticeable differences at the TPOX locus, which showed its highest frequencies at alleles 11 (0.48) and 6 (0.54) for the Ng?é and Emberá, respectively. Interestingly, these alleles are present in one population and are absent in the other, suggesting that they could be distinctive for each population. These results demonstrate that, despite the fact that each population belongs to a different linguistic stock [Chibchan (Ng?bé) and Chocoan (Emberá)], both retain strong similarities in their allele-frequency distributions. Three loci (TPOX, VWA, and F13A01) in the Ng?bé and two loci (TH01 and TPOX) in the Emberá departed from Hardy-Weinberg equilibrium. The analysis of the STR markers demonstrates that, despite their low levels of genetic polymorphisms, most of them could be informative for forensic purposes, showing a combined power of discrimination of 0.9999 for both Amerindian populations. However, powers of exclusion in the Ng?bé were very low, particularly at the TH01 (0.04) and FESFPS (0.08) loci. The combined powers of exclusion were 0.9338 and 0.9890 for the Ng?bé and the Emberá, respectively. Furthermore, the combined typical paternity index in the Ng?bé was considerably low (2.58), and in the Emberá it was 40.44, which is also very low. The low genetic polymorphism levels suggest that theuse of additional loci supplementing the battery of the nine loci is recommended for paternity and forensic tests in both populations, particularly for the Ng?bé.     

Pooling analysis of genetic data: the association of leptin receptor (LEPR) polymorphisms with variables related to human adiposity.

Analysis of raw pooled data from distinct studies of a single question generates a single statistical conclusion with greater power and precision than conventional metaanalysis based on within-study estimates. However, conducting analyses with pooled genetic data, in particular, is a daunting task that raises important statistical issues. In the process of analyzing data pooled from nine studies on the human leptin receptor (LEPR) gene for the association of three alleles (K109R, Q223R, and K656N) of LEPR with body mass index (BMI; kilograms divided by the square of the height in meters) and waist circumference (WC), we encountered the following methodological challenges: data on relatives, missing data, multivariate analysis, multiallele analysis at multiple loci, heterogeneity, and epistasis. We propose herein statistical methods and procedures to deal with such issues. With a total of 3263 related and unrelated subjects from diverse ethnic backgrounds such as African-American, Caucasian, Danish, Finnish, French-Canadian, and Nigerian, we tested effects of individual alleles; joint effects of alleles at multiple loci; epistatic effects among alleles at different loci; effect modification by age, sex, diabetes, and ethnicity; and pleiotropic genotype effects on BMI and WC. The statistical methodologies were applied, before and after multiple imputation of missing observations, to pooled data as well as to individual data sets for estimates from each study, the latter leading to a metaanalysis. The results from the metaanalysis and the pooling analysis showed that none of the effects were significant at the 0.05 level of significance. Heterogeneity tests showed that the variations of the nonsignificant effects are within the range of sampling variation. Although certain genotypic effects could be population specific, there was no statistically compelling evidence that any of the three LEPR alleles is associated with BMI or waist circumference in the general population.     

Genetic variation at minisatellite loci D1S7, D4S139, D5S110 and D17S79 among three population groups of eastern India

Genetic variation at four minisatellite loci D1S7, D4S139, D5S110 and D17S79 in three predominant population groups of eastern India, namely Brahmin, Kayastha and Garo, are reported in this study. The Brahmin and Kayastha are of Indo-Caucasoid origin while the Garo community represents the Indo-Mongoloid ethnic group. The methodology employed comprised generation of HaeIII-restricted fragments of isolated DNA, Southern blotting, and hybridization using chemiluminescent probes MS1, pH30, LH1 and V1 for the four loci. All four loci were highly polymorphic in the population groups. Heterozygosity values for the four loci ranged between 0.68 and 0.95. Neither departure from Hardy-Weinberg expectations nor evidence of any association across alleles among the selected loci was observed. The gene differentiation value among the loci is moderate (G_ST = 0.027). A neighbour-joining tree constructed on the basis of the generated data shows very low genetic distance between the Brahmin and Kayastha communities in relation to the Garo. Our results based on genetic distance analysis are consistent with results of earlier studies based on serological markers and linguistic as well as morphological affiliations of these populations and their Indo-Caucasoid and Indo-Mongoloid origin. The minisatellite loci studied here were found to be not only useful in showing significant genetic variation between the populations but also to be suitable for human identity testing among eastern Indian populations.     

New polymorphic microsatellite loci for population studies in the European anchovy, Engraulis encrasicolus (L.)

Eleven microsatellite loci were developed in the European anchovy, Engraulis encrasicolus, and tested in samples from two geographically distant populations (Atlantic and Mediterranean Sea). Number of alleles ranged from eight to 28 and observed heterozygosity from 0.440 to 0.920. There was no evidence of linkage disequilibrium, although two loci are indeed linked. All loci were in Hardy-Weinberg equilibrium, except for one locus in the Atlantic and two loci in the Mediterranean sample. These three loci plus two more showed evidence for null alleles.     

欧洲刺槐种源群体遗传结构和多样性

对来自欧洲和美国的 18个刺槐种源子代进行了等位酶分析。可进行遗传分析的 7个酶系统 (Amy,Fe,L ap,Idh,Mdh,6 Pgd,Skd)中有 14个基因位点 ,其中 12个位点具有多态性。每个多态位点平均等位基因数 (A/L )变化在 1.5 6～ 3.6 7之间 ,平均基因型数 (G/L)变化在 1.6 1～ 7.11之间 ,平均等位基因有效数目 (Ae)变化在 1.0 2～ 2 .5 0之间 ,预期杂合度 (H e)变化在0 .0 2～ 0 .5 6之间。不同种源群体之间也存在较大的遗传差异 ,在 8个德国种源中 ,各群体的 A、Ae、和 H e等相对较小 ,但不同群体间差异较大。各位点等位基因频率在不同种源群体间变化也较大 ,表明德国各种源群体内遗传变异相对较小 ,但群体间差异较大。来自匈牙利和斯洛伐克的 8个种源群则相反 ,各群体的 A、Ae、和 H e等相对较大 ,而不同种源群体间差异则较小 ,各位点等位基因频率在种源群体间变化相对一致 ,表明这两个国家的种源群体内变异较大 ,但不同种源群体间差异较小。欧洲的刺槐种源并未形成明显的地理变异模式 ,而且欧洲的种源和来自原产地的美国种源相比 ,没有发现明显的差异。经过 Hardy-Weinberg平衡检测证明 ,88.4 1%位点符合 H- W遗传平衡 ,表明各群体基因频率和基因型频率保持较高的稳定性 ,且种源内的变异大于种源间变异 ,94 .