Comparative analysis of allele polymorphism of three short tandem repeats in the Russian, Uzbek and Georgian populations

The allele polymorphism of the AGC short tandem repeat (STR) of exon 1 of the androgen receptor (AR) gene located in Xq11-12, ATCT STR of intron 40 of the von Willebrand factor (vWF) gene located in chromosome 12p12, and AGAT STR of an anonymous DNA sequence (STRX1) from the short arm of the X chromosome was analyzed in the Georgian, Uzbek, and Russian populations. Polymerase chain reaction (PCR) with DNA of unrelated persons revealed 14 AR, 7 vWF, and 7 STRX1 alleles in Georgians; 14, 8, and 6 alleles, respectively, in Uzbeks; and 16, 8, and 9 alleles, respectively, in Russians. The heterozygosity at these STR was 0.61, 0.78, and 0.46 in Georgians; 0.60, 0.83, and 0.44 in Uzbeks; and 0.80, 0.70, and 0.58 in Russians. The correspondence of genotype frequencies to the Hardy-Weinberg equilibrium was observed with AR STR in Russians and Uzbeks, STRX1 STR in Georgians, and vWF in all three populations. A significant deviation from the equilibrium was found for STRX1 in Russians and Uzbeks and AR in Georgians. The potential of individualization was 0.05 for AR, 0.13 for vWF, and 0.18 for STRX1 in Georgians; 0.04, 0.09, and 0.13, respectively in Uzbeks; and 0.05, 0.14, and 0.07, respectively, in Russians. The allele and genotype frequency distributions of each STR were analyzed in all three populations. Allele frequencies in the populations were compared by the Kolmogorov-Smirnov test. The Russian population significantly differed in allele frequencies of the three STR from Uzbeks and in those of STRX1 and AR from Georgians. Georgians and Uzbeks significantly differed in vWF and STRX1 frequencies. The possibility of using the three STR in molecular diagnosis of the corresponding monogenic diseases, population genetic studies, and personal identification is discussed.     

Development of microsatellite markers to genetically differentiate populations of Octopus minor from Korea and China

Of the more than 300 octopus species, Octopus minor is one of the most popular and economically important species in Eastern Asia, including Korea, along with O. vulgaris, O. ocellatus, and O. aegina. We developed 19 microsatellite markers from Octopus minor and eight polymorphic markers were developed to analyze the genetic diversity and relationships among four octopus populations from Korea and three from China. The number of alleles per locus varied from 10 to 49, and allelic richness per locus ranged from 2 to 16.4 across all populations. The average allele number among the populations was 11.1, with a minimum of 8.3 and a maximum of 13.6. The mean allelic richness was 8.7 in all populations. The Hardy-Weinberg equilibrium (HWE) test revealed significant deviation in 19 of the 56 single-locus sites, and null alleles were presumed in five of eight loci. The pairwise F ( ST ) values between populations from Korea and China differed significantly in all pairwise comparisons. The genetic distances between the China and Korea samples ranged from 0.161 to 0.454. The genetic distances among the populations from Korea ranged from 0.033 to 0.090, with an average of 0.062; those among populations from China ranged from 0.191 to 0.316, with an average of 0.254. The populations from Korea and China formed clearly separated into clusters via an unweighted pair group method with arithmetic mean dendrogram. Furthermore, a population from muddy flats on the western coast of the Korean Peninsula and one from a rocky area on Jeju Island formed clearly separated subclusters. An assignment test based on the allele distribution discriminated between the Korean and Chinese origins with 96.9 % accuracy.     

Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations

Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.     

Molecular genetic diversity in 5 populations of Madhya Pradesh, India

This paper presents data on the distribution of 3 amplified fragment length polymorphisms (D1S80, APOB, and YNZ22) in 5 populations of Central India. Using the polymerase chain reaction technique, 3 caste (Brahmin, Khatri, and Dhimer) and 2 tribal (Gond and Baiga) populations were studied for the 3 loci. The allelic variations observed in the caste populations are compatible with those of many Caucasian populations, but the caste populations showed significant overall and interpopulation variability within the region. D1S80 allele *24 varied from 32% (Dhimers) to 42% (Brahmins). Allele *18 was not observed in Baiga tribal populations, but in caste populations it varied from 11% (Dhimers) to 24% (Brahmins). Both tribal populations showed higher frequencies of allele *31 (17%-18%). For APOB, caste populations again showed bimodal distribution of alleles *35 and *37, but in tribal populations higher allele numbers (*47, *49) were also frequent. For YNZ22, extensive variation was observed for all populations studied. Allele *4 was the most common in caste populations, while alleles *2, *7, and *10 were prominent in tribal populations. The level of gene differentiation is not very high for the 3 systems studied in the 5 populations. Overall, allele frequency distribution, heterozygosity, and genetic diversity analysis show that the genetic diversity observed is socially and geographically structured.     

Microsatellite diversity among the primitive tribes of India

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.     

Variation at 4 short tandem repeat loci in 8 population groups of India.

We have determined the nature and extent of variation at 4 STR loci (CSF1P0, TPOX, TH01, VWA) in 8 caste and tribal population groups of eastern and northern India. Large differences in allele frequencies among the groups were found. Average heterozygosities in all populations were high (approximately 80%). The overall extent of gene differentiation among the 8 groups was high (GST = 0.04). The nature of genomic affinities based on these 4 STR loci does not completely agree with our earlier finding based on classical genetic markers that geographic proximity of habitat has a greater influence on genetic similarity between populations than sociocultural proximity does.     

STR Polymorphisms of the Henan Population and Investigation of the Central Plains Han Origin of Chaoshanese

Allele frequencies for 15 short tandem repeat (STR) loci were obtained from a Chinese Han population in Henan province of middle China. No deviation from Hardy–Weinberg equilibrium was observed for the STR loci except for D3S1358. The 15 STR loci are potentially useful for paternity testing and forensic casework in the Henan population. A phylogenetic tree based on CODIS STR allele frequencies of 25 Han populations revealed noticeable but far less clear distinctions between southern and northern Chinese populations; the Henan Han population was located at an intermediate position between south and north Chinese Han populations, relatively closer to Chaoshan and Minnan Han. Moreover, admixture analysis showed a large proportion of Central Plains Han origin in Chaoshanese and Minnanese. Admixture and phylogenetic analysis also reflected the genetic similarity shared by these two groups.     

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a polymerase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in order to estimate population genetic diversity and genetic structure parameters, one must assume that dominant (amplified) alleles are identical in state, recessive (unamplified) alleles are identical in state, AFLP fragments segregate according to Mendelian expectations and that the genotypes of an AFLP locus are in Hardy-Weinberg equilibrium (HWE). The HWE assumption is untestable for natural populations using dominant markers. Restriction fragment length polymorphism (RFLP) markers segregate as codominant alleles, and can therefore be used to test the HWE assumption that is critical for analysing AFLP data. This study examined whether the dominant AFLP markers could provide accurate estimates of genetic variability for the Aedes aegypti mosquito populations of Trinidad, West Indies, by comparing genetic structure parameters using AFLP and RFLP markers. For AFLP markers, we tested a total of five primer combinations and scored 137 putative loci. For RFLP, we examined a total of eight mapped markers that provide a broad coverage of mosquito genome. The estimated average heterozygosity with AFLP markers was similar among the populations (0.39), and the observed average heterozygosity with RFLP markers varied from 0.44 to 0.58. The average FST (standardized among-population genetic variance) estimates were 0.033 for AFLP and 0.063 for RFLP markers. The genotypes at several RFLP loci were not in HWE, suggesting that the assumption critical for analysing AFLP data was invalid for some loci of the mosquito populations in Trinidad. Therefore, the results suggest that, compared with dominant molecular markers, codominant DNA markers provide better estimates of population genetic variability, and offer more statistical power for detecting population genetic structure.     

STR polymorphisms in Philippine ethnolinguistic groups: evaluation of forensic utility

Population data was collected for the STR loci F13AO1, FES/FPS, HUMvWA, and HUMTHO1, in three major Philippine ethnolinguistic groups and used to estimate statistical parameters for identity testing in forensic work on Filipinos. The Cebuano, Ilocano, and Pampango populations in the Philippines were studied because they are among the biggest linguistic groups in the country, thus their genotypic profiles should substantially represent those of many Filipinos. The number of alleles varied from 4 to 9 at all loci, falling within the range observed for other local and world populations. Pairwise comparisons of the allele frequency distributions showed no statistical differences among the populations. The test for linkage equilibrium showed no evidence of non-random association of alleles across the physically unlinked loci in any of the three populations. The four loci combined gave an exclusion power of > or =0.9995 and a power of paternity exclusion of 0.8859-0.9389.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Genetic variation of three autosomal STR Loci D21S1435, D21S1411, and D21S1412 in Korean population

The autosomal tetranucleotide short tandem repeat loci D21S1435, D21S1411 and D21S1412 were analyzed in samples of unrelated 200 Korean individuals. The loci showed no significant deviations from Hardy–Weinberg equilibrium. Alleles were assigned according to the International Society for Forensic Haemogenetics (ISFH) recommendations. The power of discrimination of the analyzed markers was found to be high for the populations, thereby facilitating the validation and efficiency of these STR markers in forensic human identification and paternity testing. To our knowledge, this is the first report of the nomenclature and the allele frequency data for these three STR loci in Korean population.     

三个STR位点在哈萨克族中的遗传多态性

运用复合PCR扩增,6％变性聚丙烯酰胺凝胶电泳结合银染技术对我国新疆102位无关的哈萨克族个体进行D16S539,D7S820,D13S317的STR位点的调查,为建立新疆哈萨克族群体数据库提供资料。经统计学检验,3个位点的基因型频率分布符合Hardy-Weinberg平衡定律,结果显示3个位点的期望杂合度为：0.9439、0.9356、0.9304,累积PIC＝0.9905,DP＝0.9998,PE=9572。紫外,比较新疆哈萨克族与其他4个人群的等位片段频率,发现除与北京汉族在D7S820位点上无统计学意义外（P＞0.05）,其他均可见显著性差异（P＜0.05）。同时,在8个家系42人的调查中无一突变发现且均按孟德尔遗传规律传递。3个STR位点的联合分析在法医学应用及群体遗传学中显示了较高的价值。     

Early-glycation of apolipoprotein E: effect on its binding to LDL receptor,scavenger receptor A and heparan sulfates

Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) causes substantial morbidity afflicting approximately 10% of adult males. Treatment is often empirical and ineffective since the etiology is unknown. Other prostate and genitourinary diseases have genetic components suggesting that CP/CPPS may also be influenced by genetic predisposition. We recently reported a highly polymorphic short tandem repeat (STR) locus near the phosphoglycerate kinase gene within Xq11-13. Because this STR is in a region known to predispose towards other prostate diseases, we compared STR polymorphisms in 120 CP/CPPS patients and 300 control blood donors. Nine distinct allele sizes were detected, ranging from 8 to 15 repeats of the tetrameric STR plus a mutant allele (9.5) with a six base deletion in the flanking DNA sequence. The overall allele size distribution in the CP/CPPS patients differed from controls (Chi-square=19.252, df=8, P=0.0231). Frequencies of two specific alleles, 9.5 and 15, differed significantly in CP/CPPS vs. control subjects and allele 10 differed with marginal significance. Alleles 9.5 and 10 were both more common in CP/CPPS patients than controls while allele 15 was less common. These observations suggest that Xq11-13 may contain one or more genetic loci that predispose toward CP/CPPS. Further investigations involving family studies, larger patient populations, and other control groups may help elucidate this potential genetic predisposition in CP/CPPS.     

意大利蜜蜂产浆性状10个微卫星位点的遗传分析

我国培育成功的世界上蜂王浆产量最高的蜂种（Ea）是从20世纪30年代引进我国的意大利蜜蜂（Eb）中选育的。采用10个微卫星位点对蜂王浆高产蜜蜂、原种意大利蜜蜂（Ee）和本地意大利蜜蜂进行研究,以探明由于人工选择和地理隔离造成的其分子进化上的一些特征。结果,10个微卫星位点在3个蜂种中共扩增到96个等位基因,其中有48个等位基因是不同的,表明10个微卫星位点在3个蜂种中的高度多态性,而且由于人工选择和地理隔离已造成3蜂种在遗传基础上的一些分化。3蜂种的多态信息含量（PIC）分别为0．57、0．50、0．57,杂合度分别为0．60、0．57、0．61,二者均无显著差异。遗传距离的分析结果显示,Ee和Eb（0．14）、Eb和Ea（0．16）之间的遗传距离较近,而Ea和Ee（0.25）之间的遗传距离较远。等位基因频率的分析结果表明,6个位点的7个等位基因的频率（A29的159bp、A24的100bp和104bp、A7的110bp、A43的126bp、A14的221bp和A113的221bp）以Ee、Eb、Ea的顺序递增,Ea的这7个等位基因频率分别显著高于Ee和Eb。同时4个位点的4个等位基因的频率（A24的106bp、A43的140bp;A113的215bp和A14的219bp）以Ea、Eb、Ee的Ⅲ页序下降,Ea在这4个位点的频率分别显著低于Eb和Ee。这些位点的等位基因可能与蜂王浆产量有关。     

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。     

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci

We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2–6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K≥3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.     

Genetic structure of an endangered plant, Antirrhinum microphyllum (Scrophulariaceae): allozyme and RAPD analysis

Thirteen allozyme loci and 68 random amplified polymorphic DNA (RAPD) markers were analyzed to assess the genetic diversity and population structure of threatened Antirrhinum microphyllum (Scrophulariaceae), a narrow endemic of central Spain known from only four populations. According to allozyme data, species genetic diversity (p = 46.15%, A = 2.61, and H(e) = 0.218), as well as within-population genetic diversity (p = 44.23%, A = 2.10, and H(e) = 0.204), were high when compared to average estimates for other narrowly distributed plant species. Ninety-four percent of species genetic diversity corresponded to within-population genetic diversity. Nevertheless, significant differences were found among populations in allele frequencies of four of the six polymorphic loci, and three private alleles were detected. Inbreeding coefficients (F(IS)) suggest that populations are structured in genetic neighborhoods. The RAPDs also showed high levels of genetic diversity (p = 89.71% and H(e) = 0.188 at the species level, and p = 67.65% and H(e) = 0.171 at the population level). Nei's genetic distances estimated both from allozymes and RAPDs indicated low differentiation among populations. In spite of this, the low frequencies of certain alleles and the presence of private alleles indicate that efforts should be made to conserve all four remaining populations.     

Comparative study of genetic variation at 15 STR loci in three isolated populations of the Bosnian mountain area

Fifteen autosomal STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX, and FGA) were studied in three geographically close but isolated populations from the Bosnian mountain area. The three villages are Bobovica, Dejcici, and Lukomir. DNA was obtained from 83 individuals, and the allele frequencies and genetic diversity among the three sample groups were compared. In addition, seven of the STR loci (CSF1PO, D13S317, D3S1358, D5S818, D7S820, FGA, TH01) were used in a comparative population analysis of the Bjelasnica-Treskavica region and the Adriatic islands of Brac, Hvar, and Korcula. Although the sample sizes are relatively small, the observed variation within any of the small isolated populations is high and comparable to less isolated groups. In addition, even though the populations are geographically isolated, the STR data are similar among the populations. The most significant frequency differences were observed at the TH01 locus. Although the specific allele distributions in any untyped population cannot be determined a priori, we find support for a high degree of diversity for the STR loci in most populations. In addition, the multiple locus profile is highly informative not only for various population studies but also for forensic studies, even when specific population data are not available.     

Haplotype diversity of preharvest sprouting QTLs in wheat.

Preharvest sprouting (PHS) is one of the most important factors affecting wheat production worldwide in environments characterized by rainfall and high humidity at harvest. In such environments, the incorporation of seed dormancy of a limited duration is required to minimize losses associated with PHS. A global collection of 28 PHS-resistant and -susceptible wheat germplasm was characterized with microsatellite markers flanking the genomic regions associated with PHS-resistance quantitative trait loci (QTLs), particularly on chromosomes 3D and 4A. The genetic diversity analysis revealed 380 alleles at 54 microsatellite loci, with an average of 7.0 alleles per locus, among the 28 wheat genotypes. Gower's genetic similarity values among all possible pairs of genotypes varied from 0.44 to 0.97, indicating that there is considerable diversity in the PHS germplasm evaluated. Cluster and principal coordinates analysis of genetic similarity estimates differentiated the genotypes into groups, according to their source of PHS resistance. Three major SSR haplotypes were observed on chromosome 4AL, designated RL4137-type allele, Aus1408-type allele, and synthetic-hexaploid-type allele. The RL4137-type allele was prevalent in Canadian cultivars, mostly in cluster 6, followed by the Aus1408-type and its derivatives in clusters 4 and 5. The Syn36 and Syn37 alleles on chromosome 4AL were rare. On chromosome 3DL, the SSRs haplotypes derived from Syn36 and Syn37 were also rare, and proved unique to the Aegilops tauschii - derived synthetic hexaploids. They are therefore likely carrying resistance genes different from those previously reported. Based on genetic relationships, PHS resistance might be improved by selecting parental genotypes from different clusters.