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.     

中国汉族群体5个STR分子遗传标记

为了解中国人5个STR基因座等位片段结构特征,获得汉族群体D2S2955、D3S4014、D20S604、D22S689和GATA198B05基因座的群体遗传学数据。采取成都地区无血缘关系汉族个体血样EDTA抗凝血。Chelex法提取DNA,PCR扩增,非变性聚丙烯酰胺凝胶不连续缓冲系统水平电泳分型,自动激光荧光测序仪测定DNA序列。序列分析显示,中国人D2S2955、D3S4014、D20S604基因座具有简单重复序列,而D22S689、GATA198B05基因座具有复杂重复序列。5个STR基因座在成都汉族群体中均具有遗传多态性。揭示了我国汉族人群5个STR基因座的等位基因片段结构特征,为人类群体遗传研究提供了数据,建立的不连续缓冲系统水平电泳分型方法为检测这5个STR基因座提供了简便技术。     

Soybean germplasm pools in Asia revealed by nuclear SSRs

Soybean was domesticated in East Asia, where various kinds of landraces have been established as a result of adaptation to different environments and the diversification of food cultures. Asia is thus an important germplasm pool of soybean. In order to evaluate the genetic structure of the Asian soybean population, we analyzed allelic profiles at 20 simple-sequence repeat (SSR) loci of 131 accessions introduced from 14 Asian countries. The SSR loci produced an average of 11.9 alleles and a mean gene diversity of 0.782 in the accessions tested. Quantification theory III analysis and cluster analysis with the UPGMA method clearly separated the Japanese from the Chinese accessions, suggesting that the Japanese and Chinese populations formed different germplasm pools. The Korean accessions were involved in both germplasm pools, whereas most of the accessions from southeast and south/central Asia were derived from the Chinese pool. Relatively high genetic diversity and the absence of region-specific clusters in the southeast and south/central Asian populations suggest that soybean in these areas has been introduced repeatedly and independently from the diverse Chinese germplasm pool. The present study indicates that the two germplasm pools can be used as exotic genetic resources to enlarge the genetic bases of the respective Asian soybean populations.     

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     

Autosomal STR variation in five Austronesian populations

Human population characteristics at the genetic level are integral to both forensic biology and population genetics. This study evaluates biparental microsatellite markers in five Austronesian-speaking groups to characterize their intra- and interpopulation differences. Genetic diversity was analyzed using 15 short tandem repeat (STR) loci from 338 unrelated individuals from 5 Pacific islands populations, including the aboriginal Ami and Atayal groups from Taiwan, Bali and Java in Indonesia, and the Polynesian islands of Samoa. Allele frequencies from the STR profiles were determined and compared to other geographically targeted worldwide populations procured from recent literature. Hierarchical AMOVA analysis revealed a large number of loci that exhibit significant correspondence to linguistic partitioning among groups of populations. A pronounced divide exists between Samoa and the East (Formosa) and Southeast Asian (Bali and Java) islands. This is clearly illustrated in the topology of the neighbor-joining tree. Phylogenetic analyses also indicate clear distinctions between the Ami and Atayal and between Java and Bali, which belie the respective geographic proximities of the populations in each set. This differentiation is supported by the higher interpopulation variance components of the Austronesian populations compared to other Asian non-Austronesian groups. Our phylogenetic data indicate that, despite their linguistic commonalities, these five groups are genetically distinct. This degree of genetic differentiation justifies the creation of population-specific databases for human identification.     

9号染色体10个STR基因座的遗传制图

运用小规模实验初步探讨了以中国人群为基础的遗传图绘制工作的必要性。18个无关汉族3代家系共131份血样采自甘肃省白银地区,常规PCR扩增9号染色体的10个STR基因座,采用非变性聚丙烯酰凝胶电泳分析。PCR产物经克隆测序确定核心序列重复次数,采用标准命名法命名各等位基因,用POPGENE软件包计算各基因座等位基因频率,并进行Hardy-Weiberg平衡检验,用Linkage软件包进行各基因座之间连锁关系分析。根据连锁分析结果绘制了中国人群由10个STR基因座构成的9号染色体遗传图。基于中国人群体的9号染色体10个STR连分析锁分析结果与GDB检索结果之间存在较显著的差异,这种差异同时表现在个别基因座之间和0号染色体遗传图总长度上。男、女遗传结果之间在较显著的差异,这种差异同时表现在个别基因之间和9号染色体总长度上。男、女遗传图总长度为129．21cM和178．4cM,均大高加索入。说明了在运用GDB数据之前,有必要根据实验群体进行基因座的初步评估,并且有必要对基于中国人群体的遗传图进行进一步的研究。     

北京汉族群体39个短串联重复序列基因座多态性及其遗传关系

本文首次对北京地区汉族人群的13个CODIS(Combined DNA index system)和26个非CODIS系统STR基因座的遗传多态性进行了研究,建立了北京地区汉族人群39个STR基因座的群体遗传多态性数据库并对其法医学应用价值进行了评价。39个STR基因座的基因型分布均符合Hardy-Weinberg平衡且各基因座之间均不存在连锁现象,个体鉴别力(Power of discrimination, DP)在0.7740~0.9818之间,期望杂合度(Expected heterozygosity, He)在0.6000~0.9350之间,多态性信息含量(Polymorphism information content, PIC)在0.5317~0.9047之间,非父排除率(Power of exclusion, PE)在0.2909~0.8673之间,累积个体鉴别力(Cumulative probability of discrimination, CDP)为0.999999999999999999999999999999999999999964971,累积非父排除率(Cumulative probability of exclusion, CPE)为0.999999999973878。另外,结合已公开报道的国内其他11个群体相应基因座的遗传资料,根据等位基因频率计算遗传距离,构建了系统发生树。本研究可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,对北京地区汉族人群开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。     

Minisatellite MS32 Alleles Show Population Specificity Among Thai,Chinese, and Japanese

Lineages of structurally related alleles at minisatellite MS32 in human populations show considerable differentiation at the continental level. However, the regional specificity of these lineages remains unknown. We now describe the comparison of allele structures in Thai, Han Chinese, and Japanese populations with lineages previously established for North Europeans and Africans. The great majority of alignable Asian alleles showed their closest structural relative in Asia, with few instances of preferential alignment of Asian with European alleles and only one isolated incident showing a best match with an African allele. Further, there was a strong tendency, most marked for Japanese, for Asian alleles to align preferentially with other alleles from the same population, indicating strong regional specificity of allele lineages. This rapidly evolving minisatellite can therefore serve as a lineage marker for exploring recent events in human population history and dissecting population structure at the fine-scale level, as well as being an extremely informative DNA marker for personal identification.     

Austro-Asiatic tribes of Northeast India provide hitherto missing genetic link between South and Southeast Asia

Northeast India, the only region which currently forms a land bridge between the Indian subcontinent and Southeast Asia, has been proposed as an important corridor for the initial peopling of East Asia. Given that the Austro-Asiatic linguistic family is considered to be the oldest and spoken by certain tribes in India, Northeast India and entire Southeast Asia, we expect that populations of this family from Northeast India should provide the signatures of genetic link between Indian and Southeast Asian populations. In order to test this hypothesis, we analyzed mtDNA and Y-Chromosome SNP and STR data of the eight groups of the Austro-Asiatic Khasi from Northeast India and the neighboring Garo and compared with that of other relevant Asian populations. The results suggest that the Austro-Asiatic Khasi tribes of Northeast India represent a genetic continuity between the populations of South and Southeast Asia, thereby advocating that northeast India could have been a major corridor for the movement of populations from India to East/Southeast Asia.     

云南泸西汉族17个Y-STR基因座多态性及遗传关系分析

调查云南泸西县汉族群体17个Y-STR基因座的多态性分布, 探讨其群体遗传学及法医学应用价值。应用AmpF?STR?Yfiler荧光标记复合扩增系统扩增156名汉族无关男性个体的17个Y-STR基因座, 用ABI3100遗传分析仪进行基因检测, 计算等位基因及单倍型频率, 并结合已公开发表的国内外其他16个群体的遗传学资料, 分析各群体间的遗传距离。云南泸西汉族男性群体中, 共观察到154种单倍型, 其中152种为仅观察到1次的单倍型, 2种单倍型观察到2次, 单倍型多样性(HD)值为0.9998, 基因多样性(GD)值在0.3901(DYS437)—0.9632(DYS385a/b)。17个群体遗传距离分析提示, 国内人群云南泸西汉族与湖南汉族的遗传距离最小(0.005), 与闽南汉族的遗传距离最大(0.035); 在中国周边群体中,云南泸西汉族与新加坡华人的遗传距离最小(0.015), 与日本人和马来西亚印度人群的遗传距离最大(0.060)。结果表明, 17个Y-STR基因座在云南泸西汉族中具有较高的遗传多态性, 适用当地的法医学应用。与其他民族群体的遗传多样性比较, 对了解各群体的起源、迁徙及相互关系有重要意义。     

Genetic analysis of 15 STR loci in Chinese Han population from West China

Allele frequencies for 15 short tandem repeat （STR） loci （D8S1179, D21S11, D7S820, CSFIPO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA） were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001-0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.     

Dominant Contribution of Northern Chinese to the Paternal Genetic Structure of Chaoshanese in South China

We investigated the Y chromosome of various Chinese populations to determine the patrilineal origin of the Chaoshanese population. Admixture analysis of six specific Y short tandem repeat (STR) loci in 6,292 individual samples taken from 51 populations, including Chaoshanese and Minnanese of our earlier studies, showed that over 85% of the Chaoshanese Y chromosomes were derived from the Central China Han (M (RH): 0.8614; M (BE): 1.1868?±?0.2054), and a very small portion were from the southern aborigines. These results support a Central China Han origin of the Chaoshanese and additionally reveal that males from the Central China Han were the predominant contributor to the patrilineal genetics of the Chaoshanese. A phylogenetic tree and analysis of molecular variance signified a strong association between Y chromosomes of Chinese populations and their linguistic affiliations, revealing a coevolution of Y chromosome diversity and languages in East Asia.     

Phylogeography of Wild Musk Shrew (Suncus Murinus) Populations in Asia Based on Blood Protein/Enzyme Variation

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.     

Population genetics of short tandem repeat (STR) loci

To investigate the population genetics of short tandem repeat (STR) polymorphisms in human populations, we have studied the allele frequency distributions of four STR loci (HUMTH01, HUMVWA31, HUMF13A1 and HUMFES) in 16 different population surveys which can be categorised within three broadly defined ethnic groups: Caucasian, Asian (Indian subcontinent), and African (Afro-Caribbean and US black). We have observed that allele frequency distributions of populations within ethnic groups are similar; consequently, genetic distances are an order of magnitude lower than between ethnic groups. Inbreeding coefficients (F-statistics) and calculations of the number of mean heterozygous loci per individual, along with estimates of variance, did not suggest that the populations were substructured. This included a study of an immigrant Asian population known to comprise at least three different sub-groups. Finally, an indication of the discriminating power is given by calculation of likelihood ratios (LR) of each individual tested across all four loci. Approximately 70% of Caucasians give an LR of greater than 10,000; the test is even more discriminating in Afro-Caribbeans-approximately 90% of tests are greater than 10,000.Editor's commentsThe authors present data generated by the move from VNTR to STR loci for human identification. The data they present for samples within major racial groupings address some of the concerns about population substructuring discussed by Balding and Nichols in this volume.     

Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes.

Previous studies of mtDNA variation in indigenous Taiwanese populations have suggested that they held an ancestral position in the spread of mtDNAs throughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995), but the question of an absolute proto-Austronesian homeland remains. To search for Asian roots for indigenous Taiwanese populations, 28 mtDNAs representative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwan) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Alu insertion loci were analyzed, to determine if the pattern of mtDNA variation is concordant with nuclear DNA variation. Tribal groups shared considerable mtDNA sequence identity (P>.90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs with a 9-bp deletion have considerable mainland-Asian diversity and have spread to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any other populations, but these shared types were widely dispersed geographically throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overall, the results suggest that the Taiwanese have temporally deep roots, probably in central or south China, and have been isolated from other Asian populations in recent history.     

Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data

The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.     

Phylogeography of the Coastal Mosquito Aedes togoi across Climatic Zones: Testing an Anthropogenic Dispersal Hypothesis

The coastal mosquito Aedes togoi occurs more or less continuously from subarctic to subtropic zones along the coasts of the Japanese islands and the East Asian mainland. It occurs also in tropical Southeast Asia and the North American Pacific coast, and the populations there are thought to have been introduced from Japan by ship. To test this hypothesis, the genetic divergence among geographic populations of A. togoi was studied using one mitochondrial and three nuclear gene sequences. We detected 71 mitochondrial haplotypes forming four lineages, with high nucleotide diversity around temperate Japan and declining towards peripheral ranges. The major lineage (L1) comprised 57 haplotypes from temperate and subarctic zones in Japan and Southeast Asia including southern China and Taiwan. Two other lineages were found from subtropical islands (L3) and a subarctic area (L4) of Japan. The Canadian population showed one unique haplotype (L2) diverged from the other lineages. In the combined nuclear gene tree, individuals with mitochondrial L4 haplotypes diverged from those with the other mitochondrial haplotypes L1—L3; although individuals with L1—L3 haplotypes showed shallow divergences in the nuclear gene sequences, individuals from Southeast Asia and Canada each formed a monophyletic group. Overall, the genetic composition of the Southeast Asian populations was closely related to that of temperate Japanese populations, suggesting recent gene flow between these regions. The Canadian population might have originated from anthropogenic introduction from somewhere in Asia, but the possibility that it could have spread across the Beringian land bridge cannot be ruled out.     

Ethnic variations of a retinoblastoma susceptibility gene (RB1) polymorphism in eight Asian populations

An A → G single nucleotide polymorphism (SNP) at nucleotide 153,104 in the retinoblastoma susceptibility locus (RB1) at 13q14 was previously reported to be present only in Asians. In this study, we determined the distribution of this SNP in normal Southeast Asian populations (Chinese, Malay, Javanese, Thai, Filipino), in South Asian populations (Bangladeshi, Pakistani Pushtun and Indian) and in Chinese retinoblastoma cases and control subjects. TheRB1 SNP was present in all populations at an overall frequency of ≤0.18. Heterozygosity was higher in the Southeast Asian groups (0.14–0.34) than in the South Asian groups (Bangladeshi and Indian) (0.04–0.06). Significant differences in allele frequencies were found between the two population groups. Interestingly, our Pakistani population comprised of ethnic Pushtuns from northwest Pakistan was significantly different from the neighbouring Bangladeshi and Indian populations. No significant difference was found between Chinese case patients and control subjects. ThisRB1 SNP appears to be an ethnic variant prevalent in Southeast Asian populations and may be useful for studyingRB1 inheritance by pedigree analysis.     

陕西渭南地区汉族人群17个Y-STR基因座多态性及遗传关系分析

调查陕西渭南地区汉族群体17个Y-STR基因座的多态性,探讨其群体遗传学及法医学应用价值。应用Y-fi ler荧光标记复合扩增系统,对413名陕西渭南地区汉族无关男性个体17个Y-STR基因座进行复合扩增,用ABI3130遗传分析仪进行基因分型,计算各基因座的群体遗传学参数,并结合已经发表的其他10个群体相应基因座的单倍型资料,分析各群体间的遗传距离。413名陕西渭南汉族个体共检出405种单倍型,其中397种单倍型仅出现1次,单倍型多样性达0.9999,基因多样性(GD)为0.4130(DYS391)~0.9734(DYS385a/b),累计GD值为0.9999。遗传距离分析提示,陕西渭南汉族与辽宁满族的遗传距离最小(0.00110),与青海藏族的遗传距离最大(0.22333)。结果表明,17个Y-STR基因座在陕西渭南汉族群体中具有丰富的遗传多态性和较高的非父排除能力,在法医学和人类群体遗传学研究中具有重要价值。     

9号染色体短臂上7个STR基因座在基因扫描中的信息表现

为了初步探讨7个位于染色体9p区域的短串联重复序列(shorttandemrepeat,STR)基因座:D9S288、D9S157、D9S1748、D9S171、D9S161、D9S1817和D9S1805在遗传学研究及法医学应用中的意义,随机抽取225名湖南汉族无关个体,复合PCR技术扩增上述基因座,ABI377全自动测序仪进行基因分型,共检出75种等位基因,通过对基因型及等位片断频率分布的研究和数据统计分析,7个基因座基因频率分布在0.002～0.800之间,构成243种基因型。7个STR基因座基因型分布均符合Hardy Weinberg平衡定律(P>0.05),杂合度(heterozygosity,H)介于0 347～0.844之间,个体识别力(discriminationpower,DP)为0.346～0.841,非父排除率(probabilitiesofpaternityexclusion,PPE)为0.308～0.738,多态信息含量(polymorphicinformationcontent,PIC)在0.328～0.822之间。种族比较结果显示,湖南汉族与非洲黑人及欧洲白人在大多数基因座均存在显著差异(P<0.001)。研究结果丰富了中华民族基因数据库,在人类群体遗传学及法医学研究领域有重要应用价值。