Geographic contiguity and genetic affinity among five ethnic populations of Manipur,India: further molecular studies based on VNTR and STR loci

Background : Apart from traditional markers studied among a few numerically small, geographically defined surveys among Mongoloid populations in northeastern parts of India, very little is known about their genomic diversity at the molecular level. Primary objective : This study seeks to investigate how best the variable number tandem repeat (VNTR) and short tandem repeat (STR) loci together can detect the patterns of the genetic affinity among five geographically contiguous, linguistically and socio-culturally diverse Mongoloid-affiliated populations of Manipur in northeastern regions of India. Subject and methods : Blood samples were collected from unrelated and randomly selected volunteers of five ethnic populations (Meitei, Kuki, Naga, Hmar and Manipuri Muslim) from different parts of the state. Allelic variation in four minisatellite loci (D1S7, D4S139, D5S110 and D17S79) and three STR loci (vWA, FESFPS and F13AO1) was studied. Results : Average heterozygosity values among the five groups for the minisatellite range from 68% to 94%, while the hypervariable three STR loci were between 60% and 88%. In the populations, all the studied loci were highly polymorphic, with almost no departure from Hardy-Weinberg equilibrium. The gene differentiation for the VNTR loci was lower and moderate ( G st = 0.030) in comparison with microsatellites ( G st = 0.043). The neighbour-joining method of clustering based on both type of molecular markers reveals a close cluster for the tribal groups of Kuki, Naga and Hmar, while Manipur Muslim stand distinct in both the trees. The clustering pattern obtained from the combined DNA marker loci matches more closely the pattern from STR loci than that obtained from VNTR loci. Conclusions : The results reinforce that using both VNTR and STR loci in detecting regional genetic affinity among the populations is more effective than using VNTR or STR independently, and also confirm the results obtained from the serological and electrophoretic data. However, the clustering pattern obtained from combined DNA markers is more in conformity with the pattern obtained by STR loci rather than with VNTR loci. Despite linguistic, geographical and cultural barriers, the populations show genetic affinity among the four populations except in the case of the migrant Manipur Muslim group.     

Geographic contiguity and genetic affinity among five ethnic populations of Manipur,India: further molecular studies based on VNTR and STR loci

BACKGROUND: Apart from traditional markers studied among a few numerically small, geographically defined surveys among Mongoloid populations in northeastern parts of India, very little is known about their genomic diversity at the molecular level. PRIMARY OBJECTIVE: This study seeks to investigate how best the variable number tandem repeat (VNTR) and short tandem repeat (STR) loci together can detect the patterns of the genetic affinity among five geographically contiguous, linguistically and socio-culturally diverse Mongoloid-affiliated populations of Manipur in northeastern regions of India. SUBJECT AND METHODS: Blood samples were collected from unrelated and randomly selected volunteers of five ethnic populations (Meitei, Kuki, Naga, Hmar and Manipuri Muslim) from different parts of the state. Allelic variation in four minisatellite loci (D1S7, D4S139, D5S110 and D17S79) and three STR loci (vWA, FESFPS and F13AO1) was studied. RESULTS: Average heterozygosity values among the five groups for the minisatellite range from 68% to 94%, while the hypervariable three STR loci were between 60% and 88%. In the populations, all the studied loci were highly polymorphic, with almost no departure from Hardy-Weinberg equilibrium. The gene differentiation for the VNTR loci was lower and moderate (G(st) = 0.030) in comparison with microsatellites (G(st) = 0.043). The neighbour-joining method of clustering based on both type of molecular markers reveals a close cluster for the tribal groups of Kuki, Naga and Hmar, while Manipur Muslim stand distinct in both the trees. The clustering pattern obtained from the combined DNA marker loci matches more closely the pattern from STR loci than that obtained from VNTR loci. CONCLUSIONS: The results reinforce that using both VNTR and STR loci in detecting regional genetic affinity among the populations is more effective than using VNTR or STR independently, and also confirm the results obtained from the serological and electrophoretic data. However, the clustering pattern obtained from combined DNA markers is more in conformity with the pattern obtained by STR loci rather than with VNTR loci. Despite linguistic, geographical and cultural barriers, the populations show genetic affinity among the four populations except in the case of the migrant Manipur Muslim group.     

Genetic relationships of the populations in eastern India.

The genetic relationships for four sets of populations in eastern India have been studied by using gene frequency data available in the literature. The Caucasoid populations in Assam and West Bengal are genetically close but different from the Mongoloid populations in the neighbourhood. The genetic distance analysis shows that the Mongoloid populations in Assam and West Bengal cluster according to their states of residence, indicating a correlation between genetic and geographical distances.     

Genetic admixture of eight Mexican indigenous populations: Based on five polymarker,HLA‐DQA1, ABO,and RH loci

This study explores the genetic admixture of eight Mexican indigenous populations (Otomi‐Ixmiquilpan, Otomi‐Actopan, Tzeltales, Nahua‐Milpa‐Alta, Nahua‐Xochimilco, Nahua‐Zitlala, Nahua‐Ixhuatlancillo, and Nahua‐Coyolillo) on the basis of five PCR‐based polymorphic DNA loci (LDLR, GYPA, HBGG, D7S8, GC), HLA_DQA1, and the blood groups ABO and Rh (CcDEe). Among the indigenous populations, the highest gene frequencies for O and D were 0.9703 and 1.000 for Zitlala (State of Guerrero) and 0.9955 and 0.9414 for Tzeltales (State of Chiapas), respectively. Maximum likelihood estimates of admixture components yield a trihybrid model with Amerindian (assuming that Nahua‐Zitlala is the most representative indigenous population), Spanish, and African ancestry with the admixture proportions: 93.03, 6.03, and 0.94 for Tzeltales, and 28.99, 44.03, and 26.98 for Coyolillo. A contribution of the ancestral populations of Ixhuatlancillo, Actopan, Ixmiquilpan, Milpa‐Alta, and Xochimilco were found with the following average of admixture proportions: 75.84, 22.50, and 1.66. The findings herein demonstrate that the genetic admixture of the Mexican indigenous populations who at present speak the same Amer‐Indian language can be differentiated and that the majority of them have less ancestral indigenous contribution than those considered as Mestizo populations. Am. J. Hum. Biol., 2008. © 2008 Wiley‐Liss, Inc.     

Restriction fragment length polymorphism and polymerase chain reaction: HLA-DQA1 and polymarker analysis of blood samples from transfusion recipients

The effect of blood transfusion on DNA profiles of an individual is a significant issue in the forensic context. In the present study, the effects of blood transfusion in 5 recipients were studied by performing restriction fragment length polymorphism and polymerase chain reaction HLA-DQA1 and Polymarker (LDLR, GYPA, HBGG, D7S8, and GC) assays (Roche Molecular Systems, Branchburg, NJ) on serial posttransfusion blood samples. Pretransfusion and posttransfusion DNA profiles of all 5 recipients were consistent with no evidence of the donor genetic material. Currently used DNA profiling techniques in forensic science are reliable and informative for paternity and identity purposes in situations involving transfusion of 1 or 2 U of blood up to 24 hours posttransfusion.     

Antiquity, geographic contiguity and genetic affinity among Tibeto-Burman populations of India: a microsatellite study

BACKGROUND: The Tibeto-Burman (TB) populations are one of the four major linguistic population groups of India. They are considered belonging to different stocks and show wide variation in culture and language; however, their genetic relationship, antiquity and migration history among the regional populations has been little investigated. Molecular genetic studies are expected to clearly show the antiquity and genetic diversity of these populations. AIM: This paper seeks to understand the extent and magnitude of genetic affinities and diversities among 14 TB populations (12 Indian and two global groups), investigate the findings based on classical genetic markers and verify the historical accounts of their migration and genetic history based on 12 microsatellite markers. SUBJECTS AND METHODS: The allele frequency data for 12 STR loci of 13 Asian (Tibeto-Burman) populations were obtained from the literature and the Adi Pasi data was obtained by microsatellite typing of their blood samples. The 12 loci studied are D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, vWa, TPOX, D18S51. Three different distance measures, two phylogenetic trees and PCA plot have been employed to understand the genetic relationship of the studied populations. RESULTS: Average heterozygosity values range from 68 to 79% and the average G(ST) value is 4.7%. The dendrogram, based on the D(A) distance, shows the clustering of populations based on their diversities and geographical contiguity; the Mizoram and Arunachal Pradesh populations especially cluster together, populations from Sikkim form a separate subcluster and Manipur populations along with the Garo of West Bengal separate out from the other clusters. The Harpending and Ward regression model shows isolated populations positioned below the regression line and others, who experience external gene flow, placed above the line. The results support folklore migration accounts of their possible antiquity with the Tibetan and southern Chinese populations. CONCLUSIONS: Overall, geographic contiguity, punctuated by isolating barriers, is a major influencing factor of genetic affinity among the TB population; contiguous populations within a region show greater genetic relationship than with distant TB populations over a wide geographical area. The results of the microsatellite study also support the history of diverse routes of migration of these populations.     

Short tandem repeat (STR) variation in eight village populations of the island of Korcula (Croatia)

The aim of this study was to analyse short tandem repeat (STR) variation using the data on nine loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in the populations from eight villages on the island of Korcula, Croatia, in order to analyse its genetic and population structure. The analysis of STR data in this study indicated an appreciable degree of genetic homogeneity among the studied village populations on the island, even though a so-called 'east-west dichotomy' and differentiation between the inhabitants of the most recent settlement and the remaining ones was indicated with respect to the loci CSF1PO and TPOX, respectively. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among geographically closely related but reproductively isolated groups remains to be further evaluated, especially in terms of a larger number of studied loci in order to possibly find specific markers useful for resolving genetic patterns of variability at regional levels.     

D16S539、D7S820和D13S317位点在新疆哈萨克族中的遗传多态性

目的 了解新疆哈萨克族人群D16S539、D7S820和D13S317 3个STR位点的遗传多态性。方法 应用多重PCR扩增，6％变性聚丙烯酰胺凝胶电泳结合银染技术对102名无关个体及8个家系42人的哈萨克族人群进行调查，并与其他人群进行了比较。结果 3个位点分别检测出8、7、8个等位片段，多态性分布符合Hardy-Wdinberg平衡定律，期望杂合度为：0.9439、0.9356、0.9304，累积多态信息量为0.9905、个体识别为0.9998、非父排除率为0.9572，与其他人群比较差异有显著性（P＜0.05），在家系调查中无一突变发现，均按孟德尔遗传规律传递。结论 3个STR位点的综合检验在法医学应用及群体遗传学中显示了较高的价值。     

中国毛南族和仫佬族群体STR的遗传差异性分析

目的研究中国毛南族和仫佬族6个短串联重复序列基因座（STR）：D2S1338、D8S1179、D16S539、D18S51、D19S433、D21S11的遗传多态性以及他们与其他5个少数民族群体的遗传进化关系，丰富这两个群体的遗传学数据库。方法采用聚合酶链反应一短串联重复序列（PCR-STR）技术及ABI3100测序仪，研究中国毛南族（200例）和仫佬族（183例）无关个体6个STR位点的基因频率的分布特点。结果毛南族和仫佬族的6个STR位点分别共检出61和65种等位基因，其频率分布在0．0025，0．3200和0．0027～0．2842之间；共检出216和218种基因型．其频率分布在0．0050～0．1500和0．0055～0．1585之间；两者的平均H〉0．8，PIC〉0．8；累积DP达0．99999998，累积EP达0．9983以上。遗传距离和进化树结果显示：毛南族与仫佬族关系最近，彝族与水族关系最远；7个民族在进化树上被分为2类，彝族自成一类，其余6个民族聚为一类。结论毛南族和仫佬族的6个STR基因座具有高度遗传多态性的特点，实用价值较高，故以上数据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；广西7个民族STR的遗传差异性与他们的历史文化和地理分布基本一致。     

应用四个短串联重复序列基因座研究七个民族间的遗传关系

目的：调查广西黑衣壮族人群4个短串联重复序列(short tandem repeats,STR)基因座：D5S818、D7S820、D13S317、vWA的群体遗传分布资料,探讨7个民族间的遗传关系。方法：应用荧光标记STR基因扫描技术分析152名广西黑衣壮族无关个体。以遗传距离和系统发生树来分析7个民族间遗传关系。结果：4个STR基因座平均观察杂合度为0．7814;平均多态信息总量为0．7375;累积个体识别力达0．9928809,累积非父排除率达0．9928809。新疆乌孜别克族、新疆维吾尔族、甘肃裕固族、云南白族、广西黑衣壮族、浙江畲族聚为一群,东部蒙古族自成一群。结论：广西黑衣壮族的4个STR基因座属高度遗传多态性标记;新疆乌孜别克族和维吾尔族、广西黑衣壮族和浙江畲族遗传关系较近。     

中国蒙古族六个短串联重复序列基因座的遗传多态性

目的　了解中国锡盟牧区蒙古族人群 6个短串联重复序列基因座D3S13 5 8、D13S3 17、D5S818、D6S10 43、D2S1772、D7S3 0 48的遗传多态性分布并与汉族群体作对照 ,获得相应多态位点的群体遗传学数据。方法　采用多重PCR扩增技术和聚丙烯酰胺凝胶电泳方法 ,对 2 86名蒙古族个体进行调查。结果　 6个基因座D3S13 5 8、D13S3 17、D5S818、D6S10 43、D2S1772、D7S3 0 48分别检出 6、9、8、11、14、11个等位基因 ,多态性分布均符合Hardy Weinberg平衡定律 (P >0 .0 5 )。累积杂合度、个人识别能力及多态信息量分别为 0 .9998、0 .9999、0 .9998。结论　上述 6个基因座均具有较高的杂合度和多态信息量 ,是较理想的遗传标记系统。同时表明蒙汉群体基因频率分布在D3S13 5 8、D13S3 17、D5S818、D2S1772、D7S3 0 48基因座的差异有显著性 (P <0 .0 5 ) ,而在D6S10 43基因座差异无显著性 (P >0 .0 5 ) ,为人类遗传学和民族学研究提供了理论依据。     

中国北方人群14个短串联重复序列位点的遗传多态性分析

目的 分析中国北方汉族人群中染色体7p14—15区域内6个短串联重复序列(short tandem repeat，STR)位点和12q13区域内8个STR位点的遗传多态性。方法 采用荧光标记PCR扩增技术和毛细管电泳方法，对染色体7p14—15区域内D7S1808、D7S2250、D7S2251、D7S683、D7S656、D7S528位点和12q13区域内D12S1056、D12S1293、D12S83、D12S1655、D12S1662、D12S334、D12S137、D12S102位点在100名随机选取的无血缘关系的中国北方汉族人群中的遗传多态性进行分析。结果 在中国北方汉族人群中，染色体7p14-15区域的D7S1808、D7S2250、D7S2251、D7S683、D7S656和D7S528位点分别检测出7、8、7、4、6和5个等位基因，24、27、22、10、17和13种基因型，杂合度分别为86％、88％、83％、79％、85％和80％；染色体12q13区域的D12S1056、D12S1293、D12S83、D12S1655、D12S1662、D12S334、D12S137和D12S102位点分别检测出5、5、8、6、6、6、5和7个等位基因，15、15、29、17、17、19、13和24种基因型，杂合度分别为86％、84％、87％、82％、84％、85％、81％和89％。结论 染色体7p14—15区域的6个STR位点和12q13区域的8个STR位点基因频率分布符合Hardy—Weinberg平衡，并在中国北方汉族人群中呈现较好的遗传多态性。     

15个短串联重复序列在拉萨市和那曲地区藏族人群的多态性分布

目的 调查15个短串联重复序列(STR)(D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA)在408名西藏拉萨市和那曲地区藏族人群中的基因型与等位基因频率分布. 方法 提取基因组DNA,利用多重PCR和五色荧光(6FAM、VIC、NED、PET、LIZ)自动化检测技术,获得基因分型图,然后进行统计分析,获得15个STR基因座在西藏拉萨市和那曲地区藏族群体中的基因型频率和等位基因频率,并作Hardy-Weinberg平衡检测及两地区基因频率的比较分析. 结果 在拉萨市藏族群体中,15个STR基因座分别检测到11～47种基因型,5～12种等位基因,那曲地区藏族群体中,分别检测到12～58种基因型,6～14种等位基因;15个STR基因座的等位基因频率分布均符合Hardy-Weinberg平衡,拉萨和那曲地区藏族人群等位基因频率分布差异性较小. 结论 该15个STR在西藏拉萨市和那曲地区藏族群体中具有较高的遗传多态性,适合作为藏族群体的遗传标志,用于人类学、遗传疾病连锁分析、法医学亲子鉴定和个体识别等研究领域.     

Genetic structure of north-west Africa revealed by STR analysis

We have analysed a large set of autosomal short tandem repeat (STR) loci in several Arabic and Berber-speaking groups from north-west Africa (ie Moroccan Arabs, northern-central and southern Moroccan Berbers, Saharawis, and Mozabites). Two levels of analysis have been devised using two sets of 12STR loci, (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and 21 (the former set plus D9S926, D11S2010, D13S767, D14S306, D18S848, D2S1328, D4S243, F13A1, and FES/FPS). For each set, data for a number of external reference populations were gathered from the literature. Several methods of analysis based on genetic distances (neighbour-joining trees, principal coordinate analysis, boundary detection), as well as AMOVA, showed that genetic differentiation among NW African populations was very low and devoid of any spatial pattern. When the NW African populations were grouped according to cultural or linguistic differences, the partition was not associated with genetic differentiation. Thus, it is likely that Arabisation was mainly a cultural process. A clear genetic difference was found between NW African populations and Iberians, which underscores the Gilbraltar Straits as a strong barrier to genetic exchange; nonetheless, some degree of gene flow into Southern Iberia may have existed. NW Africans were genetically closer to Iberians and to other Europeans than to African Americans.     

中国汉族两群体HLA-DQA1基因的遗传构成及有关15群体DQA1基因频率的比较分析

以HLA基因的PCR-RFLP分型方法研究了哈尔滨地区(Hans-H,71例)和上海地区(Hans-S,98例)两个汉族群体HLA-DQA1座位的遗传多态性。共检出8种等位基因。两群体均以DQA1*0301频率最高,而*0401最低(哈尔滨群体未检出),频率分布符合Hardy-Weinberg平衡。综合分析华人12群体及日本人、高加索人和尼格鲁人等3群体的HLA-DQA1的基因频率显示:卡方总体检验Hans-H及Hans-S与北方华人其它4群体(除维族)间相互无显著差异(P>0.05)),但逐项检验群体间多存在一个至几个基因频率的显著差异(P<0.05～0.001)。总体检验北方华人6群体(包括Hans-S)与南方5群体间均有显著差异(P<0.05～0.001),但满族与南方汉人3群体总体检验无显著差异(P>0.05),而维族与北方华人6群体则有显著差异(P<0.05～0.001)。另外,华人与异族间总体均有非常显著差异(P<0.001),但相对而言,华人(尤其是北方人)与日本人最为接近,华人与高加索人相似性较大,与尼格鲁人差异最大,而高加索人与尼格鲁人差异也较小。并对上述结果进行了讨论。     

HLA in the Azores Archipelago: possible presence of Mongoloid genes

The HLA profile of the Azoreans has been compared with those of other world populations in order to provide additional information regarding the history of their origins. The allele frequencies, genetic distances between populations, correspondence analyses and most frequent haplotypes were calculated. Our results indicate that the Azorean population most likely contains an admixture of high-frequency Caucasoid, Mongoloid and, to a lesser degree, Negroid HLA genes. The middle Atlantic Azores Archipelago was officially colonized by the Portuguese after 1439 and historical records are concordant with the existence of Caucasoid and Negroid population. However, Mongoloid genes were not suspected, but the Oriental HLA haplotypes A24-B44-DR6-DQ1, A29-B21-DR7-DQ2 and A2-B50-DR7-DQ2 are the fourth, fifth and sixth most frequent ones in Azores. A correspondence analysis shows that the Azorean population is equidistant from Asian and European populations and genetic distances are in some cases closer to the Asian than to European ethnic groups, and never are significantly different; also, B*2707 subtype is found in Asians and Azoreans (but not in Europeans) and the same Machado-Joseph Disease founder haplotypes (Chr 14) are found in both Japanese and Azoreans. It is proposed that a Mongoloid population exists in Azores; whether, the arrival occurred prior to discovery is undetermined.     

河南汉族群体八个STR基因座遗传多态性研究

目的 对河南省汉族群体的8个短串联重复序列（short tandem repeats,STR)基因座等位基因频率进行研究,得到河南群体TH01,FES,D19S400,D7S820,D16S539,D20S161,D3S1545和D5S818基因座的群体遗传学数据。方法 EDTA抗凝血样采自河南117名无血缘关系汉族个体,酚氯仿法抽提DNA,PCR扩增,非变性聚丙烯酰胺垂直凝胶电泳,银染显色分析,结果 得到8个基因座的等位基因频率,各基因座的杂合度分别为：0．66,0.67,0.80,0.76,0.79,0.78,0.78;个体识别率:0.83,0.83,0.94,0.91,0.93,0.93,0.92,0.92.结论 8个STR基因座具较高的杂合度,等位基因分布符合HardyWeinberg平衡,是较理想的遗传标记,可用于法医学个体识别和亲权鉴定。     

云南汉族15 个短串联重复序列基因座遗传多态性特征及分析

目的:调查云南地区汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA 15 个短串联重复序列(Short tandem repeat,STR)基因座的遗传多态性。方法:收集云南汉族313 名无关个体血样,提取DNA,PCR 复合扩增并利用ABI鄄3130 型基因分析仪进行毛细管电泳检测每个样本各基因座的等位基因大小,分别统计每个STR 基因座各基因型的频率,并进行Hardy-Weinberg 遗传平衡检验。结果:云南汉族这15 个STR 基因座各基因型频率分布符合Hardy-Weinberg 平衡(P>0.05),杂合度在0.636 ~0.901,匹配概率在0.034 ~0.220,单一STR 位点的个体识别率在0.780 ~0.966、非父排除率在0.336 ~0.797、多态性信息总量在0.555 ~0.860,联合使用这15个位点所产生的累积个体识别率大于0.999 999 99,累积非父排除率等于0.999 998 408。与中国其他地区汉族群体这15 个STR 基因座等位基因频率分布相比有较高的相似性,但也有轻微的地区差异。结论:云南汉族的D8S1179、D21S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、VWA、TPOX、D18S51、D5S818、FGA 这15 个STR 基因座具有高度的多态性,与中国其他地区汉族群体有较高的相似性,在法医学中的亲子鉴定和个人识别方面具有较高应用价值。     

浙江畲族和汉族人群六个短串联重复序列位点遗传多态性的研究

目的 了解浙江畲族和汉族人群D3S1358、D16S539、TH01、TPOX、CSFlPO、D7S8206个短串联重复序列(short tandem repeat，STR)位点遗传多态性特征。方法 随机抽取108名浙江景宁畲族和102名浙江汉族无血缘关系个体的静脉血，应用AmpFlSTR Cofiler试剂盒扩增6个STR位点，PCR产物经ABI Prism377序列分析仪电泳后，用基因扫描软件进行分析。结果 畲族和汉族人群6个STR位点均符合Hardy—Weinberg平衡，畲族人群D3S1358、D16S539、TH01、TPOX、CSFlPO、D7S820位点杂合度分别为0．8028，0．9148，0．7522，0．6728，0．9123，0．8338，期望排除率分别为0．4067，0．6057，0．4437，0．3200，0．5250，0．5358，个人识别率分别为0．6690，0．7841，0．6447，0．5382，0．7298，0．7296。累积个人识别率为0．9991，累积期望排除率为0．9805，累积多态信息含量是0．9988。在D3S1358、D16S539、TPOX位点畲族人群与汉族人群之间存在显著差异。结论 浙江畲族人群有其自身的STR等位基因分布特征。所得到的数据可为法医个人识别、亲子鉴定及遗传学研究提供依据。