Genetic analysis of 15 STR loci on Chinese Tibetan in Qinghai Province

A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations

The Tibetan people are ancient and populous, constituting the seventh-largest of the fifty-five ethnic minority groups in China. The Ngawa Tibetan and Qiang Autonomous Prefecture (NTQAP), situated on the border of northwest and southwest China, has its distinct group relationships. Short tandem repeat (STR) is extremely polymorphic and extensively used in the application of forensic medicine and population genetics. However, it is not clear the genetic information including linkage disequilibrium (LD) by 36 autosomal STR (A-STR) markers in the Tibetan group from NTQAP. The Tibetan population from NTQAP of southwest China was examined for 36 A-STR loci in the research. Every marker across the 36 A-STR loci was consistent with Hardy-Weinberg equilibrium (HWE). The results of the calculation revealed that the total discrimination power (TDP) is 1-2.2552 × 10-42 and the cumulative probability of exclusion (CPE) is 1-1.3031 × 10-16. Subsequently, a total of 345 alleles with allelic frequencies ranging from 0.00382 to 0.55343 were identified, and the allelic numbers varied from 5 in both the TH01 and TPOX markers to 28 in the SE33 locus. The Ngawa Tibetan population, along with other Chinese populations, exhibited influences from historical factors and regional distribution, as indicated by the results of population genetics analysis. We thus first explored the genetic characteristics and correlated forensic parameters of the 36 A-STR markers in NTQAP to fill the gap in the Tibetan population. It was discovered that these 36 autosomal STR markers supplemented forensic STR databases and offered extremely valuable polymorphisms for Chinese forensic applications, such as parentage testing and personal identification. Moreover, the study would contribute additional information regarding the substructure and diversity in the Chinese population.

FST estimates of 94 populations in China based on STR markers

The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the F_ST values. Thus, F_ST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific F_ST values of each population, the overall F_ST values of each province, each region, and the whole country, and the locus-specific F_ST values of different loci were calculated. The LRs using different allele frequencies and different F_ST values were compared based on the combination of simulated genotypes. As a result, the F_ST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after F_ST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding F_ST values can make the LRs more accurate and reasonable.

Genetic polymorphism and forensic application of 23 autosomal STR loci in the Han population of Panjin City, Liaoning Province, Northeastern China

BACKGROUND

Short tandem repeats (STRs) are consecutive repetition of a repeat motif and widely used in forensic medicine and human genetics because of their high polymorphism.

SUBJECTS AND METHODS

In the current study, 23 autosomal STR loci were genotyped from 1263 unrelated healthy individuals living in Panjin City, Liaoning Province, Northeastern China using the VeriFiler^TM Express PCR Amplification Kit. The population comparison was performed between the Panjin Han population and the other relevant groups to further explore the structure of Panjin Han and its relationship with the other groups.

RESULTS

The results found 316 alleles across the 23 STRs and the corresponding allelic frequencies ranged from 0.5198 to 0.0004. Except for D3S1358, TPOX, TH01, and D3S1358, all STR loci were highly polymorphic (PIC > 0.7), with the Penta E locus having the highest degree of polymorphism (0.9147). For population comparison, the exact test of population differentiation found that no significant difference was observed between the Panjin Han and the other Han populations, except for Guangdong Han and Jiangxi Han.

CONCLUSION

The Panjin Han population showed significant differences with the other ethnic groups in China (Bouyei, Dong, Hui, Miao, Tibetan, and Uygur) and the foreign ethnic groups.

Genetic diversity, forensic characteristics and phylogenetic analysis of the Qiongzhong aborigines residing in the tropical rainforests of Hainan Island via 19 autosomal STRs

BACKGROUND

The genetic landscape of the Qiongzhong aborigines, who reside in "the Heart of Hainan," is still unclear. The Goldeneye™ DNA ID System 20 A is available for forensic and population genetics applications.

AIM

To obtain genetic polymorphisms of 19 autosomal STR loci in the Qiongzhong aborigines, and to explore the genetic relationships with a total of 69,132 people from forty-five populations.

SUBJECTS AND METHODS

Genotype data on 19 autosomal STRs were collected from 724 Qiongzhong aborigines and phylogenetic relationships were conducted by multidimensional scaling analysis (MDS), principal component analysis (PCA) and neighbor-joining (N-J) phylogenetic tree construction.

RESULTS

No evidence of deviation from Hardy-Weinberg equilibrium was identified. A total of 233 distinct alleles were observed with allele frequencies ranging from 0.0007 to 0.5375. The combined power of discrimination (CPD) and combined power of exclusion (CPE) for the 19 autosomal STR loci were 1-8.28 × 10^-34 and 0.999999987, respectively.

CONCLUSION

Our phylogenetic results demonstrated that (a) the populations of Southeast Asian countries have thorough integrations with southern China in terms of ethnicity and genetics due to long-term cultural and trade exchanges, and (b) based on genetic and linguistic analysis, the Qiongzhong aborigines have a close relationship with Fujian Han Chinese.HighlightsThe STR landscape of Qiongzhong aborigines inhabited in Hainan tropical rainforests was depicted by 19 autosomal STRs.A total of 69,132 people from forty-five populations were selected for a more extensive examination of genetic similarities and differences by multivariate statistical methods (MDS, PCA and N-J tree construction).The genetic analyses indicated that the populations of Southeast Asian countries are very genetically close to southern Chinese populations.From the genetic and linguistic perspective, the Qiongzhong aborigines have a close relationship with Han Chinese from Fujian Province.

Comprehensive analyses for genetic diversities of 19 autosomal STRs in Chinese Kazak group and its phylogenetic relationships with other continental populations

Short tandem repeats (STRs) play an essential role in forensic genetics due to their high degree of polymorphisms, wide distributions and easy detection method. In this study, allelic frequencies and forensic statistical parameters of the 19 autosomal STR loci in a Kazak ethnic group were calculated, and its genetic relationships with reference populations were assessed in order to understand population structure better and enrich population genetic data for forensic practice in Chinese Kazak ethnic group. There were 226 identified alleles with the corresponding allelic frequencies ranging from 0.0008 to 0.5295 in the 628 unrelated healthy Kazak individuals in Xinjiang Uygur Autonomous Region. All autosomal STRs were conformed to the Hardy-Weinberg equilibrium after Bonferroni’s correction. The cumulative power of discrimination and the combined probability of exclusion of all the 19 autosomal STRs were 0.999 999 999 999 999 999 999 997 162 and 0.999 999 994 484, respectively. Furthermore, the D_A distances and Fixation index values of pairwise populations, principal component analysis, multidimensional scaling analysis, phylogenetic tree analysis and structure analysis were conducted to probe the genetic relationships between the Kazak group and other reference populations. The population genetic results showed that these 19 autosomal STR loci were characterised by high genetic diversities in the Kazak group. Furthermore, the studied Kazak group had close genetic relationships with the Uyghur group and the Uzbek group. The present results may facilitate understanding the genetic background of the Chinese Xinjiang Kazak group.

Population genetics of 15 autosomal STR loci in the Han population of Ili Kazakh Autonomous Prefecture, Northwestern China

PURPOSE

China harbors 56 ethnic groups and Han accounts for >92% of the total Chinese population. We investigated the frequencies of 15 autosomal short tandem repeat (STR) loci in the Han population of the Ili Kazakh Autonomous Prefecture with the aim of expanding the available population information in human genetics databases and for forensic DNA analysis.

SUBJECTS AND METHODS

We explored the genetic characteristics of 15 autosomal STR loci in 552 unrelated Chinese Han individuals from Ili Kazakh Autonomous Prefecture, Northwestern China using the AmpFISTR Identifiler PCR Amplification Kit. Moreover, phylogenetic analysis was performed between the Han population and other relevant populations based on the autosomal STR genotyping. The neighbor-joining tree and principle component analysis were generated based on the Nei's standard genetic distance and allelic frequencies, respectively.

RESULTS

A total of 171 alleles were observed among 552 unrelated individuals and allelic frequencies ranged from 0.5145 to 0.0009. The combined power of discrimination and combined power of exclusion of the 15 autosomal STR loci were 0.9999999999999999964 and 0.999998243616671, respectively.

CONCLUSIONS

Population comparison revealed that the Ili Han population were lining up together with other Han populations in China while showing significant differences from other Chinese and worldwide populations.

Genetic and structural characterization of 20 autosomal short tandem repeats in the Chinese Qinghai Han population and its genetic relationships and interpopulation differentiations with other reference populations

China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%. Qinghai Province is located in the northeastern part of the Qinghai–Tibet Plateau, has an area of 72.12 km², and is the fourth largest province in China. In the present study, we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population, as well as its genetic relationships with other populations. A total of 273 alleles were identified in 2 000 individuals at 20 loci, and the allelic frequency ranged from 0.000 2 to 0.532 7. The 20 STR loci showed a relatively high polymorphic rate in the studied group. Observed and expected heterozygosities ranged 0.613 0–0.907 5 and 0.614 8–0.920 0, respectively. The combined power of discrimination, and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34, 0.999 996 0 and 0.999 999 996 5, respectively. Analyses of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian, while no significant differences were found between the Qinghai Han and Han people from Shaanxi and Jiangsu. The results of principal component analysis, multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han populations. The present results, therefore, indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications, and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.

Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population

We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.

Phylogenic analysis and forensic genetic characterization of Chinese Uyghur group via autosomal multi STR markers

We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10⁻²⁹ and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis.

Genetic structure of Tibetan populations in Gansu revealed by forensic STR loci

The origin and diversification of Sino-Tibetan speaking populations have been long-standing hot debates. However, the limited genetic information of Tibetan populations keeps this topic far from clear. In the present study, we genotyped 15 forensic autosomal short tandem repeats (STRs) from 803 unrelated Tibetan individuals from Gansu Province (635 from Gannan and 168 from Tianzhu) in northwest China. We combined these data with published dataset to infer a detailed population affinities and genetic substructure of Sino-Tibetan populations. Our results revealed Tibetan populations in Gannan and Tianzhu are genetically very similar with Tibetans from other regions. The Tibetans in Tianzhu have received more genetic influence from surrounding lowland populations. The genetic structure of Sino-Tibetan populations was strongly correlated with linguistic affiliations. Although the among-population variances are relatively small, the genetic components for Tibetan, Lolo-Burmese, and Han Chinese were quite distinctive, especially for the Deng, Nu, and Derung of Lolo-Burmese. Han Chinese but not Tibetans are suggested to share substantial genetic component with southern natives, such as Tai-Kadai and Hmong-Mien speaking populations, and with other lowland East Asian populations, which implies there might be extensive gene flow between those lowland groups and Han Chinese after Han Chinese were separated from Tibetans. The dataset generated in present study is also valuable for forensic identification and paternity tests in China.

Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui

There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China.

Genetic variability and forensic efficiency of 39 microsatellite loci in the Li ethnic group from Hainan Island in the South China Sea

BACKGROUND

Investigation of allele and genotype frequencies of microsatellite loci in various populations is an essential pre-requisite in forensic application.

AIM

The present study obtained population genetic data and forensic parameters of 39 autosomal Short Tandem Repeats (STRs) loci from a Chinese Li ethnic group and estimated the genetic relationships between Li and other reference populations.

SUBJECTS AND METHODS

Thirty-nine STR loci, which include D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSF1PO, Penta D, D2S441, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, FGA, D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D7S3048, D17S1290 and D5S2500, were amplified in two multiplex DNA-STR fluorescence detection systems for 189 unrelated healthy individuals of the Chinese Li ethnic group. The allele frequency distribution and several parameters commonly used in forensic science were statistically analysed.

RESULTS

A total of 378 alleles were observed with corresponding allelic frequencies ranging from 0.0026-0.5899. The power of discrimination and power of exclusion ranged from 0.7569-0.9672 and 0.2513-0.7355, respectively. The power of exclusion (PE) ranged from 0.2580-0.7943 for trio paternity cases and 0.1693-0.5940 for duo paternity cases. The polymorphism information content (PIC) ranged from 0.5001-0.8611. The cumulative match probability across these 39 loci was 2.4242 × 10^-38.

CONCLUSION

The results indicate that 39 STR loci are polymorphic among the Li ethnic group in Hainan Island in the South China Sea. This set of polymorphic STR loci provide highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, as well as basic population data for population genetics and anthropological research.

STR-based genetic structure of the Berber population of Bejaia (Northern Algeria) and its relationships to various ethnic groups

Patterns of genetic variation in human populations have been described for decades. However, North Africa has received little attention and Algeria, in particular, is poorly studied, Here we genotyped a Berber-speaking population from Algeria using 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA from the commercially available AmpF/STR Identifiler kit. Altogether 150 unrelated North Algerian individuals were sampled across 10 administrative regions or towns from the Bejaia Wilaya (administrative district). We found that all of the STR loci met Hardy-Weinberg equilibrium expectations, after Bonferroni correction and that the Berber-speaking population of Bejaia presented a high level of observed heterozygosity for the 15 STR system (>0.7). Genetic parameters of forensic interest such as combined power of discrimination (PD) and combined probability of exclusion (PE) showed values higher than 0.999, suggesting that this set of STRs can be used for forensic studies. Our results were also compared to those published for 42 other human populations analyzed with the same set. We found that the Bejaia sample clustered with several North African populations but that some geographically close populations, including the Berber-speaking Mozabite from Algeria were closer to Near-Eastern populations. While we were able to detect some genetic structure among samples, we found that it was not correlated to language (Berber-speaking versus Arab-speaking) or to geography (east versus west). In other words, no significant genetic differences were found between the Berber-speaking and the Arab-speaking populations of North Africa. The genetic closeness of European, North African and Near-Eastern populations suggest that North Africa should be integrated in models aiming at reconstructing the demographic history of Europe. Similarly, the genetic proximity with sub-Saharan Africa is a reminder of the links that connect all African regions.

Polymorphic distribution and forensic effectiveness study of eight miniSTR in Chinese Uyghur ethnic group

We obtained the allelic frequencies and forensic efficiency data for eight mini short tandem repeat loci including Penta E, D12S391, D6S1043, D2S1338, D19S433, CSF1PO, Penta D and D19S253 loci from a sample of 128 unrelated Uyghur individuals from China. The amplification products of the eight STR loci are <240 bp in size. A total of 94 alleles were observed and the corresponding allelic frequencies ranged from 0.0039 to 0.3438 in the present study. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. The combined power of discrimination, combined power of exclusion and combined matching probability of the eight STR loci equaled to 0.999999999963373, 0.9997770 and 3.6627 × 10(-11), respectively. Because of the small fragment length of PCR products and the high degree of polymorphisms, the eight STR loci are highly beneficial for the forensic analysis of degraded DNA samples which are commonly observed in forensic cases. The STR data of the Uyghur group were compared with the previously published population STR data of other groups from different ethnic or areas, and significant differences were observed among these groups at some loci.

A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main-island Japanese

The Sakishima islands are members of the Ryukyu island chain, stretching from the southwestern tip of the Japanese archipelago to Taiwan in the East China Sea. Archaeological data indicate cultural similarities between inhabitants of prehistoric Sakishima and Neolithic Taiwan. Recent studies based on tooth crown traits show remarkably high inter-island diversity among Ryukyu islanders, suggesting that the Sakishima islanders might have genetic backgrounds distinct from main-island Okinawa people. To investigate the genetic diversity of the Ryukyu islanders, we analyzed mtDNA, Y chromosome, and autosomal short tandem repeat loci in a sample of main-island Okinawa people and Sakishima (Miyako and Ishigaki) islanders whose participated in a previous study of tooth crown morphology. Our phylogenetic analysis of maternal (mtDNA) and paternal (Y chromosome) lineages shows that the Sakishima islanders are more closely related to people from the Japanese archipelago than to Taiwan aborigines. Miyako islanders and the Hokkaido Ainu have the first and second highest frequencies (respectively) of the Y-chromosomal Alu-insertion polymorphism, which is a presumable Jomon marker. Genetic diversity statistics show no evidence of demographic reduction or of extreme isolation in each island's population. Thus, we conclude that 1) Neolithic expansion from Taiwan did not contribute to the gene pool of modern Sakishima islanders, 2) male-lineage of the Ryukyu islanders likely shares a common ancestor with the Hokkaido Ainu who are presumably direct descendants of the Jomon people, and 3) frequent reciprocal gene flow among islands has masked the trace of common ancestry in the Ryukyu island chain.

Genetic insights into the origins of Tibeto-Burman populations in the Himalayas

The Himalayan mountain range has played a dual role in shaping the genetic landscape of the region by (1) delineating east-west migrations including the Silk Road and (2) restricting human dispersals, especially from the Indian subcontinent into the Tibetan plateau. In this study, 15 hypervariable autosomal STR loci were employed to evaluate the genetic relationships of three populations from Nepal (Kathmandu, Newar and Tamang) and a general collection from Tibet. These Himalayan groups were compared to geographically targeted worldwide populations as well as Tibeto-Burman (TB) speaking groups from Northeast India. Our results suggest a Northeast Asian origin for the Himalayan populations with subsequent gene flow from South Asia into the Kathmandu valley and the Newar population, corroborating a previous Y-chromosome study. In contrast, Tamang and Tibet exhibit limited genetic contributions from South Asia, possibly due to the orographic obstacle presented by the Himalayan massif. The TB groups from Northeast India are genetically distinct compared to their counterparts from the Himalayas probably resulting from prolonged isolation and/or founder effects.

Genetic analyzing of 15 STR loci in a Han population of Jinan (northern China)

This study reports the genetic polymorphic data of 15 autosomal STRs D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA observed in Han ethnic group living in Jinan, Shandong, China. The combined match probability and exclusion probability for 15 loci was 3.89x10(-17) and 0.99997, respectively. No mutations at these loci were found in 78 pedigrees, and Chi-test of allelic frequencies in 420 unrelated samples showed no departure from Hardy-Weinberg equilibrium at these loci. The pairwise comparisons between Jinan and 41 reference populations were performed.

A microsatellite guided insight into the genetic status of adi, an isolated hunting-gathering tribe of northeast India

Tibeto-Burman populations of India provide an insight into the peopling of India and aid in understanding their genetic relationship with populations of East, South and Southeast Asia. The study investigates the genetic status of one such Tibeto-Burman group, Adi of Arunachal Pradesh based on 15 autosomal microsatellite markers. Further the study examines, based on 9 common microsatellite loci, the genetic relationship of Adi with 16 other Tibeto-Burman speakers of India and 28 neighboring populations of East and Southeast Asia. Overall, the results support the recent formation of the Adi sub-tribes from a putative ancestral group and reveal that geographic contiguity is a major influencing factor of the genetic affinity among the Tibeto-Burman populations of India.