Genetic Polymorphisms For STR Loci In Chongqing Han Ethnicity And Phylogenetic Structure Exploration Among Chinese And Global Populations

Objective:To investigate the genetic polymorphisms and forensic effectiveness of autosomal short tandem repeats（STRs）in Chongqing Han population,and enrich the Chinese local forensic reference database,we genotyped 19 STR loci（D8S1179,D21S11,D7S820,CSF1PO,D3S1358,TH0l,D13S317,D16S539,D2S1338,D19S433,vWA,TPOX,18S51,D5S818,FGA,D6S1043,Penta D,Penta E,and D12S391）in 671unrelated Chongqing Han individuals.Additionally,to dessect the genetic relationships among populations along ethnic/geographical/linguistic divisions,we integrated our data with 58 Chinese nationwide populations and 50 worldwide populations in the comprehensive population comparisons.Methods:A total of 671 blood stains were obtained from Chongqing Han population,genomic DNA was extracted using the Chelex 100protocol,19 autosomal STR loci included in the Goldeneye^TM 20A PCR amplification kit were co-amplified.The amplified products were segregated and detected by capillary electrophoresis on an ABI 3130Genetic Analyzer and raw data analysis was performed using the GeneMapper ID 3.2 software.Allele frequencies and corresponding forensic statistical parameters were calculated in the Modified-powerstat.The Hardy-Weinberg equilibrium and Linkage disequilibrium were evaluated in the Arlequin Version 3.5.In Chinese population comparisons and polygenetic analyses,a total of 59 reference populations coming from different administrative or ethnic divisions were employed.Principal component analysis（PCA）based on allele frequency distribution was carried out in MVSP.Three different genetic distances（Nei’s genetic distance,Cavalli-Sforza genetic distance,and Reynold’s genetic distance）among 59 Chinese populations were computed using Phylip 3.695 based on allelic frequency and deliberated by the neighbor joining tree in Mega 7.0to explore the genetic differentiation.Three genetic distance matrixes were visualized as multidimensional scaling plots in the SPSS software.A total of 51 global populations were also employed to explore phylogenetic structure using aforementioned same methods.Results:All 19 STR loci were identified in agreement with the Hardy-Weinberg equilibrium and no evidence of linkage disequilibrium was found.A total of 238 alleles were observed with corresponding allele frequencies that varied from 0.0007 to 0.5119.The combined power of discrimination and the combined probability of exclusion for 19 STR loci in the Chongqing Han population were 0.99999999999999999999998954and 0.99999998387,respectively.The large genetic distances were observed between the Chongqing Han and Xinjiang Kazakh,followed by Xinjiang Uyghur.However,short genetic distances were found between the Chongqing Han and Sichuan Han,followed by Yungui Han.In Chinese population comparisons and polygenetic analyses,Altaic-speaking populations clustered together and Tibeto-Burmese-speaking populations clustered together.The other populations were clustered in two major groups:one group consisted of mainly North-China populations,the other comprised mainly South-China populations clustered together.In polygenetic analyses of global populations,different geographic populations clustered together respectively.Conclusion:The 19 autosomal STR loci were highly polymorphic in the Chongqing Han population and can be used as a powerful tool in personal identification and parentage testing.Genetic heterogeneity existed among the North-China populations and the South-China populations.Genetic similarity existed among Altaic-speaking populations,and also appeared among Tibeto-Burmese-speaking populations.The same geographic original populations have relatively close genetic relationship with each other.The results indicated that genetic affinity were tightly associated with geographic location,linguistic and ethnic origin.