Analysis Of Genetic Polymorphism And Population Genetic Structure Of 57 Autosomal InDel Loci In Sichuan Qiang Population

Objective:To evaluate the forensic application of 57 autosomal insertion/deletion polymorphic loci in the AGCU InDel 60 fluorescence detection kit in the Qiang population of Beichuan,Sichuan Province.To explore the genetic relationships between the Sichuan Qiang and 26 known populations.Method:1 Sample Collection:Blood traces were randomly collected from 200 unrelated healthy individuals in Sichuan,Sichuan Province using FTA blood cards,of which 171 were males and 29 were females.Ten sets of blood samples of triadic family lines were collected with FTA cards from the accumulation of daily examination cases at the Judicial Identification Center of North Sichuan Medical College.2 PCR amplification:PCR amplification of collected blood samples was performed using the direct amplification method according to the instructions of the AGCU InDel 60Fluorescence Assay Kit.3 InDel typing:The PCR amplification products were subjected to capillary electrophoresis in an AB 3500 Genetic Analyzer,and InDel typing was performed using GeneMapper(?)ID-X 1.4 software to record data for each sample.4 Collection of comparative population genetics data:genetic data were obtained for 26 other populations in the Thousand Genome Project Phase Ⅲdatabase,including five populations in East Asia,five in South Asia,five in Europe,four in the Americas,and seven in Africa.5 Statistical analysis:allele frequencies,probability of individual identification(PD),and polymorphic information content(PIC)were calculated for 57 autosomal InDel loci using Modified-Powerstats standard version software;Cervus 3.0.7 software was used to calculate expected heterozygosity(He),observed heterozygosity(Ho),triplet probability of non-parental exclusion(PEtrio)and diploid probability of non-parental exclusion(PEduo);Arlequin 3.5.2.2 software was used to perform Hardy-Weinberg equilibrium test(HWE),linkage disequilibrium(LD)analysis and calculate the genetic differentiation coefficient(Fst)for each locus;Phylip-3.698 software was used to calculate the Nei’s genetic distance between individual populations;based on Nei’s genetic distance,constructing phylogenetic trees of populations using MEGA5 and performing multidimensional scale analysis(MDS)using SPSS software;MVSP 3.22 software was used to perform principal component analysis(PCA);Structure2.3.4 software was used to perform cluster analysis of the populations.Results:1 All 57 autosomal InDel loci in the Sichuan Qiang population were in Hard-Weinberg equilibrium(p>0.000 88),with no linkage disequilibrium among the loci(p>0.000 031),as corrected by the Bonferroni method.2 The 57 A-InDel loci had high genetic polymorphism in the Sichuan Qiang,with deletion allele frequencies ranging from 0.2725 to 0.7600 and insertion allele frequencies ranging from 0.2400 to 0.7275,the cumulative individual identification probability of 1-2.9748×10-24,cumulative duplex non-parental exclusion probability of 0.999062660,and cumulative triplet non-parental exclusion probability was 0.999999999.3 A study of the genetic relationships between the Sichuan Qiang and 26 populations showed that the Sichuan Qiang had the fewest statistically distinct loci from the Beijing Hanand Southern Han,and the most statistically distinct loci from 2 African populations,the Barbadosand Yoruba.The population genetic results obtained using phylogenetic trees,multidimensional scale analysis,principal component analysis and population cluster analysis were similar,all showing that the Sichuan Qiang were genetically related to the Beijing Han and Southern Han,and genetically distant from seven African groups including the Barbados,Southwestern African American and Nigerian Esan.Conclusion:1 The 57 autosomal InDel loci contained in the AGCU InDel 60 fluorescence assay kit have good genetic polymorphism in the Sichuan Qiang population and can be used as a useful supplement to forensic conventional STR typing kits.2 The Sichuan Qiang are genetically most closely related to the Beijing Han and Southern Han groups and most distantly related to the African group.