| Aims and objectives1.To analyze the genetic polymorphism of 19 autosomal STR loci and 17 Y-chromosomal STR(Y-STR)loci of Ludong,Luzhong-Luxibei and Luxinan-Lunan populations and provide theoretical data for individual identification,paternity tests and population genetics research of these three Shandong populations.2.To study the genetic distance and genetic relationships among three Shandong Han populations.3.To study the genetic distance and genetic relationships between three Shandong Han populations and other Chinese populations.Methods1.Samples were collected from 1044 unrelated and healthy Han individuals residing in one of three Shandong regions for at least three generations.All of 1044 samples were analysed using autosomal STR loci and 356 male samples were analysed with Y-STR loci.2.DNA was extracted by Chelex-100 method.Autosomal STR and Y-STR loci were amplified with a GoldeneyeTM DNA identification system 20A kit and an AmpFISTR Yfiler PCR amplification kit,respectively.Amplification products were denatured,and then electrophoresed on an Applied BiosystemsTM 3500 Series Genetic Analyzer.Raw data were analysed using GeneMapper(?)ID-X software v1.3.3.Modified-PowerStates software was used to detect whether 19 autosomal STR loci could satisfy the Hardy-Weinberg equilibrium and to analyse allelic frequencies and genetic parameters of 19 autosomal STR loci of Ludong,Luzhong-Luxibei and Luxinan-Lunan populations.The genetic distance(Fst values)and the corresponding P-values among three different Shandong populations were calculated using Arlequin v3.5 software.4.Allelic and haplotype frequencies of 17 Y-STR loci were estimated using Arlequin v3.5 software.The genetic diversity and haplotype diversity were calculated according to Nei's formula.The discrimination capacity was defined as the ratio between the number of different haplotypes and total haplotypes.Pairwise genetic distance(Rst values)and the corresponding P-values were measured by the analysis of molecular variance(AMOVA)and visualized in a multi-dimensional scaling(MDS)plot via the Y-STR Haplotype Reference Database(YHRD)online tools.5.Neighbour-joining trees were conducted with the MEGA v4.0 software based on the Fst and Rst matrix.6.A heat map was drawn on the basis of Fst matrix using software R v2.11.Results1.After employing a Bonferroni correction,no significant differences were found between observed values and expected values of genetic profiles in all 19 autosomal STR loci among three Shandong populations,and full dataset satisfied the HWE(P>0.05/57=0.000877;57 is the test number).2.Of 19 autosomal STR loci,fifteen(D19S433,D5S818,D21S11,D18S51,D6S1043,D13S317,D7S820,D16S539,Penta D,vWA,D8S1179,Penta E,D12S391,D2S1338,FGA)were detected with values of heterozygosity greater than 0.7,values of polymorphism information content greater than 0.7,and values of discrimination power greater than 0.9 in all three Shandong populations,while the other four loci(D3S1358,CSF1PO,TPOX and TH01)did not meet the above criteria.The average values of combined power of discrimination and combined power of exclusion of 19 autosomal STRs were calculated to be 0.9999999999999999999999685 and 0.99999748,respectively.3.Of the 17 Y-STR loci,fourteen(DYS389?,DYS439,DYS389?,DYS456,DYS458,DYS635,DYS448,Y_GATA_H4,DYS19,DYS392,DYS393,DYS390,DYS385a/b)had high genetic polymorphism with the average value of genetic diversity higher than 0.5 in three Shandong Han populations while the locus DYS391,DYS437 and DYS438 lower than 0.5.4.In the autosomal STR analysis,Luzhong-Luxibei and Luxinan-Lunan were closest(Fst=0.00016),followed by Ludong and Luxinan-Lunan(Fst=0.00036),and Ludong and Luzhong-Luxibei were farthest(Fst=0.00066).In the Y-STR analysis,Luzhong-Luxibei and Luxinan-Lunan were closest(Rst=0.0034),followed by Ludong and Luzhong-Luxibei(Rst=0.0038)and Ludong and Luxinan-Lunan(Rst=0.0051).5.After employing a Bonferroni correction,no statistically significant differences were observed among three Shandong Han populations in both the autosomal STR and Y-STR analyses(P?0.05/3=0.0167,3 is the test number).6.In the autosomal STR analysis,significant differences were only detected between three Shandong Hans and Qinghai Tibetan as well as Xinjiang Uygur populations(P?0.05/87=0.00057471,87 is the test number),but none were found between three Shandong Hans and other reference populations(P?0.00057471).7.In the Y-STR analysis,three Shandong Han populations did not differ significantly either from most Han populations(P?0.05/93=0.00053763,93 is the test number)or from minority ethnic groups like Xibe,Manchu and Bouyei(P?0.00053763),but they differ significantly from all other seven reference ethnic minorities(P<0.00053763).Conclusions1.Both the detection system composed of 19 autosomal STR loci and that composed of 17 Y-STR loci are highly polymorphic in three Shandong Han populations,and they are suitable for forensic identification and population genetics of Shandong populations.2.Among three Shandong populations,Luzhong-Luxibei and Luxinan-Lunan population have the nearest genetic distance,while Ludong and the other two Shandong populations have the comparatively far genetic distance.No significantly genetic differences are observed among three Shandong populations.These three Shandong Hans showed remarkable homogeneity.3.In autosomal STR analysis,significantly genetic differences are only found between three Shandong Han populations and Qinghai Tibetan as well as Xinjiang Uygur.In Y-chromosomal STR analysis,three Shandong Hans do not differ significantly from the majority of Chinese Han populations,but they differ significantly from most ethnic minorities. |
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