| Background and PurposeY-STR is a short tandem repeat consisting of 2 to 6 nucleotides located on the Y chromosome.It is unique to males and is characterized by patrilineal inheritance.Y-STR is a stable typing sequence with strong flexibility and repeatability,which has been widely used in forensic medicine,biological evolution and other studies.Y-STR plays an important role in the field of physical evidence identification,such as kinship identification,pedigree screening,male individual identification and so on.Since the same male line has the same Y chromosome haplotype（unless mutated）,and Y-STR has a high mutation rate,it presents some challenges to draw conclusions in practical application.Therefore,it is necessary to investigate the population distribution of Y-STR haplotypes,the differences between the haplotypes,and the mutation rate of each locus in different male lines in specific areas.Mutation rate is an important parameter for the application of Y-STR in human origin and evolution.In addition,the study of the factors affecting the mutation rate is helpful to elucidate the evolution of Y-STR.So far,most studies on Y-STR mutation have adopted father-son pair studies.Due to the limitation of sample size,the error of mutation rate obtained is large,and there is no obvious consistent conclusion on mutation influencing factors.In order to provide reference for the practical application of Y-STR loci in this region,we conducted this study.Methods1.Sample selection According to the principle of informed consent,720 male families were selected from the population in Zhengzhou.According to the genealogy investigation,it was determined that there was no common male ancestor among the families within six generations.One individual was selected from each family,and the polymorphism and haplotype were analyzed after Y-STR typing.2～7 individuals（1723 individuals,average 2.6 male）were selected from each pedigree.After Y-STR typing,the individuals with three or more contradictory loci were excluded for mutation analysis,which represented 4673 meiosis（generations）.2.DNA typing peripheral blood samples were collected with blood collection cards.Y-STR loci were amplified using Yfiler（?）kit and Yfiler（?）Plus kit.3.Allele frequencies were statistically analyzed by manual counting method.Gene diversity（GD）,haplotype number and haplotype diversity（HD）were calculated online using Genepop software.Pairwise comparison between haplotypes represented by 720 individuals was performed using EXCEL.The number of mutations and meiosis in the same family were counted manually.The 95%confidence interval of mutation rate was calculated online by precise method.R-software linear regression was used to study the correlation between Y-STR mutation rate and allele size（repeat number）.Chi-square test was used to study the effect of length of repeat unit and complexity of repeat sequence（simple,compound and complex）on mutation rate.Results1.Allele frequency and gene diversity.A total of 201 alleles were detected at 23single-copy loci after Y-STR testing of 720 unrelated individuals,with allele frequencies ranging from 0.0014 to 0.7833.Gene diversity ranged from 0.3593（DYS391）to 0.96043（DYS385a/b）.2.Haplotype frequency haplotype diversity.There were 715 haplotypes observed,and the unique haplotypes accounted for 98.6%of the total haplotypes.There were 5haplotypes repeated twice,respectively.The HD value of haplotype diversity was0.9999807,and the DC value of individual recognition ability was 0.9930556.3.Haplotype contrast.Among 258,840 pairings of haplotypes from 720 samples,99.87%of haplotypes differed at 7 or more loci.There were 0.0019%,0.0077%,0.0197%,0.0193%,0.0243%,0.0209%and 0.0398%at 0～6 loci,respectively.4.Mutation rate and influencing factors.A total of 101971 meiosis（generations）were recorded in 1723 samples from 720 male lineages.A total of 455 mutations were found,of which 442（97.1%）were one-step mutations.Ten mutations were two-step mutations（2.2%）,and three mutations were three-step mutations（6.6‰）.The mutation rate of Y-STR ranged from 0.3×10-3of DYS393 and DYS438(95%CI:0～1.4×10-3)to 12.3×10-3of DYS449(95%CI:8.9×10-3～16.5×10-3).The mean mutation rate was 4.5×10-3(95%CI:4.1×10-3～4.9×10-3).Allele length(R=0.2765,P=6.9×10-3)was positively correlated with mutation rate,and there was no significant difference between simple and compound repeating units（P<0.05）,while there was significant difference between compound and complex repeating units（P<0.05）.That is,the longer the allele,the more complex the repeat sequence,the greater the likelihood of mutation.No significant linear correlation was found for the length of repeats,but there were significant differences in mutation rates between y-str containing 2,3,4,and 5bp.ConclusionAll 27 Y-STR loci had good haplotype diversity in Zhengzhou population,which was suitable for the construction of Y-STR database in local population.Mutation was observed at all 27 loci in the selected families,and some loci showed high mutation rate,which laid a foundation for the application of these 27 loci in this area. |
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