Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data

The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature （IUCN）（2017）. Short tandem repeats （STRs） refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software （IobSTR）, we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals （P〈0.05, t-test）. We also found a greater number of homozygous STRs than heterozygous STRs （P〈0.05, t-test）, with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

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 0.0002 to 0.5327.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 34,0.9999960 and 0.9999999965,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.

Identification of Half‑Sisters from Different Mothers by Autosomal and X Chromosomal Short Tandem Repeats:A Case Study

Complex kinship identification such as half‑sibling identification is a difficult task in forensic biology Here we represented an approach in dealing with half‑sisters from different mothers,with the combination of autosomal and X chromosomal short‑tandem repeats(STRs)data.X chromosomal STRs can offer additional information,especially in some cases where autosomal STRs alone may not provide enough information for an accurate opinion.In this case,half‑sister or unrelated relationship between two women(S_(1)and S_(2))with different mothers were distinguished.23 autosomal and 31 X chromosomal STRs of S_(1),S_(2),S_(1)’s mother(M1),S_(2)’s mother(M2)and S_(1)’s grandmother(G1)were profiled with three different commercial kits.As to X‑chromosome STRs,likelihood ratios(LRs)were calculated by FamLinkX with consideration of linkage,linkage disequilibrium,and mutations.When only the profiles of the two individuals(S_(1)and S_(2))were available,LRs between S_(1)and S_(2)were 1.1110×10^(2)based on 23 autosomal STRs and 3.2257 om107 based on 31 X chromosomal STRs.When the maternal genotypes were taken into consideration,LRs increased to 2.5297×10^(3)and 3.0563×10^(18).Therefore,both the DNA profiles of each mothers and X chromosomal STRs are important in dealing with the identification of half‑sisters from different mothers.

Genetic Polymorphism of 38 Y-chromosome Short Tandem Repeats in Beijing Han Population from China

Objective:To investigate 38 Y-chromosome short tandem repeat(Y-STR)genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations.Materials and Methods:In the study,we selected 531 unrelated male individuals of Beijing Han,and the results were statistically analyzed by testing with GSTAR™41Y reagents.Results:The allele peak heights were balanced among the Y loci,the amplified fragment ranged from 100 to 500 bps.A total of 531 haplotypes were detected in 531 samples.Eight null genotypes were observed on locus DYS448.One and three double alleles were observed on single-copy locus DYS576 and DYS19,respectively.DYS385 a/b,DYF387S1 a/b,and DYS527 a/b were more common in double copies,but 3,13,and 11 triple alleles were detected,respectively.The gene diversity values of Y-STRs except DYS391,DYS438,and DYS645 were>0.5.Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han,with Rst values ranging from 0.0002 to 0.1703.Conclusion:The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification,kinship identification,Y-STR database construction,and genetic relationship research.

A NORTHWEST DATABASE MODEL OF SHORT TANDEM REPEAT LOCI IN FORENSIC MEDICINE

Objective To establish the northwest database of short tandem repeat(STR) loci in forensic medicine. Methods Bloodstains or whole blood samples were collected from the unrelated prisoners in Xi'an city. Genetic distribution for 13 STR loci and amelogenin locus were determined in prisons based on GeneScan. One primer for each locus was labeled with the fluorescent by 5 FAM, JOE, or NED. The forensic database were generated by using multiple amplification, GeneScan, genotype, and genetic distribution analysis. Results 113 alleles and 302 genotypes were observed, with the corresponding frequency between 0.0050-0.5250 and 0.0100-0.4100. The mean H was 0.7667. The accumulative DP was 0.9999999,. The accumulative EPP was 0.9999999. The scope of PIC was 0.6036- 0.8562 . PM was less than 10 -11 . The observed and expected genotype frequencies were evaluated using χ 2 test and all were in accordance with Hardy Weinberg equilibrium ( P > 0.05 ). Conclusion STR loci is an ideal genetic marker with powerful polymorphism and stable heredity. It can be used for individual identification and paternity in forensic medicine. The forensic DNA database model can be established successfully.

Carrier Detection and Presymptomatic Identification of Wilson Disease in Chinese by Non-Isotopic Linkage Analysis with Four Short Tandem Repeat Polymorphisms

Summary: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. To establish an efficient, accurate and fast diagnostic method for carrier detection and presymptomatic identification of WD in Chinese population, we studied haplotypes of short tandem repeat (STR) polymorphisms flanking the WD gene in 40 Chinese WD families. The results suggested that this genetic diagnosis system based on the four STR polymorphisms is of high value for the detection of potential carriers and WD homozygotes in families with at least one previously affected child. It is an efficient, accurate and fast diagnostic method that can be well suited for routine use in clinical laboratories.

Application of Short Tandem Repeat in Prenatal Diagnosis for Phenmylketonuria during the First Trimester

Objective : To find a simple and rapid way far the prenatal diagnosis of phenyUce-tonuria (PKU) during the first trimester in order to prevent inborn PKU patients as early as possible. Methods :DNA was extracted respectively from the Mood sampleps of 9 families' members and chori-onic tissues of 9 embryoes by cliorionic vittus sampling (CVS). The independent short tandem repeat (STR) alleles of members in 9 families with classic form of PKU were analyzed and prenatal diagnosis were conducted using polymerase chain reaction (PCR) together with denaturing gradient gel elec-trophoresis(DGGE)and silver dyeing. Results-.We identified 1 embryo with PKU, 2 normal individuals and 5 carriers among 9 subjects. Conclusion: Prenatal diagnosis for PKU by STR is available in the first trimester. This procedure was promising and would be widely used in Chinese population.

Genetic Polymorphism and Relationship Analyses of Standard Poodle and Bichon Frise Groups Based on 19 Short Tandem Repeat Loci

Context:As the increasing number of pet canines,the identification of canine has attracted much attentions in the forensic field,however,the genetic diversities of pet canines still remained unknown.Aims:To explore genetic polymorphisms of 19 short tandem repeat(STR)loci and genetic relationships between the two studied canine groups and reference group.Subjects and Methods:In the present study,genetic polymorphisms of 19 STR loci and a sex-linked zinc finger locus were analyzed in a total of 594 canines in Standard Poodle and Bichon Frise groups from China.Results:A total of 166,159 alleles were observed in the Standard Poodle,Bichon Frise groups with the corresponding allelic frequencies ranging from 0.0030-0.6108 to 0.0012-0.6148,respectively.The combined discrimination power and probability of exclusion of 19 STR loci in Standard Poodle and Bichon Frise groups were 0.9999999999999497,0.999962884;and 0.99999999999999995,0.999965955,respectively.Furthermore,the genetic distances between the two canine groups and Labrador retriever group were calculated,and the results indicated that Standard Poodle and Bichon Frise groups showed a closer genetic relationship,while the two canine groups had distant genetic relationships with Labrador retriever group.The result of population genetic structure revealed that genetic component distributions in the three canine groups were different.The predicted accuracies of the constructed random forest prediction model for three validation sets(25%individuals randomly selected from three populations with 808 individuals)were higher than 0.9,especially for the individuals in validation set from the Bichon Frise group is 1.Conclusions:The 19 STR loci could be used for individual identification,canine breed identification and paternity testing in the two canine groups.

A Brief Review of Short Tandem Repeat Mutation

Short tandem repeats （STRs） are short tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp. Because of their polymorphisms and high mutation rates, STRs are widely used in biological research. Strand-slippage replication is the predominant mutation mechanism of STRs, and the stepwise mutation model is regarded as the main mutation model. STR mutation rates can be influenced by many factors. Moreover, some trinucleotide repeats are associated with human neurodegenerative diseases. In order to deepen our knowledge of these diseases and broaden STR application, it is essential to understand the STR mutation process in detail. In this review, we focus on the current known information about STR mutation.

Comparison of STR polymorphism among a Kirgiz ethnic group from Sinkiang and other groups

Objective To study the genetic relationship between Kirgiz individuals living in Sinkiang China and analyze the difference among Kirgiz and the other population with STR polymorphisms.Methods PCR amplification was performed using PE9700,the PCR products were typed by automated sequencer and genescan.Results A database of nine STR loci of Kirgiz was established.It shows there are at least 73 STR alleles and 191 genotypes in Kirgiz.Genotype frequencies distribution showed no deviation from Hardy-Weinberg equilibrium by χ2-test.Kirgiz was compared with the other Chinese ethnic groups,then the American Black and the White.Conclusion These results suggested that the nine STR loci and Amelogenin locus were very useful in human identification,biological archaeology and gene resource studies.

Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05×10-10 within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.

Association Studies of 3 Candidate Genes with Type 2 Diabetes Mellitus in a Chinese Population

Objectives To explore the relationship between the polymorphisms of the selected short tandem repeats (STRs) of the candidate genes and type 2 diabetes mellitus (DM) in a Chinese population,the role of genetic and environmental factors in the development of type 2 diabetes. Methods STRs including D11S916 of uncoupling protein 3 (UCP3) gene,binucleotide repeat (CA)n within intron 6 [HSLi6(CA)] of hormone-sensitive lipase(HSL)gene and D20S501 of protein tyrosine phosphatase-1B (PTP-1B)gene polymorphisms were detected, by poiymerase chain reaction(PCR) ,poly-acrylamide gel electrophoresis and silver staining in 106 patients with type 2 DM and 102 control subjects. Results The allele distribution of UCP3 and HSL gene differed significantly between patients with type 2 diabetes and control subjects (X2 = 26. 12,P<0. 005; X2 = 10. 33,P<0. 005,respectively). For UCP3 and HSL gene,the frequencies of alleles A6,A7,A8 and allele B9 were much higher in diabetic patients than in control subjects (0. 090 vs 0. 020,P<0. 005; 0. 109 vs 0. 015,P <0. 005; 0. 033 vs 0. 000,P<0. 05; 0. 033 vs 0. 005,P<0. 05,respectively),while the frequencies of allele A1 and allele B5 were lower in diabetic patients than in control subjects (0. 090 vs 0. 206,P<0. 005; 0. 057 vs 0. 118,P<0. 05,respectively). At D20S501 locus,The allele distribution of PTP-1B gene had no significant difference in two groups (X2 = 3. 77, P>0. 05). Multi-variate logistic regression analysis showed positive correlation between alleles A6,A7 of UCP3 gene,systolic blood pressure, apolipoprotein B, lipoprotein (a) and type 2 diabetes. Conclusion Our data show that D11S916 of UCP3 gene and HSLi6(CA) of HSL gene polymorphisms are associated with type 2 diabetes in Chinese suggesting that UCP3 and HSL might represent susceptibility genes for type 2 diabetes. D20S501 of PTP-IB gem polymorphism is not associated with type 2 diabetes in Chinese. Alleles A6, A7 of UCP3 gene, systolic blood pressure, apolipoprotein B,Upoprotein (a) may play some role in the development of type 2 diabetes.

POLYMORPHISM OF THE vWF LOCUS AND ITS FORENSIC APPLICATION IN COMPACT BONE

The allele rrequencles or the vWF locus were determined in a chinese Han populationsample (n=112) using the polymerase chain reaction (PCR). 7 alleies and 23 genotypes were observed. Distribution of allellc frequencies in our data showed a different pattern from those reportedin the literature ror European Caucasians. No deviation from Hardy--Weinberg equilibrium wasfound. The observed heterozygoslty was 79. I %. The vWF Is one of the useful genetic markers forpaternity testing and identity testing, with an exclusion power (EP) value or 0. 7337 and a discrimination power (DP) value of 0. 9438. The results of compact bone and dens were in perrect agreementwith those of the blood and blood stains.

THE STUDY OF POPULATION GENETIC RELATION AMONG TEN ETHNIC GROUPS IN NORTHWEST CH INA

Objective To investigate the genetic relation am on g ten ethnic groups in northwest China. Methods Allele frequ encies of six STR(short tandem repeat ) loci in D13S1358, VWA, FGA, D5S818, D13S 317, and D7S820 were collected from Lasa Tibetan, Changdu Tibetan, Xi'an Han, G ansu Dongxiang, Gansu Yugu, Xinjiang Uygur, Ozbak, Kirgiz, Sibe, Ningxia Hui by the results of State Key laboratory, Forensic Science Department, school of medi cal, Xi'an Jiaotong University and internet biological information data bank, a nd compared with that of the Mongolian, Zhuang in China, and White and Negro in USA. The polymorphism index (H, DP, PPE, PIC) and genetic distance, then the phy logenetic tree of all population were reported. Results The res ulting tree topology exhibited strong geographic and racial partitioning consist ent with that obtained with HLA and classical genetic polymorphisms. Conclusion The results suggest that forensic STR loci may be particular ly powerful tools and provide the necessary fine resolution for the reconstructi on of recent human evolutionary history.

The development and application of a multiplex short tandem repeat(STR)system for identifying subspecies,individuals and sex in tigers

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world’s last remaining wild tigers.Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species.We developed a multiplex genotyping system“tigrisPlex”to simultaneously assess 22 short tandem repeat(STR,or microsatellite)loci and a gender-identifying SRY gene,all amplified in 4 reactions using as little as 1 ng of template DNA.With DNA samples used for between-run calibration,the system generates STR genotypes that are directly compatible with voucher tiger subspecies genetic profiles,hence making it possible to identify subspecies via bi-parentally inherited markers.We applied“tigrisPlex”to 12 confiscated specimens from Russia and identified 6 individuals(3 females and 3 males),each represented by duplicated samples and all designated as Amur tigers(Panthera tigris altaica)with high confidence.This STR multiplex system can serve as an effective and versatile approach for genetic profiling of both wild and captive tigers as well as confiscated tiger products,fulfilling various conservation needs for identifying the origins of tiger samples.

Genotypic diagnosis of long QT syndrome by analysis of candidate genes

Objective To diagnose 6 LQTS families by genetic analysis.Methods A total aof 6 LQTS pedigrees with 43 family members were brought together for genetic diagnosis by using short-sequence tandem-repeat(STR)markers or sequencing.Genomic DNA was extracted from blood samples by standard procedure.STR markers or KCNQ1,KCNH2 and SCN5A were amplified.The haplotype analysis for LQTS was performed.If the family got the negative haplotype analysis,the sequencing was performed.Results LQTS patients were always linkaged with the SCN5A gene in family 1.KCNH2 was linkaged with the disease in family 2 to 5.21 gene carriers were identified from these 5 families.A mutation(A561V-KCNH2)was only found in the proband of family 6 and an SNP(G1691A)was found in all the members of the family.Conclusion Genetic diagnosis can not only improve presymptomatic diagnosis,but also provide the basis for personal therapy and research on disease-causing mutations.