Analysis of two susceptibility SNPs in HLA region and evidence of interaction between rs6457617 in <Emphasis Type="BoldItalic">HLA-DQB1</Emphasis> and <Emphasis Type="BoldItalic">HLA-DRB1</Emphasis>*04 locus on Tunisian rheumatoid arthritis

Previous genomewide association studies (GWAS) and meta-analyses have enumerated several genes/loci in major histocompatibility complex region, which are consistently associated with rheumatoid arthritis (RA) in different ethnic populations. Given the genetic heterogeneity of the disease, it is necessary to replicate these susceptibility loci in other populations. In this case, we investigate the analysis of two SNPs, rs13192471 and rs6457617, from the human leukocyte antigen (HLA) region with the risk of RA in Tunisian population. These SNPs were previously identified to have a strong RA association signal in several GWAS studies. A case–control sample composed of 142 RA patients and 123 healthy controls was analysed. Genotyping of rs13192471 and rs6457617 was carried out using real-time PCR methods by TaqMan allelic discrimination assay. A trend of significant association was found in rs6457617 TT genotype with susceptibility to RA (\(P = 0.04\), \(p_{c} = 0.08\), \(\hbox {OR} = 1.73\)). Moreover, using multivariable analysis, the combination of rs6457617*TT–HLA-DRB1*\(04^{+}\) increased risk of RA (\(\hbox {OR} = 2.38\)), which suggest a gene–gene interaction event between rs6457617 located within the HLA-DQB1 and HLA-DRB1. Additionally, haplotypic analysis highlighted a significant association of rs6457617*T–HLA-DRB1*\(04^{+}\) haplotype with susceptibility to RA (\(P = 0.018\), \(p_{c} = 0.036\), \(\hbox {OR} = 1.72\)). An evidence of association was shown subsequently in \(\hbox {antiCCP}^{+}\) subgroup with rs6457617 both in T allele and TT genotype (\(P = 0.01\), \(p_{c} = 0.03\), \(\hbox {OR} = 1.66\) and \(P = 0.008\), \(p_{c} = 0.024\), \(\hbox {OR} = 1.28\), respectively). However, no association was shown for rs13192471 polymorphism with susceptibility and severity to RA. This study suggests the involvement of rs6457617 locus as risk variant for susceptibility/severity to RA in Tunisian population. Secondly, it highlights the gene–gene interaction between HLA-DQB1 and HLA-DRB1.     

Oestrogen regulates the expression of cathepsin E-A-like gene through ER$$\upbeta $$ in liver of chicken ( Gallus gallus)

The cathepsin E-A-like, also known as ‘similar to nothepsin’, is a new member of the aspartic protease family, which may take part in processing of egg yolk macromolecules, due to it was identified in the chicken egg-yolk. Previously, studies have suggested that the expression of cathepsin E-A-like increased gradually during sexual maturation of pullets, but the exact regulation mechanism is poorly understood. In this study, to gain insight into the function and regulation mechanism of the gene in egg-laying hen, we cloned the cathepsin E-A-like gene and evaluated its evolutionary origin by using both phylogenetic and syntenic methods. The mode of the gene expression regulation was analysed through stimulating juvenile hens with \(17\upbeta \)-estradiol and chicken embryo hepatocytes with \(17\upbeta \)-estradiol combined with oestrogen receptor antagonists including MPP, ICI 182,780 and tamoxifen. Our results showed that cathepsin E-A-like was an orthologoues gene with nothepsin, which is present in birds but not in mammals. The expression of cathepsin E-A-like significantly increased in a dose-dependent manner after the juvenile hens were treated with \(17\upbeta \)-estradiol (\(P~<~0.05\)). Compared with the \(17\upbeta \)-estradiol treatment group, the expression of cathepsin E-A-like was not significantly changed when the hepatocytes were treated with \(17\upbeta \)-estradiol combined with MPP (\(P~<~0.05\)). In contrast, compared with the \(17\upbeta \)-estradiol combined with MPP treatment group, the expression of cathepsin E-A-like was significantly downregulated when the hepatocytes were treated with \(17\upbeta \)-estradiol combined with tamoxifen or ICI 182,780 (\(P~<~0.05\)). These results demonstrated that cathepsin E-A-like shared the same evolutionary origin with nothepsin. The expression of cathepsin E-A-like was regulated by oestrogen, and the regulative effect was predominantly mediated through ER-\(\upbeta \) in liver of chicken.     

Association of <Emphasis Type="BoldItalic">lactase</Emphasis> 13910 C/T polymorphism with bone mineral density and fracture risk: a meta-analysis

A number of studies have investigated the association of lactase (LCT, C/T-13910) gene polymorphism with bone mineral density (BMD) and fracture risk, but previous results were inconclusive. In this study, a meta-analysis was performed to quantify the association of LCT (C/T-13910) polymorphism with BMD and fracture risk. Eligible publications were searched in the PubMed, Web of Science, Embase databases, Google Scholar, Yahoo and Baidu. Pooled weighed mean difference (WMD) or odds ratio (OR) with their 95% confidence interval (CI) were calculated using a fixed-effects or random-effects model. A total of nine articles with 8871 subjects were investigated in the present meta-analysis. Overall, the TT/TC genotypes of LCT 13910 C/T polymorphism showed significantly higher BMD than those with the CC genotype at femur neck (FN) (\(\hbox {WMD} = 0.011\,\hbox {g/cm}^{2}\), 95% CI \(=\) 0.004–0.018, \(P = 0.003\)). Besides, LCT 13910 C/T polymorphism may decrease the risk of any site fractures (for TT versus TC \(+\) CC, OR \(=\) 0.813, 95% CI \(=\) 0.704–0.938, \(P = 0.005\); for T allele versus C allele, OR \(=\) 0.885, 95% CI \(=\) 0.792–0.989, \(P = 0.032\)). However, there was no significant association of LCT 13910 C/T polymorphism with BMD at lumbar spine and risk of vertebral fractures under all genetic contrast models (all P values were \({>}0.05\)). The meta-analysis suggests that there are significant effects of LCT 13910 C/T polymorphism on BMD and fracture risk. Large-scale studies with different ethnic populations will be needed to further investigate the possible race-specific effect of LCT 13910 C/T polymorphism on BMD and fracture risk.     

Glutathione <Emphasis Type="BoldItalic">S</Emphasis>-transferase P1 gene polymorphisms and susceptibility to coronary artery disease in a subgroup of north Indian population

The present study aimed to investigate the association of \(\hbox {g}.313\hbox {A}{>}\hbox {G}\) and \(\hbox {g}.341\hbox {C}{>}\hbox {T}\) polymorphisms of GSTP1 with coronary artery disease (CAD) in a subgroup of north Indian population. In the present case–control study, CAD patients (\(n = 200\)) and age-matched, sex-matched and ethnicity-matched healthy controls (\(n = 200\)) were genotyped for polymorphisms in GSTP1 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Genotype distribution of \(\hbox {g}.313\hbox {A}{>}\hbox {G}\) and \(\hbox {g}.341\hbox {C}{>}\hbox {T}\) polymorphisms of GSTP1 gene was significantly different between cases and controls (\(P = 0.005\) and 0.024, respectively). Binary logistic regression analysis showed significant association of A/G (odds ratio (OR): 1.6, 95% CI: 1.08–2.49, \(P = 0.020\)) and G/G (OR: 3.1, 95% CI: 1.41–6.71, P \(=\) 0.005) genotypes of GSTP1 \(\hbox {g}.313\hbox {A}{\!>\!}\hbox {G}\), and C/T (OR: 5.8, 95% CI: 1.26–26.34, \(P = 0.024\)) genotype of GSTP1 \(\hbox {g}.341\hbox {C}{>}\hbox {T}\) with CAD. The A/G and G/G genotypes of \(\hbox {g}.313\hbox {A}{>}\hbox {G}\) and C/T genotype of \(\hbox {g}.341\hbox {C}{>}\hbox {T}\) conferred 6.5-fold increased risk for CAD (OR: 6.5, 95% CI: 1.37–31.27, \(P = 0.018\)). Moreover, the recessive model of GSTP1 \(\hbox {g}.313\hbox {A}{>}\hbox {G}\) is the best fit inheritance model to predict the susceptible gene effect (OR: 2.3, 95% CI: 1.11–4.92, \(P = 0.020\)). In conclusion, statistically significant associations of GSTP1 \(\hbox {g}.313\hbox {A}{>}\hbox {G}\) (A/G, G/G) and \(\hbox {g}.341\hbox {C}{>}\hbox {T}\) (C/T) genotypes with CAD were observed.     

Invasions Slow Down or Collapse in the Presence of Reactive Boundaries

Motivated by the propagation of thin bacterial films around planar obstacles, this paper considers the dynamics of travelling wave solutions to the Fisher–KPP equation \(u_t = u(1-u) + u_{xx} + u_{yy}\) in a planar strip \(-\infty< x < \infty \), \(0 \le y \le L\). We examine the propagation of fronts in the presence of a mixed boundary condition (also referred to as a ‘partially absorbing’ or ‘reactive’ boundary) \(u_y = \alpha u\), with \(\alpha >0\), at \(y=0\). The presence of boundary conditions of this kind leads to the development of front solutions that propagate in x but contain transverse structure in y. Motivated by the observation that the speed of propagation in the Fisher–KPP equation is determined (for exponentially decaying initial conditions) by the behaviour at the leading edge, we analyse the linearised Fisher–KPP equation in order to estimate the speed of the stable travelling front, a function of the width L and the imposed boundary conditions. For wide strips the speed estimate based on the linearised equation agrees well with the results of numerical simulations. For narrow channels numerical simulations indicate that the stable front propagates more slowly, and for sufficiently small L or sufficiently large \(\alpha \) the front speed falls to zero and the front collapses. The reason for the collapse is the non-existence, far behind the front, of a stable positive equilibrium solution u(x, y). While existence of these equilibrium states can be demonstrated via phase plane arguments, the investigation of stability is similar to calculations of critical patch sizes carried out in similar ecological models.     

Identification and association of novel lncRNA <Emphasis Type="BoldItalic">pouMU1</Emphasis> gene mutations with chicken performance traits

The biological functions of long noncoding RNAs (lncRNAs), which play an important role in regulating development and gene expression, may be affected by variations in lncRNA gene loci or associated genomic sequences. However, the functions of many lncRNAs remain unknown. To analyse correlations between mutations in pouMU1 with chicken growth and carcass traits, 860 chickens from a Gushi \(\times \) Anka F2 resource population and 96 Lushi, Xichuan, Changshun and recessive white chickens were used to evaluate the genetic effect of the pouMU1 gene. We performed quantitative real-time polymerase chain reaction (qRT-PCR) to analyse the relative expression levels of pouMU1 in nine different tissues and stages of development. pouMU1 expression was highest in pectoralis and leg muscles, whereas no expression was observed in the heart, liver and abdominal fat. Using direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods, two novel sequence mutations (g.1198A>G and g.1238-1239del/insGA) were detected in the pouMU1 gene. SPSS software was used for statistical analysis in association studies. Based on the association data, the presence of both variants was significantly associated with leg muscle fibre width and leg muscle fibre roundness (\(P < 0.05\)) and highly associated with leg muscle fibre girth and body weight at 0 week of age (\(P < 0.01\)). These data suggest that pouMU1 might participate in regulating chicken muscle development and growth, and the findings offer new insight into the functions of sequence mutations in lncRNAs.     

Competition of Multiple Species in Advective Environments

We study the effect of changes in flow speed on competition of an arbitrary number of species living in advective environments, such as streams and rivers. We begin with a spatial Lotka–Volterra model which is described by n reaction–diffusion–advection equations with Danckwerts boundary conditions. Using the dominant eigenvalue \(\lambda \le 0\) of the diffusion–advection operator subject to boundary conditions, we reduce the model to a system of ordinary differential equations. We impose a “transitive arrangement” of the competitors in terms of their interspecific coefficients and growth rates, which means that in the absence of advection, we have the following situation: for all \(1\le i<j\le n\), species i out-competes species j, while species j has higher intrinsic growth rate than species i. Changing advection speed in the original spatial model corresponds to changing the value of \(\lambda \) in the spatially implicit model. Considering the cases of the odd and even n separately, we obtain explicit intervals of the values of \(\lambda \) that allow all n species to be present in the habitat (coexistence interval). Stability of this equilibrium is shown for \(n\le 4\).     

Genetic variability and structure of an isolated population of <Emphasis Type="Italic">Ambystoma altamirani</Emphasis>, a mole salamander that lives in the mountains of one of the largest urban areas in the world

Amphibians are globally threatened by habitat loss and fragmentation; species within the order Ambystoma are not the exception, as there are 18 species of mole salamanders in México, of which 16 are endemic and all species are under some national or international status of protection. The mole salamander, Ambystoma altamirani is a microendemic species, which is distributed in central México, within the trans-Mexican volcanic belt, and is one of the most threatened species due to habitat destruction and the introduction of exotic species. Nine microsatellite markers were used to determine the genetic structure, genetic variability, effective population size, presence of bottlenecks and inbreeding coefficient of one population of A. altamirani to generate information which might help to protect and conserve this threatened species. We found two genetic subpopulations with significant level of genetic structure (\(F_{\mathrm{ST}}= 0.005\)) and high levels of genetic variability (\(H_{\mathrm{o}}= 0.883\); \(H_{\mathrm{e}}= 0.621\)); we also found a small population size (\(N_{\mathrm{e}} = 8.8\)), the presence of historical (\(M =\) 0.486) and recent bottlenecks under IAM and TPM models, with a low, but significant coefficient of inbreeding (\(F_{\mathrm{IS}} = -\)0.451). This information will help us to raise conservation strategies of this microendemic mole salamander species.     

Forecasting next season’s <Emphasis Type="Italic">Ixodes ricinus</Emphasis> nymphal density: the example of southern Germany 2018

The castor bean tick, Ixodes ricinus (L.) (Ixodida: Ixodidae), is the principal vector of pathogens causing tick-borne encephalitis or Lyme borreliosis in Europe. It is therefore of general interest to make an estimate of the density of I. ricinus for the whole year at the beginning of the tick season. There are two necessary conditions for making a successful prediction: a long homogeneous time series of observed tick density and a clear biological relationship between environmental predictors and tick density. A 9-year time series covering the period 2009–2017 of nymphal I. ricinus flagged at monthly intervals in southern Germany has been used. With the hypothesis that I. ricinus density is triggered by the fructification of the European beech 2 years before, the mean annual temperature of the previous year, and the current mean winter temperature (December–February), a forecast of the annual nymphal tick density has been made. Therefore, a Poisson regression model was generated resulting in an explained variance of 93.4% and an error of \(\hbox {RMSE} = 21\) ticks per \(100\,\hbox {m}^2\) (annual \(\hbox {MEAN} = 260\) collected ticks/\(100\,\hbox {m}^2\)). An independent verification of the forecast for the year 2017 resulted in 187 predicted versus 180 observed nymphs per \(100\,\hbox {m}^2\). For the year 2018 a relatively high number of 443 questing I. ricinus nymphs per \(100\,\hbox {m}^2\) is forecasted, i.e., a “good” tick year.     

StreAM-$$T_g$$: algorithms for analyzing coarse grained RNA dynamics based on Markov models of connectivity-graphs

Background

In this work, we present a new coarse grained representation of RNA dynamics. It is based on adjacency matrices and their interactions patterns obtained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. These interactions can be represented as adjacency matrices of k nucleotides. Based on those, we define transitions between states as changes in the adjacency matrices which form Markovian dynamics. The intense computational demand for deriving the transition probability matrices prompted us to develop StreAM-\(T_g\), a stream-based algorithm for generating such Markov models of k-vertex adjacency matrices representing the RNA.

Results

We benchmark StreAM-\(T_g\) (a) for random and RNA unit sphere dynamic graphs (b) for the robustness of our method against different parameters. Moreover, we address a riboswitch design problem by applying StreAM-\(T_g\) on six long term molecular dynamics simulation of a synthetic tetracycline dependent riboswitch (500 ns) in combination with five different antibiotics.

Conclusions

The proposed algorithm performs well on large simulated as well as real world dynamic graphs. Additionally, StreAM-\(T_g\) provides insights into nucleotide based RNA dynamics in comparison to conventional metrics like the root-mean square fluctuation. In the light of experimental data our results show important design opportunities for the riboswitch.

     

Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs

Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown. To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups, \(A_\mathrm{R}\) and \(B_\mathrm{R}\), each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics. Specifically, based on a system of ordinary differential equations for \(A_\mathrm{R}\) and \(B_\mathrm{R}\), we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point, T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e., \(f \Delta t\)-long for DrugA and \((1-f) \Delta t\)-long for DrugB with \(0 \le f \le 1\) and \(\Delta t \ge 0\)). We prove that the optimal duration of the initial stage, in which the first drug is administered, T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition. We further analyzed the relationship between population makeup, \(\mathcal {A/B} = A_\mathrm{R}/B_\mathrm{R}\), and the effect of each drug. We determine a critical ratio, which we term \(\mathcal {(A/B)}^{*}\), at which the two drugs are equally effective. As the first stage of the optimal strategy is applied, \(\mathcal {A/B}\) changes monotonically to \(\mathcal {(A/B)}^{*}\) and then, during the second stage, remains at \(\mathcal {(A/B)}^{*}\) thereafter. Beyond our analytic results, we explored an individual-based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.     

An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding

Background

The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known \(O(n^3)\)-time dynamic programming method. Recently three methodologies—Valiant, Four-Russians, and Sparsification—have been applied to speedup RNA secondary structure prediction. The sparsification method exploits two properties of the input: the number of subsequence Z with the endpoints belonging to the optimal folding set and the maximum number base-pairs L. These sparsity properties satisfy \(0 \le L \le n / 2\) and \(n \le Z \le n^2 / 2\), and the method reduces the algorithmic running time to O(LZ). While the Four-Russians method utilizes tabling partial results.

Results

In this paper, we explore three different algorithmic speedups. We first expand the reformulate the single sequence folding Four-Russians \(\Theta \left(\frac{n^3}{\log ^2 n}\right)\)-time algorithm, to utilize an on-demand lookup table. Second, we create a framework that combines the fastest Sparsification and new fastest on-demand Four-Russians methods. This combined method has worst-case running time of \(O(\tilde{L}\tilde{Z})\), where \(\frac{{L}}{\log n} \le \tilde{L}\le min\left({L},\frac{n}{\log n}\right)\) and \(\frac{{Z}}{\log n}\le \tilde{Z} \le min\left({Z},\frac{n^2}{\log n}\right)\). Third we update the Four-Russians formulation to achieve an on-demand \(O( n^2/ \log ^2n )\)-time parallel algorithm. This then leads to an asymptotic speedup of \(O(\tilde{L}\tilde{Z_j})\) where \(\frac{{Z_j}}{\log n}\le \tilde{Z_j} \le min\left({Z_j},\frac{n}{\log n}\right)\) and \(Z_j\) the number of subsequence with the endpoint j belonging to the optimal folding set.

Conclusions

The on-demand formulation not only removes all extraneous computation and allows us to incorporate more realistic scoring schemes, but leads us to take advantage of the sparsity properties. Through asymptotic analysis and empirical testing on the base-pair maximization variant and a more biologically informative scoring scheme, we show that this Sparse Four-Russians framework is able to achieve a speedup on every problem instance, that is asymptotically never worse, and empirically better than achieved by the minimum of the two methods alone.

     

A Malaria Transmission Model with Temperature-Dependent Incubation Period

Malaria is an infectious disease caused by Plasmodium parasites and is transmitted among humans by female Anopheles mosquitoes. Climate factors have significant impact on both mosquito life cycle and parasite development. To consider the temperature sensitivity of the extrinsic incubation period (EIP) of malaria parasites, we formulate a delay differential equations model with a periodic time delay. We derive the basic reproduction ratio \(R_0\) and establish a threshold type result on the global dynamics in terms of \(R_0\), that is, the unique disease-free periodic solution is globally asymptotically stable if \(R_0<1\); and the model system admits a unique positive periodic solution which is globally asymptotically stable if \(R_0>1\). Numerically, we parameterize the model with data from Maputo Province, Mozambique, and simulate the long-term behavior of solutions. The simulation result is consistent with the obtained analytic result. In addition, we find that using the time-averaged EIP may underestimate the basic reproduction ratio.     

WNT10A variants in relation to nonsyndromic hypodontia in eastern Slovak population

Nonsyndromic hypodontia is a congenital absence of less than six permanent teeth, with a most common subtype maxillary lateral incisor agenesis (MLIA). Mutations in several genes have been described in severe tooth agenesis. The aim of this study was to search for the variants in wingless-type MMTV-integration site family member (WNT10A), paired box 9 (PAX9) and axis inhibitor 2 (AXIN2) genes, and investigate their potential role in the pathogenesis of non-syndromic hypodontia. Clinical examination and panoramic radiograph were performed in the cohort of 60 unrelated Slovak patients of Caucasian origin with nonsyndromic hypodontia including 37 MLIA cases and 48 healthy controls. Genomic DNA was isolated from buccal swabs and Sanger sequencing of WNT10A, PAX9 and AXIN2 was performed. Altogether, we identified 23 single-nucleotide variants, of which five were novel. We have found three rare nonsynonymous variants in WNT10A (p.Gly165Arg; p.Gly213Ser and p.Phe228Ile) in eight (13.33%) of 60 patients. Analysis showed potentially damaged WNT10A variant p.Phe228Ile predominantly occurred only in MLIA patients, and with a dominant form of tooth agenesis (odds ratio \(({\hbox {OR}}_{\mathrm{dom}}) = 9.841\); \(P=0.045\); 95% confidence interval (CI) 0.492–196.701; \({\hbox {OR}}_{\mathrm{rec}} = 0.773\); \(P =1.000\); 95% CI 0.015–39.877). In addition, the WNT10A variant p.Phe228Ile showed a trend associated with familial nonsyndromic hypodontia (\(P =0.024\); OR = 1.20; 95% CI 0.97–1.48). After Bonferroni correction, these effects remained with borderline tendencies. Using a 3D WNT10A protein model, we demonstrated that the variant Phe228Ile changes the protein secondary structure. In PAX9 and AXIN2, common variants were detected. Our findings suggest that the identified WNT10A variant p.Phe228Ile could represent risk for the inherited nonsyndromic hypodontia underlying MLIA. However, further study in different populations is required.     

Y-chromosome polymorphisms of the domestic Bactrian camel in China

Single-nucleotide polymorphisms (SNPs), microsatellites and copy number variation (CNV) were studied on the Y chromosome to understand the paternal origin and phylogenetic relationships for resource protection, rational development and utilization of the domestic Bactrian camel in China. Our sample set consisted of 94 Chinese domestic Bactrian camels from four regions (Inner Mongolia, Gansu, Qinghai and Xinjiang), we screened 29 Y-chromosome-specific loci for SNPs, analysed 40 bovine-derived microsatellite loci and measured CNVs of HSFY and SRY through Sanger sequencing, automated fluorescence-based microsatellite analysis and quantitative real-time PCR, respectively. A multicopy gene, SRY, was first found, and sequence variation was only detected in SRY in a screen of 29 loci in 13 DNA pools of individual camels. In addition, a TG repeat in the USP9Y gene was identified as the first polymorphic microsatellite in the camel Y chromosome, whereas microsatellite based on bovine sequences were not detected. The frequency of each allele varied among different populations. For the Nanjiang, Hexi and Alashan populations, a 243-bp allele was found. For the Sunite population, 241-bp, 243-bp and 247-bp alleles were detected, and the frequencies of these alleles were \(22.2\%\), \(44.5\%\) and \(33.3\%\), respectively; 241-bp and 243-bp alleles were found in other populations. Finally, CNVs in two Y-chromosomal genes were detected; CNV for HSFY and SRY ranged from 1 to 3 and from 1 to 9, respectively.