Guangxi Population Research Articles

Disparity of HIV-1 Pretreatment Drug Resistance in Men Who Have Sex With Men and the Heterosexual Population in Guangxi, China.

The prevalence of human immunodeficiency type 1 (HIV-1) pretreatment drug resistance (PDR) in men who have sex with men (MSM) in Guangxi remains unclear, and its effect on antiretroviral therapy (ART) needs to be further studied. Individuals newly diagnosed with HIV in Guangxi from 2016 to 2020, which mainly included MSM and the heterosexual (HES) population, were recruited in this study. Pol sequences were sequenced to analyze PDR and construct a genetic network. The risk factors for PDR and the effect on ART were respectively analyzed. The PDR of MSM in Guangxi was 4.7% (34/716), consisting of nonnucleoside reverse transcriptase inhibitors (3.5%), protease inhibitors (0.8%), integrase strand transfer inhibitors (0.7%), and nucleoside reverse transcriptase inhibitors (0.4%), and lower than that of HES (9.3% [77/827]). The subtype was associated with PDR, and MSM was lower than HES (CRF01_AE: 3.0% vs 8.0%; CRF07_BC: 4.1% vs 7.2%). CRF55_01B (adjusted odds ratio [aOR], 3.35) was a risk factor for PDR in MSM, while CRF08_BC (aOR, 2.34) and older (aOR, 2.75) were risk factors for PDR in HES. Six of 18 (33.3%) PDR of MSM in the network connected to each other, lower than that of HES (61.1% [22/36]). CRF55_01B (aOR, 5.69) was a risk factor for PDR transmission in MSM, while CRF08_BC (aOR, 4.08) was a risk factor in HES. Pretreatment CD4+ T-cell count, age, infection route, and subtype were associated with recovery of CD4+ count and suppression of viral load. The prevalence of PDR was different between MSM and HES, which may be associated with subtype. Thus, the monitoring of subtype and PDR should be strengthened.

Study of the association of lncRNA-GAS5 gene polymorphisms with systemic lupus erythematosus in Guangxi population

To assess the association of rs55829688 and rs75315904 polymorphisms of the lncRNA-GAS5 gene with susceptibility to systemic lupus erythematosus (SLE) in Guangxi population. Peripheral venous blood samples were collected from the SLE group and control group. Following extraction of genomic DNA, SNPscan and Sanger sequencing were carried out to determine the genotypes for the rs55829688 and rs75315904 loci of the lncRNA-GAS5 gene. No difference was found between the two groups with regard to the genotypic frequencies for rs55829688 and rs75315904 (P > 0.05). However, the frequencies of C allele of rs55829688 between the two groups was significantly different (P < 0.05). In the SLE group, the frequencies of C allele and CT+CC genotype for rs55829688 among SLE patients with nephritis were significantly lower than those of SLE patients without nephritis (P < 0.05). In addition, haplotype analysis showed that the frequency of rs55829688 C/rs75315904 A allele in the SLE group was lower than that of the control group (P < 0.05). In Guangxi population, the carrier status of rs55829688 C allele of the lncRNA-GAS5 gene may reduce the risk of SLE and its complicated nephritis, and the rs55829688 C/rs75315904 A haplotype may reduce the risk for SLE.

MTOR gene polymorphism may be associated with microscopic polyangiitis susceptibility in a Guangxi population of China

ObjectiveMicroscopic polyangiitis (MPA) onset is affected by genetic predisposition. Autophagy plays a certain role in antineutrophil cytoplasmic antibody-associated vasculitis developing. A key factor in autophagy regulating, the genetic polymorphism of MTOR gene is essential. The objective was to explore the associations between MTOR gene polymorphism and MPA susceptibility in a Guangxi population of China. MethodsA sum of 208 MPA cases and 209 healthy volunteers from Guangxi in this case-control study, four important single nucleotide polymorphism (SNP) loci of MTOR gene including rs3806317, rs1064261, rs1883965 and rs2295080 were examined. Multiplex polymerase chain reaction combined with high-throughput sequencing was performed. Subgroup analysis was evaluated by gender and ethnicity. Linkage disequilibrium and haplotype analysis were tested. Multi-SNPs interaction among mTOR signaling pathway was assessed. ResultsFor rs2295080, homozygous mutant GG genotype was associated with a decreased susceptibility of MPA in recessive model (OR = 0.38, 95%CI: 0.14–1.00, p = 0.040), particularly in the subgroup of female (OR = 0.16, 95%CI: 0.03–0.74, p = 0.006) and Han population (OR = 0.32, 95%CI: 0.10–1.00, p = 0.034). Individual carrying G allele was linked with decreasing MPA susceptibility in Han population of Guangxi (OR = 0.65, 95%CI: 0.44–0.97, p = 0.036). In haplotype analysis, the haplotype AAT was correlated with increasing susceptibility of MPA (OR = 1.347, 95%CI: 1.004–1.807, p = 0.046). Moreover, in the multi-SNPs interaction analysis, the six-locus model was identified as the best interaction model (p < 0.05). ConclusionThese findings suggest that rs2295080 polymorphism of MTOR gene may be associated with MPA susceptibility in a Guangxi population of China and G allele might be an important protective factor.

The Glu69Asp Polymorphism of EME1 Gene is Associated with an Increased Risk of Hepatocellular Carcinoma in Guangxi Population, China.

BackgroundThe dysfunction of Essential meiotic endonuclease 1 homolog 1 (EME1) can lead to genomic instability and tumorigenesis. Single nucleotide polymorphisms (SNPs) in the EME1 gene have been reported to be associated with the risk of several cancers, but its association with hepatocellular carcinoma (HCC) has not been investigated. This study aimed to determine the association between EME1 SNPs and the risk of HCC.MethodsThis study included 645 HCC patients and 649 healthy controls from a Guangxi population of Southern China, and genotyped three functional SNPs (Glu69Asp: rs3760413A>C, Ile350Thr: rs12450550T>C, and rs11868055A>G) of the EME1 gene utilizing the Agena MassARRAY platform.ResultsThe rs3760413C variant genotypes (AC+CC: Glu/Asp+Asp/Asp) conferred a 1.419-fold risk of HCC compared to the AA (Glu/Glu) genotype (adjusted OR = 1.419, 95% CI = 1.017–1.980), and the allele C increased the risk of HCC in a dose-dependent manner (Ptrend = 0.017). Moreover, the effects of the rs3760413C variant genotypes were more pronounced in individuals who drank pond/ditch water (adjusted OR = 3.956, 95% CI = 1.413–11.076) than in those who never drank (P = 0.033). We further observed that a potential carcinogen microcystin-LR induced more DNA oxidative damages in peripheral blood mononuclear cells from the carriers of rs3760413C variant genotypes than those from the subjects with AA genotype (P = 0.006). A nomogram was also constructed combining the rs3760413A>C polymorphism and environmental risk factors for predicting HCC risk with a good discriminatory ability (concordance index = 0.892, 95% CI: 0.874–0.911) and good calibration (mean absolute error = 0.005).ConclusionOur data suggest that the Glu69Asp missense polymorphism (rs3760413) of EME1 gene is associated with the risk of HCC, which may be a susceptible biomarker of HCC in the Guangxi population.

Associations between ATG16L1 gene polymorphism and antineutrophil cytoplasmic antibody-associated vasculitis in the Chinese Guangxi population: A case-control study.

BackgroundAntineutrophil cytoplasmic antibody (ANCA)‐associated vasculitis (AAV) is an autoimmune disease often accompanied by rapidly progressive renal failure, and the genetic background is still unknown. Our study was performed to test whether autophagy‐related 16 like 1 (ATG16L1) rs4663402 and rs4663396 single nucleotide polymorphisms (SNPs) were associated with AAV in the Chinese Guangxi population.MethodsOne hundred seventy seven unrelated AAV patients and 216 healthy controls were included in this case–control study. Multiplex polymerase chain reaction combined with high‐throughput sequencing was used for typing, and SNPStats and SHEsis were used for association analysis, pairwise linkage disequilibrium, and haplotype analysis.Resultsrs4663402 and rs4663396 were in Hardy–Weinberg equilibrium in AAV and control groups. The frequencies of rs4663402 AA, AT, and TT genotypes were 82.5%, 16.9%, and 0.6%, respectively, in patients with AAV, and 83.5%, 16.2%, and 0.5%, respectively, in controls. The frequencies of rs4663396 CC, CT, and TT genotypes were 63.8%, 33.9%, and 2.3%, respectively, in patients with AAV, and 69.2%, 26.6%, and 4.2%, respectively, in controls. Haplotype analysis revealed two SNPs in a single haplotype block (D′ = 1.0). Our logistic regression adjusted for sex and age showed no association between rs4663402 and rs4663396 and the risk for AAV in genetic models (p > 0.05). However, ATG16L1 rs4663396 CC and CT + TT genotypes exhibited statistically significant differences in the incidence of arthralgia (p = 0.03).ConclusionsOur results indicated that ATG16L1 rs4663402 and rs4663396 polymorphisms were not associated with AAV in the Chinese Guangxi population. ATG16L1 rs4663396 CT + TT genotype may be associated with arthralgia.

Insights into evolutionary dynamics of East Asians through Ancient DNA

<p indent="0mm">Human origins and evolution are a principal focus of the Earth and Life Sciences. To address these important scientific subjects, the extraction, sequencing, and analysis of ancient DNA from subfossil materials and sediments has emerged as a powerful tool, forming a cutting-edge research field for the country’s innovation competitions. Ancient DNA provides unique advantages by allowing the direct observation of the changing genetic composition of ancient populations to unveil an expanding picture of the origin and evolution of humans in rich detail. Since 2010, the genomic data of ancient humans have grown exponentially, which has dramatically increased our knowledge of important questions such as the interaction between archaic humans and early modern humans, and the genetic components of past modern human lineages. However, compared to other regions worldwide, China had lagged far behind in the ancient DNA research field, and the genetic history of humans in East Asia, especially China, remained poorly understood. Before 2017, while hundreds of genomes of past Europeans and North Asians had been generated, those of East Asians were extremely limited (only four ancient human genomes had been generated from Japan), highlighting large gaps in our knowledge of past population histories between eastern and western Eurasia. In 2017, Qiaomei Fu’s research team had published the oldest East Asian genome sequenced to date, from the approximately 40000-year-old Tianyuan individual near Beijing, which opened up new prospects for the genetic study of past East Asians. Since then, they have continued to extensively sequence large numbers of ancient human genomes across different times and regions of China, including genomes from approximately 33000-to-300-year-old humans from Heilongjiang, Inner Mongolia, Shandong, Fujian, Guangxi, Xinjiang and the Taiwan Strait. This data has been used to identify the genetic characteristics of different ancient populations in East Asia, such as Basal East Asians (represented by the Tianyuan individual) and the Ancient Guangxi population (represented by the Longlin individual) which did not contribute to present-day Eurasians, as well as explore the primary ancestries of Ancient Northern East Asians and Ancient Southern East Asians, which compose the genetic makeup of East Asians today. These studies revealed the previously unknown genetic connections among past East Asians and other ancient and present-day populations in different regions of the world, elucidated the migration and interaction models of related populations, and characterized the genetic variation associated with environmental adaptations. These pioneering works have untangled the evolutionary dynamics of East Asians over a large timescale, challenged, supported, or revised several existing hypotheses, and played a significant role in a more comprehensive reconstruction of human history. The results of these studies have additionally provided important scientific value and practical significance for human microevolution and medical genetics research.

1H NMR-Based Metabolomics Reveals the Intrinsic Interaction of Age, Plasma Signature Metabolites, and Nutrient Intake in the Longevity Population in Guangxi, China.

Health and longevity populations have distinct metabolic and nutrient intake profiles. However, the relationship between biomarkers of longevity-related metabolites and dietary nutrient intake profiles, as well as metabolic markers associated with longevity features, have not been fully elucidated. Therefore, 1H nuclear magnetic resonance (1H NMR)-based plasma metabolomics profiling was conducted in the present study to identify potential metabolites which can be used as specific markers for the evaluation of healthy aging. Plasma samples were obtained from centenarians and nonagenarians from the longevous region, and elderly participants aged 60–89 from the longevous region, as well as a low centenarian ratio region. The results showed that participants from longevous regions exhibited higher plasma levels of citrate, tyrosine, choline, carnitine, and valine, as well as lower contents of VLDL, lactate, alanine, N-acetyl glycoprotein (NAG), trimethylamine oxide (TMAO), α-glucose, β-glucose, and unsaturated lipids. The differential plasma metabolites were associated with an alteration in glycolysis/gluconeogenesis; aminoacyl-tRNA biosynthesis; alanine, aspartate, and glutamate metabolism; and phenylalanine, tyrosine, and tryptophan biosynthesis in participants from longevous regions. The signature metabolites were associated with higher dietary fiber intake, as well as lower energy and fat intake. The results of the present study demonstrate key longevity signature metabolites in plasma, and the dietary patterns identified provide a basis for further health and longevity research.

Novel and recurrent ASPM mutations of founder effect in Chinese population

PurposeMutations in ASPM are the most common causes of primary microcephaly (MCPH), which is a rare brain developmental disorder with few studies in Chinese population so far. This study aimed to identify the common pathogenic variants of ASPM and estimated the incidence of MCPH5 in Guangxi population. MethodsWe ascertained six MCPH cases caused by ASPM mutations in Guangxi Zhuang Autonomous Region, Whole-exome sequencing (WES) was performed to uncover the causal variants. The haplotype analysis was used to estimate the age of the recurrent variation. ResultsFive different pathogenic variants were identified in this batch of MCPH5 cases, including two novel variants p.Ser842fs*9 and p.Lys1340Argfs*29. An rarely reported pathogenic variant, c.1789C>T/p.Arg597* was found to be a founder mutation in local population. We evaluated all ASPM variants detected among 2674 non-microcephalic individuals and estimated the MCPH5 incidence to be 5.03/1,000,000 in Guangxi population. ConclusionsWe reported the first case series of Chinese MCPH cases with ASPM mutation and revealed a highly recurrent founder mutation in this local population. MCPH5 may be the major type of congenital microcephaly in Chinese population.

Whole-genome sequencing revealed genetic diversity and selection of Guangxi indigenous chickens.

Guangxi chickens play a crucial role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chickens from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except for HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was slight. MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes had received strong selection in local breeds. These also provided novel breeding visual and data basis for future breeding.

Environmental Factors for Epstein-Barr Virus Reactivation in a High-Risk Area of Nasopharyngeal Carcinoma: A Population-Based Study.

BackgroundEpstein-Barr virus (EBV) reactivation from latent to lytic infection has been considered as a key step in nasopharyngeal carcinoma oncogenesis. However, epidemiological evidence regarding environmental risk factors for EBV reactivation on a population level remains largely lacking.MethodsWe enrolled 1916 randomly selected adults from the general population of Guangdong and Guangxi, China, from 2010 to 2014. Information on environmental factors was collected via a structured interview. Serum immunoglobulin A antibodies against EBV viral capsid antigen and nuclear antigen 1 were measured by enzyme-linked immunosorbent assay to evaluate EBV reactivation status. We used logistic regression to calculate odds ratios (ORs) with 95% confidence intervals (CIs) for the associations of EBV reactivation with various environmental factors.ResultsNo associations were observed between EBV reactivation and extensive environmental factors, including alcohol or tea drinking, a history of chronic ear/nose/throat diseases, use of medications or herbs, consumption of salted fish or preserved foods, oral hygiene, sibship structure, and various residential and occupational exposures. Only cigarette smoking was associated with EBV reactivation (current smokers vs never smokers; OR = 1.37; 95% CI = 1.02–1.83), with positive exposure-response trends with increasing intensity, duration, and pack-years of smoking.ConclusionsConsistent with previous studies, we found an association between cigarette smoking and EBV reactivation. Other examined exposures were not associated with EBV reactivation. These null results could suggest either more complex interactions between exposures and EBV reactivation or a predominant role of host and/or viral genetic variation.

Lack of Genetic Structure Among Populations of Striped Flea Beetle Phyllotreta striolata (Coleoptera: Chrysomelidae) Across Southern China

The striped flea beetle (SFB) Phyllotreta striolata (Fabricius) (Coleoptera: Chrysomelidae) is a major pest of cruciferous vegetables in southern China. The population diversity and genetic structure of SFB are unknown. Here, we assembled a draft genome for the SFB and characterized the distribution of microsatellites. Then, we developed 12 novel microsatellite markers across the genome. We used a segment of the cox1 gene and newly developed microsatellite markers to genotype the genetic diversity of SFB across southern China. There were 44 mitochondrial haplotypes in the SFB populations, with haplotype 2 as the most widespread. The population genetic differentiation was very low, indicated by FST-values (&amp;lt;0.05 except for Guangxi population with other populations based on cox1), high gene flow (4.10 and 44.88 of cox1 and microsatellite, respectively) and Principal Coordinate Analysis across all populations. Mantel test showed genetic distance in SFB was significantly associated with geographic distance based on microsatellites (R2 = 0.2373, P = 0.014) while result based on cox1 (R2 = 0.0365, P = 0.155) showed no significant difference. The phylogenetic analysis did not find any geographically related clades among all haplotypes. Analyses based on microsatellites showed a lack of population genetic structure among all populations. Our study provides a foundation for the future understanding of the ecology and evolution of SFB and its management.

Assessment of cognitive function of the elderly by serum metabolites of brain-gut axis

Objective: To investigate the feasibility of assessing cognitive function of the elderly by serum metabolites of brain-gut axis. Methods: Convenience sampling was used to select 100 and 60 participants from the healthy population cohort and microecological balance cohort of the longevity population in Guangxi, to constitute subset of healthy population and longevity population, respectively. A questionnaire was used to investigate the demographic characteristics of the subjects, 2-5 ml of fasting venous blood was collected from the subjects, and the serum untargeted metabolomics was determined by liquid chromatography tandem mass spectrometry. The biomarkers related to the brain-gut axis were collected through literature retrieval, and the results were intersected with the untargeted metabolites and annotated. Spearman correlation analysis was used to screen serum metabolites of brain-gut axis associated with aging, and multiple linear regression method was used to construct biological age model. The mini mental status examination was used to evaluate the cognitive function of longevity population subsets. The differences of biological age and chronological age of longevity population subsets with different cognitive function were compared. Results: The M (Q1, Q3) of subset of healthy population and longevity population were 64 (38, 72) and 97 (95, 99) years old, respectively, and there were 50 (50.0%) and 44 (73.3%) females, respectively. Nine serum metabolites of brain-gut axis were obtained by initial screening, which were propionic acid, glutamic acid, γ-aminobutyric acid (GABA), lactic acid, 5-hydroxytryptamine (5-HT), tryptophan, trimethylamine oxide, dopamine and canine urea. Spearman correlation analysis showed that glutamic acid and dopamine were positively correlated with aging (r values were 0.208 and 0.524, respectively, all P values<0.05), and tryptophan, 5-HT and GABA were negatively correlated with aging (r values were -0.308, -0.533 and -0.213, respectively, all P values<0.05). The biological age model was constructed as: y=49.81-1.18×10-5× GABA-1.82×10-4×5-HT+1.99×10-3×dopamine+1.65×10-6×glutamic acid -2.04×10-6×tryptophan+2.36×gender, where y was the biological age (years), the items on the right were the intercept item, the relative concentration of each metabolite, and gender (male=1, female=2). The coefficient of determination of model was 0.50 (P<0.001). The M (Q1, Q3) of the chronological age of the subset of longevity population with poor, moderate and good cognitive function were 97 (94, 100), 97 (93, 101) and 96 (94, 101) years old, respectively, and there was no statistical significance in pairwise comparison (all P values>0.05). The M (Q1, Q3) of the biological age of the subjects with better cognitive function was 51 (38, 54) years old, which was lower than that of the subjects with poor cognitive function [57 (47, 61)] (P=0.040). Conclusion: The biological age model can be constructed based on serum metabolites of brain-gut axis and used to evaluate the cognitive function of the elderly.

Analysis of rs1864182 and rs1864183 variants in ATG10 gene and antineutrophil cytoplasmic autoantibody‐associated vasculitis in Chinese Guangxi population

ObjectivesTo investigate the association of autophagy‐associated gene 10 (ATG10) gene polymorphisms (rs1864182 and rs1864183) with antineutrophil cytoplasmic autoantibody (ANCA)‐associated vasculitis (AAV) in Chinese Guangxi population.MethodsThe single nucleotide polymorphisms (SNPs) of ATG10 rs1864182 and rs1864183 in 395 participants (195 AAVs and 200 healthy controls) were genotyped. Generalized multiple dimensionality reduction (GMDR) was used to analyze the SNP‐SNP interactions among two SNPs of ATG10 gene and other SNPs of autophagy gene previously studied by our research team.ResultsIn this study, we found that the two ATG10 SNPs were not associated with AAV risk in Chinese Guangxi population. However, there were statistically significant differences in the incidence of hemoptysis, hematuria, and proteinuria among the three genotypes of ATG10 rs1864182 and rs1864183 (p < 0.05). Moreover, permutation test of GMDR suggested that immunity‐related GTPase M(IRGM) rs4958847, autophagy‐associated gene 7 (ATG7) rs6442260, ATG7 rs2594966, ATG10 rs1864183, protein kinase B(AKT2) rs3730051, and AKT2 rs11552192 might interact with each other in the process of developing AAV (p < 0.05).ConclusionsOur results indicated that there existed no association between ATG10 SNPs and AAV, and SNP‐SNP interactions among IRGM rs4958847, ATG7 rs6442260, ATG7 rs2594966, ATG10 rs1864183, AKT2 rs3730051, and AKT2 rs11552192 may confer AAV risk in the Chinese Guangxi population.

Gene polymorphisms in ULK1 and PIK3CA are associated with the risk of microscopic polyangiitis in the Guangxi Zhuang Autonomous Region in China.

BackgroundMicroscopic polyangiitis (MPA) is a systemic autoimmune disease characterized by inflammation of small- and medium-sized blood vessels. Autophagy-related protein polymorphisms are involved in autoimmune disease. The aim of this study was to evaluate the effects of single-nucleotide polymorphisms (SNPs) in the ULK1 and PIK3CA genes on the risk of MPA.MethodA total of 208 patients with MPA and 211 controls in the Guangxi Zhuang Autonomous Region were recruited and analyzed. The SNPs selected were detected by polymerase chain reaction and high-throughput sequencing. The differences in allele and genotype frequency, various genetic models, and stratification analyses were evaluated, haplotype evaluation was performed after linkage disequilibrium analysis, and the interaction between gene alleles was analyzed.ResultsA statistically significant difference was detected in the genotypic distribution of two SNPs between the two groups: ULK1 rs4964879 (p = 0.019) and PIK3CA rs1607237 (p = 0.002). The results of the genetic models revealed that ULK1 rs4964879 and rs9481 were statistically significantly associated with an increased risk of MPA, whereas PIK3CA rs1607237 was associated with a reduced risk. The association between SNPs and MPA risk was affected by age, sex, and ethnicity. The ULK1 haplotype (G-T-A-C-G-A) and PIK3CA haplotype (T-G) were associated with a reduced risk of MPA, while the PIK3CA haplotype (C-G) was associated with an increased risk.ConclusionIn this study, polymorphisms in the autophagy-related genes ULK1 and PIK3CA and their association with MPA were examined. The results showed that the polymorphisms in ULK1 (rs4964879 and rs9481) and PIK3CA (rs1607237) were significantly associated with MPA risk in the Guangxi population. However, the molecular mechanisms are still unclear; basic science research and studies with larger samples are needed to confirm our conclusions and explore the underlying mechanisms.

Association of four gene polymorphisms in Chinese Guangxi population with diabetic retinopathy in type 2 diabetic patients

sBackgroundDiabetic retinopathy (DR) is one of the most common chronic microvascular complications of diabetes. Many studies have suggested that genetic factors are important in the context of DR. This study evaluated the associations of GWAS (Genome-wide association study) -identified DR-associated SNPs in a Chinese population in Guangxi Province with type 2 diabetes mellitus (T2DM).MethodsA total of 386 hospitalized T2DM patients without proliferative diabetic retinopathy (PDR) and 316 hospitalized T2DM patients with PDR were included in this case–control study. Four tag SNPs, including rs1800896 in the IL-10 gene, rs2010963 in the VEGFA gene, rs2070600 in the RAGE gene and rs2910164 in the miR-146a gene, were examined using KASP (kompetitive allele specific PCR) genotyping assays.ResultsThere were no significant differences in the genotype or allele frequencies of the miR-146a polymorphism (rs2910164) between subjects with PDR and those without DR. The TC genotype of rs1800896 was determined to be associated with an increased risk of PDR (the odds ratio (OR) was 2.366, with a 95% confidence interval (CI) ranging from 1.144 to 4.894). The CG genotypes of rs2010963 was associated with an decreased risk of PDR (the OR was 0.588, with a 95% CI ranging from 0.366 to 0.946). Regarding rs2070600, 2 genotypes (TT and CT) were associated with a decreased risk of PDR (the OR of the TT genotype was 0.180, with a 95% CI ranging from 0.037 to 0.872, and the OR of the CT genotype was 0.448, with a 95% CI ranging from 0.266 to 0.753).ConclusionsThe rs1800896 polymorphisms in the IL-10 gene, rs2010963 in the VEGFA gene and rs2070600 in the RAGE gene are associated with the risk of PDR in the Han Chinese population of Guangxi Province. Our findings provide suggestive evidence that these polymorphisms may be involved in the pathogenesis of PDR and should be investigated further.

Correlations between allocation to foliar phosphorus fractions and maintenance of photosynthetic integrity in six mangrove populations as affected by chilling.

Chilling restrains the distribution of mangroves. We tested whether foliar phosphorus (P) fractions and gene expression are associated with cold tolerance in mangrove species. We exposed seedlings of six mangrove populations from different latitudes to favorable, chilling and recovery treatments, and measured their foliar P concentrations and fractions, photochemistry, nighttime respiration, and gene expression. A Kandelia obovata (KO; 26.45°N) population completely and a Bruguiera gymnorhiza (Guangxi) (BGG; 21.50°N) population partially (30%) survived chilling. Avicennia marina (24.29°N), and other B. gymnorhiza (26.66°N, 24.40°N, and 19.62°N) populations died after chilling. Photosystems of KO and photosystem I of BGG were least injured. During chilling, leaf P fractions, except nucleic acid P in three populations, declined and photoinhibition and nighttime respiration increased in all populations, with the greatest impact in B. gymnorhiza. Leaf nucleic acid P was positively correlated with photochemical efficiency during recovery and nighttime respiration across populations for each treatment. Relatively high concentrations of nucleic acid P and metabolite P were associated with stronger chilling tolerance in KO. Bruguiera gymnorhiza exhibited relatively low concentrations of organic P in favorable and chilling conditions, but its partially survived population showed stronger compensation in nucleic acid P and Pi concentrations and gene expression during recovery.

Genetic diversity analysis of the invasive gall pest Leptocybe invasa (Hymenoptera: Apodemidae) from China.

Leptocybe invasa Fisher et LaSalle is a global invasive pest that seriously damages Eucalyptus plants. Studying the genetic diversity, genetic structure and introgression hybridization of L. invasa in China is of great significance for clarifying the breeding strategy, future invasion and diffusion trends of L. invasa in China and developing scientific prevention and control measures. Genetic diversity and phylogenetic analyses of 320 L. invasa female adults from 14 geographic populations in China were conducted using 10 polymorphic microsatellite loci (SSRs) and mitochondrial DNA cytochrome oxidase I gene sequences (COIs). (1) The Bayesian phylogenetic tree and haplotype network diagram showed that only haplotype Hap3 existed in L. invasa lineage B in China, while haplotypes Hap1 and Hap2 existed in lineage A, among which haplotype Hap2 was found for the first time. The nucleotide and haplotype diversities of lineage A were higher than those of lineage B. (2) The SSR genetic diversity of the Wuzhou Guangxi, Ganzhou Jiangxi and Panzhihua Sichuan populations was higher than that of the other 11 populations, and the SSR genetic diversity of lineage A was higher than that of lineage B. (3) The AMOVA analysis of mitochondrial COI data showed that 75.55% of the variation was among populations, and 99.86% of the variation was between lineages, while the AMOVA analysis of nuclear SSR data showed that 35.26% of the variation was among populations, and 47.04% of the variation was between lineages. There were obvious differences in the sources of variation between the COI and SSR data. (4) The optimal K value of COI and SSR data in structure analysis was 2, and PCoA analysis also divided the dataset into two obvious categories. The UPMGA phylogenetic tree based on SSR data clustered 14 geographic species into two groups. The results of genetic structure analysis supported the existence of two lineages, A and B, in China. (5) Structural analysis showed that there was obvious introgressive hybridization in Wuzhou Guangxi, Ganzhou Jiangxi, Panzhihua Sichuan and other populations. These results suggest that lineage introgressive hybridization has occurred in the L. invasa population in China. The introgressive hybridization degree and genetic diversity of lineage A are obviously higher than those of lineage B. Lineage introgressive hybridization may be the driving force for further L. invasa invasion and diffusion in China in the future.

Genetic polymorphisms of interluekin-17A gene in Black-clothes Zhuang population in Guangxi

Objective To explore the distribution characteristics of rs3819024 and rs2275913 polymorphisms of interleukin-17A (IL-17A) gene in Black-clothes Zhuang population in Guangxi and the polymorphism different among ethnic populations. Methods The polymorphisms of rs3819024 and rs2275913 of IL-17A gene in 115 Black-clothes Zhuang subjects were genotyped by SNaPshot technique. And used statistical methods to compare the differences in the distribution of these polymorphisms across sexes and populations. Results There were AA, AG and GG genotypes at rs3819024 and rs2275913 of IL-17A gene of Black-clothes Zhuang population in Guangxi, and AG genotype was the most common genotype in both loci. The frequencies of AA, AG and GG genotypes at rs3819024 were 15.6%, 54.8% and 29.6%, respectively, and the frequencies of AA, AG and GG genotypes at rs2275913 were 27.8%, 51.3% and 20.9%, respectively. G and A alleles were commonly found at rs3819024 and rs2275913, respectively, and their distribution frequencies were 57.0% and 53.5%, respectively. The genotype and allele frequency of rs3819024 and rs2275913 had no significant difference between male and female ( P>0.05). The genotype and allele of rs3819024 were significantly different from Japanese in Tokyo, Japan (JPT), Yoruba in Ibadan, Nigeria (YRI), Gujarati Indians in Houston (GIH) and Utah residents with Northern and Western European ancestry from the CEPH collection (CEU) populations published by the 1000 Genome Project (all P<0.05). There was no statistically significant different from Han Chinese in Beijing, China (CHB) population ( P>0.05)。The distribution frequency of each genotype and allele at rs2275913 site were significantly different from YRI, GIH and CEU ( P<0.05), and there was no statistically significant different from HCB ( P>0.05). Compared with JPT, the difference in genotype distribution frequency was not statistically significant ( P<0.05), but the difference in allele distribution frequency was statistically significant ( P<0.05). Conclusion The locus polymorphisms of rs3819024 and rs2275913 of IL-17A gene have difference among different races and regions. 摘要： 目的 探讨广西黑衣壮人群白细胞介素 17A 基因 ( IL-17A) rs3819024、rs2275913 位点的多态性分布特点和 不同人群间的多态性差异。 方法 采取多重单碱基延伸法 (SNaPshot) 方法对 115 例广西黑衣壮人群 IL-17A 基因 rs3819024、rs2275913 位点进行基因分型检测, 并比较不同性别及人群分布差异。 结果 广西黑衣壮人群 IL-17A 基因 rs3819024 和 rs2275913 位点均存在 AA、AG、GG 3 种基因型, 两位点基因型分布均以 AG 基因型多见, 其中 rs3819024 位 点 AA、AG、GG 基因型的分布频率分别为 15.6%、54.8%、29.6%; rs2275913 位点 AA、AG、GG 基因型的分布频率分别为 27.8%、51.3%、20.9%。rs3819024 和 rs2275913 位点分别以 G 和 A 等位基因多见, 分布频率分别为 57.0% 和 53.5%。rs3819024 和 rs2275913 两位点基因型及等位基因频率在广西黑衣壮人群男女性别间比较, 差异无统计学意义 ( P>0.05)。rs3819024 位点基因型及等位基因频率与千人基因组计划 (1000 Genomes) 数据库公布的日本人群 (JPT)、非洲 尼日利亚人群 (YRI)、印第安人群 (GIH)、欧洲人群 (CEU) 比较, 差异均有统计学意义 ( P<0.05); 与北京汉族人群 (HCB) 比较差异无统计学意义 ( P>0.05)。rs2275913 位点基因型及等位基因频率与 YRI、GIH、CEU 人群比较差异均有统计学 意义 ( P<0.05), 与 HCB 人群比较差异无统计学意义 ( P>0.05); 而与 JPT 人群相比, 基因型频率差异无统计学意义 ( P>0.05), 但等位基因频率差异有统计学意义 ( P<0.05)。 结论 IL-17A 基因rs3819024、rs2275913 基因位点多态性在不同 种族和地区间存在差异。

Human population history at the crossroads of East and Southeast Asia since 11,000 years ago

Past human genetic diversity and migration between southern China and Southeast Asia have not been well characterized, in part due to poor preservation of ancient DNA in hot and humid regions. We sequenced 31 ancient genomes from southern China (Guangxi and Fujian), including two ∼12,000- to 10,000-year-old individuals representing the oldest humans sequenced from southern China. We discovered a deeply diverged East Asian ancestry in the Guangxi region that persisted until at least 6,000 years ago. We found that ∼9,000- to 6,000-year-old Guangxi populations were a mixture of local ancestry, southern ancestry previously sampled in Fujian, and deep Asian ancestry related to Southeast Asian Hòabìnhian hunter-gatherers, showing broad admixture in the region predating the appearance of farming. Historical Guangxi populations dating to ∼1,500 to 500 years ago are closely related to Tai-Kadai and Hmong-Mien speakers. Our results show heavy interactions among three distinct ancestries at the crossroads of East and Southeast Asia.

Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

Bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.