With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genet...With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.展开更多
The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy...The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.展开更多
Suzhong swine is a hybrid breed derived from Taihu sows and Landraee boars. To identify Suzhong swine individuals and trace the source of pork products, single nucleotide polymorphisms （SNPs） identification of Suzho...Suzhong swine is a hybrid breed derived from Taihu sows and Landraee boars. To identify Suzhong swine individuals and trace the source of pork products, single nucleotide polymorphisms （SNPs） identification of Suzhong swine individuals was studied. A total of 29 pairs of primers were designed and sev- en pairs of primers were used for identification of Suzhong swine individuals. The products amplified by seven pairs of primers could be directly sequenced, with clean sequencing map background and no ambiguity in sequence read. Totally 52 SNPs loci were amplified by seven pairs of primers, and 41 SNPs loci were reserved for identification of Suzhong swine individuals through correlation analysis and heterezygosity filtration （ H ≥0.1 ）. Meantime, the digital barcodes for SNP identification of 96 individuals of Suzhong swine derived from seven boars and 12 sows were developed, which well distinguished 96 individuals of Suzhong swine. Theoretically, 41SNPs amplified by seven pairs of primers could be used for identification of 5.0 × 10^6 pig individuals. Therefore, digital barcode devel- opment method for SNP identification of Suzbong swine individuals can be used for individual identification of Suzhong swine in scale pig farm and meat product traceability.展开更多
Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sect...Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sectional study,between May and November 2022,peripheral venous blood of151 VS patients(case group)and 233 volunteers(control group)were collected.Fourteen SNPs were identified in five genes encoding the components of the MMP-2 signaling pathway,assessed through carotid-femoral pulse wave velocity(cf PWV),and analyzed using multivariate logistic regression.The multigene influence on the risk of VS was assessed using multifactor dimensionality reduction(MDR)and generalized multifactor dimensionality regression(GMDR)modeling.Results Within the multivariate logistic regression models,four SNPs were screened to have significant associations with VS:chemokine(C-C motif)ligand 2(CCL2)rs4586,MMP2 rs14070,MMP2rs7201,and MMP2 rs1053605.Carriers of the T/C genotype of MMP2 rs14070 had a 2.17-fold increased risk of developing VS compared with those of the C/C genotype,and those of the T/T genotype had a19.375-fold increased risk.CCL2 rs4586 and MMP-2 rs14070 exhibited the most significant interactions.Conclusion CCL2 rs4586,MMP-2 rs14070,MMP-2 rs7201,and MMP-2 rs1053605 polymorphisms were significantly associated with the risk of VS.展开更多
Background:Platinum chemotherapy(CT)remains the backbone of systemic therapy for patients with smallcell lung cancer(SCLC).The nucleotide excision repair(NER)pathway plays a central role in the repair of the DNA damag...Background:Platinum chemotherapy(CT)remains the backbone of systemic therapy for patients with smallcell lung cancer(SCLC).The nucleotide excision repair(NER)pathway plays a central role in the repair of the DNA damage exerted by platinum agents.Alteration in this repair mechanism may affect patients’survival.Materials and Methods:We conducted a retrospective analysis of data from 38 patients with extensive disease(ED)-SCLC who underwent platinum-CT at the Clinical Oncology Unit,Careggi University Hospital,Florence(Italy),from 2015 to 2020.mRNA expression analysis and single nucleotide polymorphism(SNP)characterization of three NER pathway genes—namely ERCC1,ERCC2,and ERCC5—were performed on patient tumor samples.Results:Overall,elevated expression of ERCC genes was observed in SCLC patients compared to healthy controls.Patients with low ERCC1 and ERCC5 expression levels exhibited a better median progression-free survival(mPFS=7.1 vs.4.9 months,p=0.39 for ERCC1 and mPFS=6.9 vs.4.8 months,p=0.093 for ERCC5)and overall survival(mOS=8.7 vs.6.0 months,p=0.4 for ERCC1 and mOS=7.2 vs.6.2 months,p=0.13 for ERCC5).Genotyping analysis of five SNPs of ERCC genes showed a longer survival in patients harboring the wild-type genotype or the heterozygous variant of the ERCC1 rs11615 SNP(p=0.24 for PFS and p=0.14 for OS)and of the rs13181 and rs1799793 ERCC2 SNPs(p=0.43 and p=0.26 for PFS and p=0.21 and p=0.16 for OS,respectively)compared to patients with homozygous mutant genotypes.Conclusions:The comprehensive analysis of ERCC gene expression and SNP variants appears to identify patients who derive greater survival benefits from platinum-CT.展开更多
Single nucleotide polymorphisms （SNPs） are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in cultivar identification and genetic diversity studies. The ...Single nucleotide polymorphisms （SNPs） are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in cultivar identification and genetic diversity studies. The objective of this study was to identify SNP markers useful for discrimination of citrus cultivars, since large numbers of expressed sequence tags （ESTs） of sweet orange are available from the National Center for Biotechnology Information （NCBI）. We now have the opportunity to discover SNP markers suitable for determining the haplotypes with which to distinguish very closely related cultivars and to assess genetic diversity within or between related species of citrus. SNPs and small insertions/deletions （Indels） from ESTs of sweet orange and satsuma were identified by the in silico SNP discovery strategy. 55 296 EST sequences of sweet orange and 2 575 of satsuma retrieved from the NCBI repository were mined for potential SNPs. Cleaved amplified polymorphic sequences （CAPS） and sequencing approaches were used to validate putative SNPs in a sample of 30 citrus accessions. A total of 3 348 putative SNPs were identified based on the abundance of sequences and haplotype cosegregation. Of these 3 348 SNPs, the transitions, transversions and Indels ratios were 47.9, 36.1 and 16.0%, respectively. The SNPs occurred on average at a frequency of 1 per 164 bp in the coding region of citrus. 14 SNPs were randomly selected and genotyped according to 30 citrus accessions including 23 accessions of sweet orange; 11 SNPs displayed polymorphism with an average polymorphism information content （PIC） of 0.20 among 30 citrus accessions. The genetic diversity present in sweet orange was low, so the 14 SNP markers failed to discriminate different cultivars of sweet orange, but they did succeed in distinguishing accessions of inter-species of citrus. In this study, SNPs were mined from EST sequences of sweet orange and satsuma, which displayed potential capability as molecular markers to discriminate inter-species accessions of citrus. It is anticipated that these putative SNPs could be applied in citrus genetics research and breeding.展开更多
Objectives To determine whether -238G/A and -857C/T polymorphisms of tumor necrosis factor-alpha （TNF-o0 gene promoter were associated with outcomes of hepatitis B virus infection. Methods A total of 246 HBV self-lim...Objectives To determine whether -238G/A and -857C/T polymorphisms of tumor necrosis factor-alpha （TNF-o0 gene promoter were associated with outcomes of hepatitis B virus infection. Methods A total of 246 HBV self-limited infected subjects and 443 chronic hepatitis B （HB） patients were recruited in this case-control study. TNF-α-238G/A and -857C/T gene promoter polymorphisms were examined by polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Results The frequency of TNF-α-238 GG （90.7%） in chronic HB group was significantly lower than that （95.1%） in self-limited group （P=0.041）. The frequency of TNF-oc-857 CC （79.7%） in chronic HB patients was significantly higher than that （70.9%） in self-limited infected subjects （P=0.021）. Multiple logistic regression analysis revealed that both TNF-oc-238GA and -857CC were independently associated with chronic HB. Conclusions TNF-α promoter variants are likely to play a substantial role in influencing the outcomes of HBV infection.展开更多
The insulin-like growth factor 1（IGF1） gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffal...The insulin-like growth factor 1（IGF1） gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms（SNPs）, G64 A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly（P〈0.05） higher body weight（BW） and average daily gain（ADG） than those with other genotypes at ages of 3–6 months in G64A SNP and 6–9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated（P〈0.0001） with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with m RNA levels of IGF1 and IGF1 receptor（IGF1 R） in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher m RNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.展开更多
Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken ...Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken with restricton fragment length polymorphisms. The associations of the SNPs with the total egg production （NE）, average days of continual laying （ADCL）, and number of double-yolked eggs （DYE） traits were analyzed. The frequency of restriction enzyme A/a alleles in the population was for GnRHR 0.69 （Bpu1102 Ⅰ A） and 0.31 （Bpu1102 Ⅰ a） and for NPY 0.46 （Dra Ⅰ B） and 0.54 （Dra Ⅰ b）. Trait data from a total of 120 hens, which were purebred introduced from Hainan Province, China from one generation were recorded. Two significant effects of genes＇ marker were found： for GnRHR and number of eggs （dominant; t= 2.67, df= 116） and NPY and number of eggs （additive; t= 1.97, df= 116）. The current research supports the effects of GnRHR and NPY genes on egg-laying traits of chickens.展开更多
Objective： The inhibition of the neovascularization in tumors is a potential therapeutic target of cancer. Vascular endothelial growth inhibitor （VEGI） is a member of the TNF superfamily which has the ability to su...Objective： The inhibition of the neovascularization in tumors is a potential therapeutic target of cancer. Vascular endothelial growth inhibitor （VEGI） is a member of the TNF superfamily which has the ability to suppress the formation of new vessels in tumors. In order to study the association between VEGI gene polymorphisms and breast cancer risk, a case-control study was conducted in Chinese Han women in Northeast China. Methods： Our study involved 708 female breast cancer patients and 685 healthy volunteers. Four SNPs of VEGI gene were analyzed through the polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） method. The association between VEGI gene polymorphisms and breast cancer risk was analyzed in our study. The relation between VEGI gene variants and clinical features of breast cancer including lymph node （LN） metastasis, esl^ogen receptor （ER）, progestrogen receptor （PR）, tumor protein 53 （1953）, human epidermal growth factor receptor 2 （Her-2） and triple negative （ER-/PR-/Her-2-） status was analyzed as well. Results： We found that the CT genotype and T allele of rs6478106 were more frequent in patients than in controls. There was also a statistical difference in the distribution of Crs6478106Grs4263839 haplotype between patients and controls. In addition, SNP rs6478106 and rs4979462 were related with the Her-2 status. Conclusions： Our results suggest that VEGI gene variants may be related to the breast cancer risk and the clinical features of breast cancer in Chinese Han women in Northeast China.展开更多
The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 3...The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 38 single nucleotide polymorphisms （SNPs） from a fragment of the IGFBP-3 gene spanning 1 823 bp using the denaturing high-performance liquid chromatography （DHPLC） method and confirmed them by direct sequencing. Among these SNPs, 36 located in introns and the remaining 2 in the 3 prime untranslated region （3UTR）. In addition, 16 PCR-RFLP polymorphisms were identified within these SNPs. Three SNPs were then selected to genotype 272 F2 individuals with PCR-RFLP method and the association of polymorphism with growth and carcass traits were analyzed. The results showed that no significant associations were observed between polymorphisms of A265G and A952G and traits. However, the A2670G significantly related with live body length, loin muscle area, and skin and fat percentage （P〈0.05）; highly significantly associated with weight of carcass lean and lean percentage （P〈 0.01）.展开更多
The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron re...The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.展开更多
Silent information regulator 2 （Sir2） proteins, or sirtuins, are nicotine adenine dinucleotide （NAD）-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Si...Silent information regulator 2 （Sir2） proteins, or sirtuins, are nicotine adenine dinucleotide （NAD）-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 homologs, namely, silent information regulators （SIRT1-7）. SIRT4 and SIRT7 genes play a crucial role in regulating lipid metabolism, cellular growth and metabolism. This suggests that they are potential candidate genes for affecting body size and meat quality traits in animals. Hence, this study aimed to detect genetic variations of both SIRT4 and SIRT7 bovine genes in Qinchuan cattle, and to evaluate the effect of these variations on economically important body size and meat quality traits. Expression analysis using quantitative real-time PCR （qPCR） indicated that SIRT4 and SIRT7 were broadly expressed in all thirteen studied tissues. The expression of SIRT4 was higher in liver, muscle, and in subcutaneous fat tissue. In the case of SIRT7, the expression was higher in lung, abomasum, and subcutaneous fat. Using DNAsequencing, a total of three single nucleotide polymorphisms （SNPs） were identified within SIRT4 and SIRT7 genes in 468 Qinchuan cattle. These included one novel SNP within 3＇ untranslated regions （UTR） of SIRT4 （SNP1： g. 13915A〉G） and two novel synonymous substitutions in SIRT7 （SNP2： g.3587C〉T and SNP3： g.3793T〉C）. Statistical analyses indicated that all three SNPs could significantly influence some body size and meat quality traits in Qinchuan cattle. These novel findings will provide a background for application of bovine SIRT4 and SIRT7 genes in the selection program of Chinese cattle.展开更多
A total of 64 patients with β-lactam allergy and 30 control subjects were enrolled in a case-control study. This study is aimed to analyze the relationship between β-lactam allergy and 10 single nucleotide polymorph...A total of 64 patients with β-lactam allergy and 30 control subjects were enrolled in a case-control study. This study is aimed to analyze the relationship between β-lactam allergy and 10 single nucleotide polymorphisms（SNPs） in interleukin-10（IL-10）, IL-13, IL-4Rα, high-affinity immunoglobulin E-receptor β chain（FcεRIβ）, interferon γ receptor 2（IFNGR2）, and CYP3A4, and within the Han Chinese population of Northwest China. Genotyping for the SNPs was conducted using the Sequenom Mass ARRAY platform. SPSS 17.0 was employed to analyze the statistical data and SHEsis was used to perform the haplotype reconstruction and analyze linkage disequilibrium of SNPs of IL-10 and IL-13. The results showed that the genotype distribution of CYP3A4 rs2242480/CT differed significantly between case and control groups of males（P=0.022; odds ratio（OR）=0.167, 95% confidence interval（CI）： 0.032–0.867）. Further analysis showed that CCA, CCG, and TAA haplotypes of IL-10 had no significant correlation in patients with β-lactam allergy. The correlation between CCT and CAC haplotypes of IL-13 and β-lactam allergy needs to be further studied. The analysis did not reveal any differences in the distribution of others gene polymorphisms between cases and controls.展开更多
The aim of present study was to investigate the relationship between nerve injury-induced protein 2 （NINJ2） gene polymorphism and stroke in Chinese Han population. Fifty-two patients with large-artery atheroscleros...The aim of present study was to investigate the relationship between nerve injury-induced protein 2 （NINJ2） gene polymorphism and stroke in Chinese Han population. Fifty-two patients with large-artery atherosclerosis （LAA） infarction, 85 patients with small-artery occlusion lacunar （SAO） infarction, 50 patients with intracerebral hemorrhage （ICH） and 66 controls were included. Genotypes and alleles frequencies of the two single nucleotide polymorphisms （SNPs） of NINJ2 among different groups were analyzed and compared. In regard to rs12425791, the frequencies of the AG and AA＋AG genotypes of the LAA and SAO groups were significantly higher than those in the control group; the frequency of the A allele of the SAO group was significantly higher than that of the control group. In regard to rs11833579, there were not any significant differences between the case and the control groups. The SNP rs12425791 is significantly associated with ischemic stroke, and the A allele increases the susceptibility to stroke. The SNP rs11833579 is not significantly associated with stroke.展开更多
Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or ...Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.展开更多
We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by ...We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by using radial basis function （RBF） networks. The result of the forward sliding windows sug-gests that the accuracies and Matthews correlation coefficient （MCC values） ascend with the increasing of length of sliding windows. The accuracies range from 73.27 % to 80.69 %,and MCC values range from 0.465 to 0.614. The backward sliding windows and the sliding windows with fixed length three are de-signed to find the crucial sites related to SNP. The results imply that the occurrence possibility of SNP relies heavily on the above physical and chemical features of sites which are at a distance around 20 bases from the SNP site. Compared with the support vector machine （SVM）,our RBF network approach has achieved more satisfactory results.展开更多
The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blo...The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blood mononuclear cells(PBMCs)of CHB patients and healthy controls and evaluated using the Human Methylation 450 K Assay.The DNA methylation level at hg37 chromosome(CHR)X:7810800 was further validated using pyrosequencing.SNP genotypes,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were further examined using SNaPshot,RT-qPCR,and Western blot,respectively.Results showed that a total of 5529 CpG loci were differentially methylated between male and female CHB patients.DNA methylation level and CC+CT frequency at CHR X:7810800,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were higher in female than in male CHB patients.The CHR X:7810800 locus was hypermethylated in CHB patients with CC+CT genotypes in comparison with those with the TT genotype.In cases of CC-f CT genotypes,VCX mRNA expression was negatively correlated with the DNA methylation level.CHB patients with higher levels of HBV DNA,AST,and GGT or higher GPRI scores exhibited lower VCX expression.In conclusion,SNPs and DNA methylation at the CHR X:7810800 locus cooperatively regulate VCX expression in CHB.The upregulated VCX expression in female CHB patients might represent a mechanism of protection from more severe liver dysfunction and extensive fibrosis,as observed in male CHB patients.展开更多
Objective Findings from the previous studies have suggested a relationship between ectonucleotide pyrophosphatase /phosphodiesterase 1 （ENPP‐1） or plasma cell membrane glycoprotein 1 （PC‐1） gene single nucleotid...Objective Findings from the previous studies have suggested a relationship between ectonucleotide pyrophosphatase /phosphodiesterase 1 （ENPP‐1） or plasma cell membrane glycoprotein 1 （PC‐1） gene single nucleotide polymorphism （K121Q, rs1044498） and genetic susceptibility to obesity. However, such relationship is not reproduced by some currently available studies. In this context, the present study is aimed to quantitatively analyze the association of K121Q variant with obesity in all published case‐control studies in European adult populations. Methods Published literature from PubMed, EMBASE, and ISI web of science databases were retrieved. The studies evaluating the association of ENPP1/PC1 gene K121Q polymorphism with obesity were included, in which sufficient data were presented to calculate the odds ratio （OR） with 95% confidence intervals （CIs）. Results Ten case‐control studies meeting the inclusion criteria identified a total of 24,324 subjects including 11,372 obese and 12,952 control subjects. The meta‐analysis results showed a statistically significant association of K121Q with obesity [OR （95%CI）： 1.25 （1.04‐1.52） P=0.021] under a recessive model of inheritance （QQ vs. KK＋KQ） without heterogeneity or publication bias. Conclusions The results from the present study have indicated that ENPP1/PC1 Q121 variant may increase the risk of obesity and that more well‐designed studies based on a larger population will be required to further evaluate the role of ENPP1/PC1 gene K121Q polymorphism in obesity and other related metabolic syndromes.展开更多
The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate ...The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate the oyster growth traits and the associations with bHLH genes variations,we analyzed the gene polymorphisms-traits association in a wild population,and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis.After screening the single nucleotide polymorphisms(SNPs)in three candidate genes of the bHLH family(88 bHLH genes in two wild oyster populations in total),we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene.This allele is a non-synonymous mutation(Phe/Leu)with an extremely significant association with shell width(P<0.01)and allele G is beneficial to shell width.This SNP on the CgLoblHLH4 gene might have a potential value as a genetic marker of growth traits that could be used in breeding in C.gigas in the future.展开更多
文摘With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.
基金Supported by the National Key R&D Program of China(Nos.2018YFD0900106,2018YFC1406700)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(No.2018SDKJ0302-4)the MOA Modern Agricultural Talents Support Project。
文摘The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.
基金Supported by Agricultural Science and Technology Innovation Project of Jiangsu Province[CX(16)1006]Fundamental Research Fund of Jiangsu Academy of Agricultural Sciences[ZX(15)3003]
文摘Suzhong swine is a hybrid breed derived from Taihu sows and Landraee boars. To identify Suzhong swine individuals and trace the source of pork products, single nucleotide polymorphisms （SNPs） identification of Suzhong swine individuals was studied. A total of 29 pairs of primers were designed and sev- en pairs of primers were used for identification of Suzhong swine individuals. The products amplified by seven pairs of primers could be directly sequenced, with clean sequencing map background and no ambiguity in sequence read. Totally 52 SNPs loci were amplified by seven pairs of primers, and 41 SNPs loci were reserved for identification of Suzhong swine individuals through correlation analysis and heterezygosity filtration （ H ≥0.1 ）. Meantime, the digital barcodes for SNP identification of 96 individuals of Suzhong swine derived from seven boars and 12 sows were developed, which well distinguished 96 individuals of Suzhong swine. Theoretically, 41SNPs amplified by seven pairs of primers could be used for identification of 5.0 × 10^6 pig individuals. Therefore, digital barcode devel- opment method for SNP identification of Suzbong swine individuals can be used for individual identification of Suzhong swine in scale pig farm and meat product traceability.
基金supported by the Construction of Prevention and Treatment System of Geriatric Syndromes Focusing on Disability and Dementia(No.21-1-2-2-zyyd-nsh)。
文摘Objective This study aimed to explore the association of single nucleotide polymorphisms(SNP)in the matrix metalloproteinase 2(MMP-2)signaling pathway and the risk of vascular senescence(VS).Methods In this cross-sectional study,between May and November 2022,peripheral venous blood of151 VS patients(case group)and 233 volunteers(control group)were collected.Fourteen SNPs were identified in five genes encoding the components of the MMP-2 signaling pathway,assessed through carotid-femoral pulse wave velocity(cf PWV),and analyzed using multivariate logistic regression.The multigene influence on the risk of VS was assessed using multifactor dimensionality reduction(MDR)and generalized multifactor dimensionality regression(GMDR)modeling.Results Within the multivariate logistic regression models,four SNPs were screened to have significant associations with VS:chemokine(C-C motif)ligand 2(CCL2)rs4586,MMP2 rs14070,MMP2rs7201,and MMP2 rs1053605.Carriers of the T/C genotype of MMP2 rs14070 had a 2.17-fold increased risk of developing VS compared with those of the C/C genotype,and those of the T/T genotype had a19.375-fold increased risk.CCL2 rs4586 and MMP-2 rs14070 exhibited the most significant interactions.Conclusion CCL2 rs4586,MMP-2 rs14070,MMP-2 rs7201,and MMP-2 rs1053605 polymorphisms were significantly associated with the risk of VS.
文摘Background:Platinum chemotherapy(CT)remains the backbone of systemic therapy for patients with smallcell lung cancer(SCLC).The nucleotide excision repair(NER)pathway plays a central role in the repair of the DNA damage exerted by platinum agents.Alteration in this repair mechanism may affect patients’survival.Materials and Methods:We conducted a retrospective analysis of data from 38 patients with extensive disease(ED)-SCLC who underwent platinum-CT at the Clinical Oncology Unit,Careggi University Hospital,Florence(Italy),from 2015 to 2020.mRNA expression analysis and single nucleotide polymorphism(SNP)characterization of three NER pathway genes—namely ERCC1,ERCC2,and ERCC5—were performed on patient tumor samples.Results:Overall,elevated expression of ERCC genes was observed in SCLC patients compared to healthy controls.Patients with low ERCC1 and ERCC5 expression levels exhibited a better median progression-free survival(mPFS=7.1 vs.4.9 months,p=0.39 for ERCC1 and mPFS=6.9 vs.4.8 months,p=0.093 for ERCC5)and overall survival(mOS=8.7 vs.6.0 months,p=0.4 for ERCC1 and mOS=7.2 vs.6.2 months,p=0.13 for ERCC5).Genotyping analysis of five SNPs of ERCC genes showed a longer survival in patients harboring the wild-type genotype or the heterozygous variant of the ERCC1 rs11615 SNP(p=0.24 for PFS and p=0.14 for OS)and of the rs13181 and rs1799793 ERCC2 SNPs(p=0.43 and p=0.26 for PFS and p=0.21 and p=0.16 for OS,respectively)compared to patients with homozygous mutant genotypes.Conclusions:The comprehensive analysis of ERCC gene expression and SNP variants appears to identify patients who derive greater survival benefits from platinum-CT.
基金supported by the National Natural Science Foundation of China(2006BAD13B06-1-4)the Natural Science Foundation of Chongqing,China (CSTC,2007BB1343)
文摘Single nucleotide polymorphisms （SNPs） are the most abundant sequence variations found in plant genomes and are widely used as molecular genetic markers in cultivar identification and genetic diversity studies. The objective of this study was to identify SNP markers useful for discrimination of citrus cultivars, since large numbers of expressed sequence tags （ESTs） of sweet orange are available from the National Center for Biotechnology Information （NCBI）. We now have the opportunity to discover SNP markers suitable for determining the haplotypes with which to distinguish very closely related cultivars and to assess genetic diversity within or between related species of citrus. SNPs and small insertions/deletions （Indels） from ESTs of sweet orange and satsuma were identified by the in silico SNP discovery strategy. 55 296 EST sequences of sweet orange and 2 575 of satsuma retrieved from the NCBI repository were mined for potential SNPs. Cleaved amplified polymorphic sequences （CAPS） and sequencing approaches were used to validate putative SNPs in a sample of 30 citrus accessions. A total of 3 348 putative SNPs were identified based on the abundance of sequences and haplotype cosegregation. Of these 3 348 SNPs, the transitions, transversions and Indels ratios were 47.9, 36.1 and 16.0%, respectively. The SNPs occurred on average at a frequency of 1 per 164 bp in the coding region of citrus. 14 SNPs were randomly selected and genotyped according to 30 citrus accessions including 23 accessions of sweet orange; 11 SNPs displayed polymorphism with an average polymorphism information content （PIC） of 0.20 among 30 citrus accessions. The genetic diversity present in sweet orange was low, so the 14 SNP markers failed to discriminate different cultivars of sweet orange, but they did succeed in distinguishing accessions of inter-species of citrus. In this study, SNPs were mined from EST sequences of sweet orange and satsuma, which displayed potential capability as molecular markers to discriminate inter-species accessions of citrus. It is anticipated that these putative SNPs could be applied in citrus genetics research and breeding.
基金This work was supported by Beijing Municipal Government Commission for Science & Technology, (No. H020920020590)
文摘Objectives To determine whether -238G/A and -857C/T polymorphisms of tumor necrosis factor-alpha （TNF-o0 gene promoter were associated with outcomes of hepatitis B virus infection. Methods A total of 246 HBV self-limited infected subjects and 443 chronic hepatitis B （HB） patients were recruited in this case-control study. TNF-α-238G/A and -857C/T gene promoter polymorphisms were examined by polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Results The frequency of TNF-α-238 GG （90.7%） in chronic HB group was significantly lower than that （95.1%） in self-limited group （P=0.041）. The frequency of TNF-oc-857 CC （79.7%） in chronic HB patients was significantly higher than that （70.9%） in self-limited infected subjects （P=0.021）. Multiple logistic regression analysis revealed that both TNF-oc-238GA and -857CC were independently associated with chronic HB. Conclusions TNF-α promoter variants are likely to play a substantial role in influencing the outcomes of HBV infection.
基金Project supported by the Science Technology Development Fund(STDF,No.2585),Ministry of Scientific Research,Egypt
文摘The insulin-like growth factor 1（IGF1） gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms（SNPs）, G64 A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly（P〈0.05） higher body weight（BW） and average daily gain（ADG） than those with other genotypes at ages of 3–6 months in G64A SNP and 6–9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated（P〈0.0001） with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with m RNA levels of IGF1 and IGF1 receptor（IGF1 R） in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher m RNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.
文摘Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken with restricton fragment length polymorphisms. The associations of the SNPs with the total egg production （NE）, average days of continual laying （ADCL）, and number of double-yolked eggs （DYE） traits were analyzed. The frequency of restriction enzyme A/a alleles in the population was for GnRHR 0.69 （Bpu1102 Ⅰ A） and 0.31 （Bpu1102 Ⅰ a） and for NPY 0.46 （Dra Ⅰ B） and 0.54 （Dra Ⅰ b）. Trait data from a total of 120 hens, which were purebred introduced from Hainan Province, China from one generation were recorded. Two significant effects of genes＇ marker were found： for GnRHR and number of eggs （dominant; t= 2.67, df= 116） and NPY and number of eggs （additive; t= 1.97, df= 116）. The current research supports the effects of GnRHR and NPY genes on egg-laying traits of chickens.
基金supported by a grant from the National Natural Science Foundation of China(31070780)the Major Project of Technology Department,Heilongjiang Province(GB05C402)
文摘Objective： The inhibition of the neovascularization in tumors is a potential therapeutic target of cancer. Vascular endothelial growth inhibitor （VEGI） is a member of the TNF superfamily which has the ability to suppress the formation of new vessels in tumors. In order to study the association between VEGI gene polymorphisms and breast cancer risk, a case-control study was conducted in Chinese Han women in Northeast China. Methods： Our study involved 708 female breast cancer patients and 685 healthy volunteers. Four SNPs of VEGI gene were analyzed through the polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） method. The association between VEGI gene polymorphisms and breast cancer risk was analyzed in our study. The relation between VEGI gene variants and clinical features of breast cancer including lymph node （LN） metastasis, esl^ogen receptor （ER）, progestrogen receptor （PR）, tumor protein 53 （1953）, human epidermal growth factor receptor 2 （Her-2） and triple negative （ER-/PR-/Her-2-） status was analyzed as well. Results： We found that the CT genotype and T allele of rs6478106 were more frequent in patients than in controls. There was also a statistical difference in the distribution of Crs6478106Grs4263839 haplotype between patients and controls. In addition, SNP rs6478106 and rs4979462 were related with the Her-2 status. Conclusions： Our results suggest that VEGI gene variants may be related to the breast cancer risk and the clinical features of breast cancer in Chinese Han women in Northeast China.
基金the projects under the National High Technology Research and Development Program of China(2006CB 102107)the National Natu-ral Science Foundation of China(30571327)the Key Program of Science and Technology of Guangdong Province,China(2006B20201051).
文摘The insulin-like growth factor binding protein-3 （IGFBP-3） was known as a key factor that regulates the effect of insulin- like growth factors （IGF-1 and IGF-2） on pig growth and development. We first identified 38 single nucleotide polymorphisms （SNPs） from a fragment of the IGFBP-3 gene spanning 1 823 bp using the denaturing high-performance liquid chromatography （DHPLC） method and confirmed them by direct sequencing. Among these SNPs, 36 located in introns and the remaining 2 in the 3 prime untranslated region （3UTR）. In addition, 16 PCR-RFLP polymorphisms were identified within these SNPs. Three SNPs were then selected to genotype 272 F2 individuals with PCR-RFLP method and the association of polymorphism with growth and carcass traits were analyzed. The results showed that no significant associations were observed between polymorphisms of A265G and A952G and traits. However, the A2670G significantly related with live body length, loin muscle area, and skin and fat percentage （P〈0.05）; highly significantly associated with weight of carcass lean and lean percentage （P〈 0.01）.
基金Supported by the National Basic Research Program of China(973Program)(No.2010CB126304)the Special Fund for Agro-scientific Research in the Public Interest(No.200903046)the Project from the Ministry of Science and Technology of China(No.2006DKA30470017)
文摘The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.
基金supported by the National 863 Program of China (2013 AA102505)the National Natural Science Foundation of China (31272411 and 31402044)+2 种基金the National Beef and Yak Industrial Technology System,China (CARS-38)the China Postdoctoral Science Foundation (2016M590976)the Key Technologies R&D Program of Henan Province,China (122102110062)
文摘Silent information regulator 2 （Sir2） proteins, or sirtuins, are nicotine adenine dinucleotide （NAD）-dependent deacetylases that connect metabolism with longevity in lower organisms. In mammals, there are seven Sir2 homologs, namely, silent information regulators （SIRT1-7）. SIRT4 and SIRT7 genes play a crucial role in regulating lipid metabolism, cellular growth and metabolism. This suggests that they are potential candidate genes for affecting body size and meat quality traits in animals. Hence, this study aimed to detect genetic variations of both SIRT4 and SIRT7 bovine genes in Qinchuan cattle, and to evaluate the effect of these variations on economically important body size and meat quality traits. Expression analysis using quantitative real-time PCR （qPCR） indicated that SIRT4 and SIRT7 were broadly expressed in all thirteen studied tissues. The expression of SIRT4 was higher in liver, muscle, and in subcutaneous fat tissue. In the case of SIRT7, the expression was higher in lung, abomasum, and subcutaneous fat. Using DNAsequencing, a total of three single nucleotide polymorphisms （SNPs） were identified within SIRT4 and SIRT7 genes in 468 Qinchuan cattle. These included one novel SNP within 3＇ untranslated regions （UTR） of SIRT4 （SNP1： g. 13915A〉G） and two novel synonymous substitutions in SIRT7 （SNP2： g.3587C〉T and SNP3： g.3793T〉C）. Statistical analyses indicated that all three SNPs could significantly influence some body size and meat quality traits in Qinchuan cattle. These novel findings will provide a background for application of bovine SIRT4 and SIRT7 genes in the selection program of Chinese cattle.
基金Project supported by the Natural Science Foundation of Gansu Province,China(Nos.3ZS061-A25-084 and 1208RJZA192)the Key Laboratory of Digestive System Tumors of Gansu Provincethe Fundamental Research Funds for the Central Universities(No.lzujbky-2011-t03-15),China
文摘A total of 64 patients with β-lactam allergy and 30 control subjects were enrolled in a case-control study. This study is aimed to analyze the relationship between β-lactam allergy and 10 single nucleotide polymorphisms（SNPs） in interleukin-10（IL-10）, IL-13, IL-4Rα, high-affinity immunoglobulin E-receptor β chain（FcεRIβ）, interferon γ receptor 2（IFNGR2）, and CYP3A4, and within the Han Chinese population of Northwest China. Genotyping for the SNPs was conducted using the Sequenom Mass ARRAY platform. SPSS 17.0 was employed to analyze the statistical data and SHEsis was used to perform the haplotype reconstruction and analyze linkage disequilibrium of SNPs of IL-10 and IL-13. The results showed that the genotype distribution of CYP3A4 rs2242480/CT differed significantly between case and control groups of males（P=0.022; odds ratio（OR）=0.167, 95% confidence interval（CI）： 0.032–0.867）. Further analysis showed that CCA, CCG, and TAA haplotypes of IL-10 had no significant correlation in patients with β-lactam allergy. The correlation between CCT and CAC haplotypes of IL-13 and β-lactam allergy needs to be further studied. The analysis did not reveal any differences in the distribution of others gene polymorphisms between cases and controls.
基金supported by a grant from the National Science Foundation of Jiangsu Province (No. BK2010116)
文摘The aim of present study was to investigate the relationship between nerve injury-induced protein 2 （NINJ2） gene polymorphism and stroke in Chinese Han population. Fifty-two patients with large-artery atherosclerosis （LAA） infarction, 85 patients with small-artery occlusion lacunar （SAO） infarction, 50 patients with intracerebral hemorrhage （ICH） and 66 controls were included. Genotypes and alleles frequencies of the two single nucleotide polymorphisms （SNPs） of NINJ2 among different groups were analyzed and compared. In regard to rs12425791, the frequencies of the AG and AA＋AG genotypes of the LAA and SAO groups were significantly higher than those in the control group; the frequency of the A allele of the SAO group was significantly higher than that of the control group. In regard to rs11833579, there were not any significant differences between the case and the control groups. The SNP rs12425791 is significantly associated with ischemic stroke, and the A allele increases the susceptibility to stroke. The SNP rs11833579 is not significantly associated with stroke.
基金Supported by the Key Program of National Natural Science Foundation of China (No.30730071)the National High Technology R&D Program of China(863 Program)(No.2012AA10A404)the Agricultural Science and Technology Achievements Transformation Funds Project(No.2010GB24910700)
文摘Pacific white shrimp has become a major aquaculture and fishery species worldwide.Although a large scale EST resource has been publicly available since 2008,the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure.In this study,a set of 155 411 expressed sequence tags(ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms(SNPs) were predicted,including 9 546 transitions,5 124 transversions and 2 481 indels.Among the 7 298 SNP substitutions located in functionally annotated contigs,58.4%(4 262) are non-synonymous SNPs capable of introducing amino acid mutations.Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding.Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous,suggesting negative selection.Distribution of non-synonymous to synonymous substitutions(Ka/Ks) ratio ranges from 0 to 4.01,(average 0.42,median 0.26),suggesting that the majority of the affected genes are under purifying selection.Enrichment analysis identified multiple gene ontology categories under positive or negative selection.Categories involved in innate immune response and male gamete generation are rich in positively selected genes,which is similar to reports in Drosophila and primates.This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species.The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.
基金Supported by Discipline-Crossing Research Foundation of Huazhong Agricultural University(2008XKJC006)the Fundamental Research Funds for the Central Universities of China
文摘We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by using radial basis function （RBF） networks. The result of the forward sliding windows sug-gests that the accuracies and Matthews correlation coefficient （MCC values） ascend with the increasing of length of sliding windows. The accuracies range from 73.27 % to 80.69 %,and MCC values range from 0.465 to 0.614. The backward sliding windows and the sliding windows with fixed length three are de-signed to find the crucial sites related to SNP. The results imply that the occurrence possibility of SNP relies heavily on the above physical and chemical features of sites which are at a distance around 20 bases from the SNP site. Compared with the support vector machine （SVM）,our RBF network approach has achieved more satisfactory results.
基金supported by the Key Program of National Natural Science Foundation of China (81330084)the E-institutes of Shanghai Municipal Education Commission (No E03008)+1 种基金supported by the National Science and Technology Major Project of China (2012ZX10005001-004)supported by the Science and Technology Commission of Shanghai Municipality (19YF1449900)
文摘The study was conducted to explore the mechanisms of sex differences in the response to chronic hepatitis B(CHB)in terms of DNA methylation,SNP genotype,and gene expression.Genomic DNA was isolated from peripheral blood mononuclear cells(PBMCs)of CHB patients and healthy controls and evaluated using the Human Methylation 450 K Assay.The DNA methylation level at hg37 chromosome(CHR)X:7810800 was further validated using pyrosequencing.SNP genotypes,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were further examined using SNaPshot,RT-qPCR,and Western blot,respectively.Results showed that a total of 5529 CpG loci were differentially methylated between male and female CHB patients.DNA methylation level and CC+CT frequency at CHR X:7810800,VCX mRNA expression of PBMCs,and plasma VCX protein concentration were higher in female than in male CHB patients.The CHR X:7810800 locus was hypermethylated in CHB patients with CC+CT genotypes in comparison with those with the TT genotype.In cases of CC-f CT genotypes,VCX mRNA expression was negatively correlated with the DNA methylation level.CHB patients with higher levels of HBV DNA,AST,and GGT or higher GPRI scores exhibited lower VCX expression.In conclusion,SNPs and DNA methylation at the CHR X:7810800 locus cooperatively regulate VCX expression in CHB.The upregulated VCX expression in female CHB patients might represent a mechanism of protection from more severe liver dysfunction and extensive fibrosis,as observed in male CHB patients.
文摘Objective Findings from the previous studies have suggested a relationship between ectonucleotide pyrophosphatase /phosphodiesterase 1 （ENPP‐1） or plasma cell membrane glycoprotein 1 （PC‐1） gene single nucleotide polymorphism （K121Q, rs1044498） and genetic susceptibility to obesity. However, such relationship is not reproduced by some currently available studies. In this context, the present study is aimed to quantitatively analyze the association of K121Q variant with obesity in all published case‐control studies in European adult populations. Methods Published literature from PubMed, EMBASE, and ISI web of science databases were retrieved. The studies evaluating the association of ENPP1/PC1 gene K121Q polymorphism with obesity were included, in which sufficient data were presented to calculate the odds ratio （OR） with 95% confidence intervals （CIs）. Results Ten case‐control studies meeting the inclusion criteria identified a total of 24,324 subjects including 11,372 obese and 12,952 control subjects. The meta‐analysis results showed a statistically significant association of K121Q with obesity [OR （95%CI）： 1.25 （1.04‐1.52） P=0.021] under a recessive model of inheritance （QQ vs. KK＋KQ） without heterogeneity or publication bias. Conclusions The results from the present study have indicated that ENPP1/PC1 Q121 variant may increase the risk of obesity and that more well‐designed studies based on a larger population will be required to further evaluate the role of ENPP1/PC1 gene K121Q polymorphism in obesity and other related metabolic syndromes.
基金Supported by the National Key R&D Program of China(No.2018YFD0901400)National Natural Science Foundation of China(No.31672678)+1 种基金Ningbo Municipal Science and Technology International Cooperation Research Projects(No.2016D10017)the Zhejiang Provincial Major Program of Science and Technology(No.2016C02055-9)。
文摘The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate the oyster growth traits and the associations with bHLH genes variations,we analyzed the gene polymorphisms-traits association in a wild population,and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis.After screening the single nucleotide polymorphisms(SNPs)in three candidate genes of the bHLH family(88 bHLH genes in two wild oyster populations in total),we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene.This allele is a non-synonymous mutation(Phe/Leu)with an extremely significant association with shell width(P<0.01)and allele G is beneficial to shell width.This SNP on the CgLoblHLH4 gene might have a potential value as a genetic marker of growth traits that could be used in breeding in C.gigas in the future.
