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
Background: More and more chronic kidney disease (CKD) patients are accompanied with hyperuricaemia. As is known, hyperuricaemia is an independent hazard of both cardiovascular diseases (CVD) and chronic kidney diseas...Background: More and more chronic kidney disease (CKD) patients are accompanied with hyperuricaemia. As is known, hyperuricaemia is an independent hazard of both cardiovascular diseases (CVD) and chronic kidney diseases. We aim at identifying Single Nucleotide Polymorphism (SNP) difference of hURAT1 (rs7932775) and ABCG2 (rs3825016) on CKD patient with hyperuricemia and/or gout. Methods: All forty-two CKD patients were divided into two groups: hyperuricemia, and control group. 24 hours urine sample and serum were prepared for testing biochemistry parameters. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method is used to analyze hURAT1 and ABCG2 single nucleotide polymorphisms in different groups. Results: 17 patients have CT SNP of hURAT1 (rs7932775) and 13 patients have CT SNP of ABCG2 (rs3825016) in hyperuricemia group, while only 5 persons and 6 persons have the same mutations in control group respectively. 7 patients have CT SNP of both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group, while only 2 persons have the same mutations in control group. CT mutation rates of hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 60.7% (17/28) and 50% (13/28) respectively, higher than that of control group (35.7% (5/14) and 42.8% (6/14)). What is more, Double SNP mutations in both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 25% (7/28), higher than that of control group (14.2%, 2/14). Conclusion: There are higher mutation rates of CT SNP in hURAT1 (rs7932775) and/or ABCG2 (rs3825016) in hyperuricemia group. We can conclude that hyperuricemia is a high risk factor in progress of CKD, which is necessary to take measures of decreasing serum uric acid to delay CKD progress.展开更多
Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been report...Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer(CRC) have been described.Case presentation: Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a micro RNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers.Conclusions: By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.展开更多
This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association stu...This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.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
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
In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide as...In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide association study.In Japanese populations,the correlation between 2 SNPs on 17q and the risk of prostate cancer and tumor aggressiveness was also confirmed by a large-scale experiment.However,whether 17q is associated with prostate cancer and its clinical manifestations in Chinese populations is still unknown.Therefore,we conducted a case-control study in a northern Chinese population and tested 2 SNPs,rs4430796 and rs1859962,on 17q in 124 prostate cancer patients and 111 controls using polymerase chain reaction-high resolution melting curve(PCR-HRM) combined with sequencing.We analyzed the association of the 2 SNPs with the risk of prostate cancer as well as patients' lifestyles,onset ages,Gleason scores,PSA levels,and pathologic stages.We found a significant difference in the G allele of SNP rs1859962(P = 0.035,OR = 1.51,95% CI = 1.03-2.21) but not in the rs4430796 genotype frequency or allele frequency distribution between prostate cancer patients and the controls(P > 0.05).Neither of the SNPs was significantly associated with the onset age,Gleason score,PSA level,pathologic stage,or other clinical indicators of patients with prostate cancer(P > 0.05).Our results show that polymorphism of the G allele of SNP rs1859962 is associated with the risk of prostate cancer in a Chinese population.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： Available study revealed advanced tumors have a higher expression rate of MAGE-A3 gene which has a lot of single nucleotide polymorphism（SNP） loci with polymorphisms. This study aimed to analyze the all...Background： Available study revealed advanced tumors have a higher expression rate of MAGE-A3 gene which has a lot of single nucleotide polymorphism（SNP） loci with polymorphisms. This study aimed to analyze the allele frequency of SNP loci in MAGE-A3 gene and investigate the relationship between MAGE-A3 gene polymorphisms and clinical factors.Methods： Tumor samples of a cohort of 191 NSCLC patients were collected. EGFR m RNA expression were detected by q RT-PCR. SNPs in whole length of MAGE-A3 gene were detected by direct sequencing. Frequencies of the SNPs were correlated to gene expression, mutation status of EGFR and clinical factors.Results： Sequencing analysis confirmed that allele frequencies of genotypes on SNP loci rs5970360, rs5925210, rs5970361, rs5925211 and rs35123853 were CC（0.681）/CT（0.319）, CC（0.660）/CG（0.340）, CC（0.681）/CA（0.319）, AA（0.984）/AT（0.016） and GG（1.000）/GA（0.000）, respectively, which were different from the frequencies and genotypes of MAGE-A3 in SNP database. Chi-square tests showed the EGFR mR NA expression level had significant correlation with the genotypes of SNP loci rs5970360 and rs5925210. But all frequencies of each MAGE-A3 SNPs were not found significantly different between EGFR mutant and wild type patients. MAGE-A3 gene polymorphisms had no significant effects on survival of NSCLC patients.Conclusions： Chinese patients with NSCLC had different SNP patterns of MAGE-A3 in comparison with those in international SNP database. These MAGE-A3 SNP loci might have not prognostic significance. MAGE-A3 SNP loci rs5970360 and rs5925210 might be predictive for EGFR m RNA expression levels and helpful to the selection of patients for epidermal growth factor receptor（EGFR） targeted immunotherapy.展开更多
Objective To identify single nucleotide polymorphisms (SNPs) of human CatSper gene, themouse homologous gene product, which plays a crucial role in mouse male sterility.Methods We demonstrated a systematic screening o...Objective To identify single nucleotide polymorphisms (SNPs) of human CatSper gene, themouse homologous gene product, which plays a crucial role in mouse male sterility.Methods We demonstrated a systematic screening of SNPs in coding regions and flankingintronic regions of human CatSper gene in a sample subset from a total 210 male individuals byDNA sequencing. Then we used PCR single-strand conformation polymorphism (SSCP) analy-sis to determine the allele frequencies of the possible SNPs among the whole 210 Chinese Hanmale individuals.Results Three SNPs, including two novels, were identified and their allele frequencies weredetermined in the 210 Chinese Han male individuals. These SNPs were assembled into largeSNP database that promises to enable the dissection of the genetic basis of disease.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
Three breeds of sows were observed to investigate the relationship between Single Nucleotide Polymorphisms（SNPs） in Mu Opioid Receptor（MOR）and stereotypic behaviour,such as,sham-chewing,bar biting and standing sti...Three breeds of sows were observed to investigate the relationship between Single Nucleotide Polymorphisms（SNPs） in Mu Opioid Receptor（MOR）and stereotypic behaviour,such as,sham-chewing,bar biting and standing still in order to better understand the mechanism of stereotypic development of the animals in restrained conditions.MOR exon 2 partial sequences were amplified to analyze single nucleotide polymorphisms by PCR-SSCP.One SNP,a silence mutant was found.A significant difference （P〈0.01）was found in the frequency of genotypes in these 3 breeds where only the BB genotype,which was identical to that published in GenBank,was found in the Duroc breed,while no AA genotype was found in Landrace,3 genotypes AA,BB and AB were found in Yorkshire.The result also indicated that the individuals with AA and AB genotypes tended to be more active in sham-chewing than those with the BB genotype（P〈0.05）.The overall results of this study suggested that sham-chewing of sows may be subjected to both genetic control and environmental conditions,but activity level was more likely to be affected by their environment.We can putatively draw the conclusion that MOR gene has effect on the sham-chewing behavioral traits of sow.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： Nonsyndromic cleft lip with or without cleft palate（NSCL/P） is a common birth defect with unclear etiology. Both genetic and environmental factors may contribute to NSCL/P. Many genes have been identifie...Objective： Nonsyndromic cleft lip with or without cleft palate（NSCL/P） is a common birth defect with unclear etiology. Both genetic and environmental factors may contribute to NSCL/P. Many genes have been identified as candidate genes associated with this disease. Interferon regulatory factor 6（IRF6） gene and transforming growth factor-a（TGFA） gene seem to be crucial in the predisposition of NSCL/ P. Here we evaluated some single nucleotide polymorphisms（SNPs） loci of TGFA and IRF6 genes in Chinese nuclear families consisting of fathers, mothers and affected offspring with NSCL/P. Methods：Fifty patients of NSCL/P were confirmed by the plastic surgeons. They and their parents were included in the study, all with the informed consents. SNPs loci of TGFA and IRF6 genes were analyzed by microarray technology. Some PCR products were randomly chosen and sequenced to check microarray results. The distribution of gene type and allele frequency between patient group and parents group were compared. Then a Haplotype Relative Risk（HRR） and Transmission Disequilibrium Test（TDT） were performed. Results：The sequences of randomly selected PCR products were all consistent with the microarray results. All loci were in Hardy-Weinberg equilibrium. There were no significant differences in the distribution of genotypes and alleles between patients and their parents. Using HRR and TDT analyses the V274I of IRF6 was associated with NSCL/P, while another SNP locus oflRF6 was not. Strong evidence of linkage disequilibrium was found between the 2 SNP loci of TGFA and disease with the HRR analysis, but not with the TDT analysis. Conclusion：Our study confirms the contribution of IRF6 in the etiology of NSCL/P in populations of Asian ancestry. The association of TGFA with NSCL/P requires further research.展开更多
Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins,The association of Single Nucleotide Polymorphism(SNP)in the calpastatin gene with meat tenderness is a...Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins,The association of Single Nucleotide Polymorphism(SNP)in the calpastatin gene with meat tenderness is an important topic in meat production.Therefore efficient procedure to investigate the SNP is necessary.The objectives of this study were to detect the SNP of calpastatin gene at domain L marker(G/C transversion)of the Kamphaengsaen beef breed(KPS cattle;n=26)by the Amplification Refractory Mutation System(ARMS)compared with the Restriction Fragment Length Polymorphism(RFLP)methods and to determine the genotypes of the KPS cattle at that marker.Genomic DNA of calpastatin gene extracted from blood of the KPS cattle was detected with ARMS and RFLP methods.The ARMS system has utilized two primer pairs to amplify the two different alleles of a polymorphism in single PCR reaction to detected single base mutation.In this method,the alleles-specific primers had a mismatch at 3'terminal base and a second deliberate mismatch at position-2 from 3'terminus.While the RFLP method detected a polymorphism using PCR-base technique follow by RsaI restriction enzyme.Amplification of the ARMS method revealed that the results were not different from the conventional method of RFLP.Analysis of genotypes revealed that the KPS cattle inherited the CC,CG and GG genotypes at domain L marker.These were reliable when verified by nucleotide sequence analysis of PCR products.The animals were genotyped and determined for tenderness phenotype with this marker that predicted variation of an intronic polymorphism at domain L of the calpastatin gene.Therefore,the ARMS method was simple,efficient technique,and suitable for detecting SNP at domain L marker of the calpastatin gene.展开更多
Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression t...Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.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.
文摘Background: More and more chronic kidney disease (CKD) patients are accompanied with hyperuricaemia. As is known, hyperuricaemia is an independent hazard of both cardiovascular diseases (CVD) and chronic kidney diseases. We aim at identifying Single Nucleotide Polymorphism (SNP) difference of hURAT1 (rs7932775) and ABCG2 (rs3825016) on CKD patient with hyperuricemia and/or gout. Methods: All forty-two CKD patients were divided into two groups: hyperuricemia, and control group. 24 hours urine sample and serum were prepared for testing biochemistry parameters. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method is used to analyze hURAT1 and ABCG2 single nucleotide polymorphisms in different groups. Results: 17 patients have CT SNP of hURAT1 (rs7932775) and 13 patients have CT SNP of ABCG2 (rs3825016) in hyperuricemia group, while only 5 persons and 6 persons have the same mutations in control group respectively. 7 patients have CT SNP of both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group, while only 2 persons have the same mutations in control group. CT mutation rates of hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 60.7% (17/28) and 50% (13/28) respectively, higher than that of control group (35.7% (5/14) and 42.8% (6/14)). What is more, Double SNP mutations in both hURAT1 (rs7932775) and ABCG2 (rs3825016) in hyperuricemia group were 25% (7/28), higher than that of control group (14.2%, 2/14). Conclusion: There are higher mutation rates of CT SNP in hURAT1 (rs7932775) and/or ABCG2 (rs3825016) in hyperuricemia group. We can conclude that hyperuricemia is a high risk factor in progress of CKD, which is necessary to take measures of decreasing serum uric acid to delay CKD progress.
基金supported in part by funds obtained through an Italian law that allows taxpayers to allocate 0.5 percent share of their income tax contribution to a research institution of their choice
文摘Background: Androgen insensitivity syndrome(AIS), a disorder of sexual development in 46, XY individuals, is caused by loss-of-function mutations in the androgen receptor(AR) gene. A variety of tumors have been reported in association with AIS, but no cases with colorectal cancer(CRC) have been described.Case presentation: Here, we present a male patient with AIS who developed multiple early-onset CRCs and his pedigree. His first cousin was diagnosed with AIS and harbored the same AR gene mutation, but with no signs of CRC. The difference in clinical management for the two patients was that testosterone treatment was given to the proband for a much longer time compared with the cousin. The CRC family history was negative, and no germline mutations in well-known CRC-related genes were identified. A single nucleotide polymorphism array revealed a microduplication on chromosome 22q11.22 that encompassed a micro RNA potentially related to CRC pathogenesis. In the proband, whole exome sequencing identified a polymorphism in an oncogene and 13 rare loss-of-function variants, of which two were in CRC-related genes and four were in genes associated with other human cancers.Conclusions: By pathway analysis, all inherited germline genetic events were connected in a unique network whose alteration in the proband, together with continuous testosterone stimulation, may have played a role in CRC pathogenesis.
基金Project supported by Ovita Limited, Dunedin, New Zealand
文摘This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.
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 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.
文摘In European populations,7 single nucleotide polymorphisms(SNPs) on chromosome 17q,3 SNPs on 17q12,and 4 SNPs on 17q24.3 were recently identified to be closely related to the risk of prostate cancer by a genome-wide association study.In Japanese populations,the correlation between 2 SNPs on 17q and the risk of prostate cancer and tumor aggressiveness was also confirmed by a large-scale experiment.However,whether 17q is associated with prostate cancer and its clinical manifestations in Chinese populations is still unknown.Therefore,we conducted a case-control study in a northern Chinese population and tested 2 SNPs,rs4430796 and rs1859962,on 17q in 124 prostate cancer patients and 111 controls using polymerase chain reaction-high resolution melting curve(PCR-HRM) combined with sequencing.We analyzed the association of the 2 SNPs with the risk of prostate cancer as well as patients' lifestyles,onset ages,Gleason scores,PSA levels,and pathologic stages.We found a significant difference in the G allele of SNP rs1859962(P = 0.035,OR = 1.51,95% CI = 1.03-2.21) but not in the rs4430796 genotype frequency or allele frequency distribution between prostate cancer patients and the controls(P > 0.05).Neither of the SNPs was significantly associated with the onset age,Gleason score,PSA level,pathologic stage,or other clinical indicators of patients with prostate cancer(P > 0.05).Our results show that polymorphism of the G allele of SNP rs1859962 is associated with the risk of prostate cancer in a Chinese population.
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.
基金supported by grants from the Foundation of Guangdong Science and Technology Department(Grant No.2010B031600158,XN Yang)Key Lab System Project of Guangdong Science and Technology Department(Grant No.2012A061400006,YL WU)
文摘Background： Available study revealed advanced tumors have a higher expression rate of MAGE-A3 gene which has a lot of single nucleotide polymorphism（SNP） loci with polymorphisms. This study aimed to analyze the allele frequency of SNP loci in MAGE-A3 gene and investigate the relationship between MAGE-A3 gene polymorphisms and clinical factors.Methods： Tumor samples of a cohort of 191 NSCLC patients were collected. EGFR m RNA expression were detected by q RT-PCR. SNPs in whole length of MAGE-A3 gene were detected by direct sequencing. Frequencies of the SNPs were correlated to gene expression, mutation status of EGFR and clinical factors.Results： Sequencing analysis confirmed that allele frequencies of genotypes on SNP loci rs5970360, rs5925210, rs5970361, rs5925211 and rs35123853 were CC（0.681）/CT（0.319）, CC（0.660）/CG（0.340）, CC（0.681）/CA（0.319）, AA（0.984）/AT（0.016） and GG（1.000）/GA（0.000）, respectively, which were different from the frequencies and genotypes of MAGE-A3 in SNP database. Chi-square tests showed the EGFR mR NA expression level had significant correlation with the genotypes of SNP loci rs5970360 and rs5925210. But all frequencies of each MAGE-A3 SNPs were not found significantly different between EGFR mutant and wild type patients. MAGE-A3 gene polymorphisms had no significant effects on survival of NSCLC patients.Conclusions： Chinese patients with NSCLC had different SNP patterns of MAGE-A3 in comparison with those in international SNP database. These MAGE-A3 SNP loci might have not prognostic significance. MAGE-A3 SNP loci rs5970360 and rs5925210 might be predictive for EGFR m RNA expression levels and helpful to the selection of patients for epidermal growth factor receptor（EGFR） targeted immunotherapy.
文摘Objective To identify single nucleotide polymorphisms (SNPs) of human CatSper gene, themouse homologous gene product, which plays a crucial role in mouse male sterility.Methods We demonstrated a systematic screening of SNPs in coding regions and flankingintronic regions of human CatSper gene in a sample subset from a total 210 male individuals byDNA sequencing. Then we used PCR single-strand conformation polymorphism (SSCP) analy-sis to determine the allele frequencies of the possible SNPs among the whole 210 Chinese Hanmale individuals.Results Three SNPs, including two novels, were identified and their allele frequencies weredetermined in the 210 Chinese Han male individuals. These SNPs were assembled into largeSNP database that promises to enable the dissection of the genetic basis of disease.
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 National Natural Sciences Foundation of China(39970533)
文摘Three breeds of sows were observed to investigate the relationship between Single Nucleotide Polymorphisms（SNPs） in Mu Opioid Receptor（MOR）and stereotypic behaviour,such as,sham-chewing,bar biting and standing still in order to better understand the mechanism of stereotypic development of the animals in restrained conditions.MOR exon 2 partial sequences were amplified to analyze single nucleotide polymorphisms by PCR-SSCP.One SNP,a silence mutant was found.A significant difference （P〈0.01）was found in the frequency of genotypes in these 3 breeds where only the BB genotype,which was identical to that published in GenBank,was found in the Duroc breed,while no AA genotype was found in Landrace,3 genotypes AA,BB and AB were found in Yorkshire.The result also indicated that the individuals with AA and AB genotypes tended to be more active in sham-chewing than those with the BB genotype（P〈0.05）.The overall results of this study suggested that sham-chewing of sows may be subjected to both genetic control and environmental conditions,but activity level was more likely to be affected by their environment.We can putatively draw the conclusion that MOR gene has effect on the sham-chewing behavioral traits of sow.
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 Medical Technology Development Foundation of Jiangsu Provincial Health Bureau of China (H200513)Changjiang Scholars and Innovative Research Team in University (IRT0631) and National 973 Program(2006CB944005)
文摘Objective： Nonsyndromic cleft lip with or without cleft palate（NSCL/P） is a common birth defect with unclear etiology. Both genetic and environmental factors may contribute to NSCL/P. Many genes have been identified as candidate genes associated with this disease. Interferon regulatory factor 6（IRF6） gene and transforming growth factor-a（TGFA） gene seem to be crucial in the predisposition of NSCL/ P. Here we evaluated some single nucleotide polymorphisms（SNPs） loci of TGFA and IRF6 genes in Chinese nuclear families consisting of fathers, mothers and affected offspring with NSCL/P. Methods：Fifty patients of NSCL/P were confirmed by the plastic surgeons. They and their parents were included in the study, all with the informed consents. SNPs loci of TGFA and IRF6 genes were analyzed by microarray technology. Some PCR products were randomly chosen and sequenced to check microarray results. The distribution of gene type and allele frequency between patient group and parents group were compared. Then a Haplotype Relative Risk（HRR） and Transmission Disequilibrium Test（TDT） were performed. Results：The sequences of randomly selected PCR products were all consistent with the microarray results. All loci were in Hardy-Weinberg equilibrium. There were no significant differences in the distribution of genotypes and alleles between patients and their parents. Using HRR and TDT analyses the V274I of IRF6 was associated with NSCL/P, while another SNP locus oflRF6 was not. Strong evidence of linkage disequilibrium was found between the 2 SNP loci of TGFA and disease with the HRR analysis, but not with the TDT analysis. Conclusion：Our study confirms the contribution of IRF6 in the etiology of NSCL/P in populations of Asian ancestry. The association of TGFA with NSCL/P requires further research.
文摘Calpastatin is an endogenous inhibitor of calpain which is responsible for the breakdown of myofibrillar proteins,The association of Single Nucleotide Polymorphism(SNP)in the calpastatin gene with meat tenderness is an important topic in meat production.Therefore efficient procedure to investigate the SNP is necessary.The objectives of this study were to detect the SNP of calpastatin gene at domain L marker(G/C transversion)of the Kamphaengsaen beef breed(KPS cattle;n=26)by the Amplification Refractory Mutation System(ARMS)compared with the Restriction Fragment Length Polymorphism(RFLP)methods and to determine the genotypes of the KPS cattle at that marker.Genomic DNA of calpastatin gene extracted from blood of the KPS cattle was detected with ARMS and RFLP methods.The ARMS system has utilized two primer pairs to amplify the two different alleles of a polymorphism in single PCR reaction to detected single base mutation.In this method,the alleles-specific primers had a mismatch at 3'terminal base and a second deliberate mismatch at position-2 from 3'terminus.While the RFLP method detected a polymorphism using PCR-base technique follow by RsaI restriction enzyme.Amplification of the ARMS method revealed that the results were not different from the conventional method of RFLP.Analysis of genotypes revealed that the KPS cattle inherited the CC,CG and GG genotypes at domain L marker.These were reliable when verified by nucleotide sequence analysis of PCR products.The animals were genotyped and determined for tenderness phenotype with this marker that predicted variation of an intronic polymorphism at domain L of the calpastatin gene.Therefore,the ARMS method was simple,efficient technique,and suitable for detecting SNP at domain L marker of the calpastatin gene.
文摘Background: A deletion of 32 bp in the nucleotide sequence of CCR5 gene results in a defective CCR5 which confers protection from HIV infection in the homozygous state, while reducing the rate of disease progression to AIDS and death in the heterozygous state. The status of the CCR5Δ32 gene has not been reported in Nigeria. Aim: This study was aimed at analyzing single nucleotide polymorphism of CCR5 gene among the Ijaws resident in Yenagoa, Nigeria. Methods: 100 subjects (75 HIV negative and 25 HIV positive control) were recruited for this study. The CCR5 genes were amplified by 2 Stage PCR reaction using GeneAmp 9700 PCR system utilizing specific primers that would flank 32 bp deletion, followed by agarose gel electrophoresis, DNA sequencing of 20 subjects was done followed by phylogenetic and polymorphism analysis. Results: The results showed that 75 (100%) of the HIV negative subjects had 189 base pair in their CCR5 gene. Nucleotide of the 20 (100%) of the sequenced samples were conservatively same and no SNP was observed. Conclusion: This study documented no SNPs in CCR5 gene of the study population hence;the study population has no protection from HIV infection.
