Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-...Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-wide association analysis to identify the EPN4 gene,which is allelic to NARROW LEAF1(NAL1).Overexpression lines containing the Teqing allele(TQ)of EPN4 had significantly increased EPN.NIL-EPN4^(TQ) in japonica(geng)cultivar Lemont(LT)exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT.Haplotype analysis indicated that accessions with EPN4-1 had medium EPN,medium grain number,and medium grain weight,but had the highest grain yield among seven haplotypes,indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield.Furthermore,accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations.Therefore,pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.展开更多
Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been ass...Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been assessed yet. Therefore the objective of this study is to identify in Abidjan the HbS haplotypes that modulate HU treatment responses. Methods: In a cross-sectional descriptive and analytical study, children aged 5 to 15 years with SCD, and carrying the hemoglobin phenotypes SSFA2 and SFA2, were recruited into a HU treatment cohort. Various parameters on the haplotypes and the outcomes of the treatment were analyzed. Results: Thirty nine children with SCD were included. The phenotypic profile of the cohort was 86.6% of SSFA2 and 15.4% of SFA2. Three haplotypes were found, the Benin haplotype, the Senegal haplotype, and an atypical one. The participants belonged to three genotypes, Benin/atypical (64.1%), Benin/Senegal (33.3%) and Senegal/Senegal (2.6%). Overall, HU treatment was successful in all haplotypes with 12 out of 39 patients failing treatment after 12 months in the Benin haplotype group. The association between HU treatment success and the Benin haplotype was found in terms of the decrease in the number of white blood cells and the students missing class. Conclusion: The study revealed that inferring haplotype based on the phenotypic profile could be inaccurate. The proportion of atypical haplotype that were not previously described in Côte d’Ivoire was high. All the haplotypes seemed to be associated with HU treatment success but some patients with Benin haplotype did not respond well.展开更多
Rice is sensitive to salinity stress at both the seedling and reproductive stages.The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions o...Rice is sensitive to salinity stress at both the seedling and reproductive stages.The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions of India.These genotypes were evaluated in hydroponics under control[electrical conductivity(ECe)~1.2 dS/m]and saline(ECe~10.0 dS/m)environments along with susceptible(IR29)and tolerant(FL478)checks.The stress susceptibility index for eight morphophysiological traits was estimated.Analysis of variance showed significant differences among the genotypes for all the parameters studied in control,stress and relative stress conditions.We identified 3 landraces(Kuttimanja,Tulasimog and IET-13713I)as tolerant and 14 lines as moderately tolerant to salt stress.Strong correlations in the morphological(root and shoot lengths)and physiological traits(shoot Na^(+),Ca^(2+)and Mg^(2+)contents,and Na^(+)/K^(+)ratio)were observed under all the conditions.The hierarchical cluster analysis grouped the genotypes into five clusters,among which cluster Ⅱ comprised salt-tolerant lines.Haplotyping of Saltol region using 11 simple sequence repeat markers on 17 saline tolerant and moderately tolerant lines was conducted.Markers AP3206F,RM10793 and RM3412b,located close to SKC1 gene(11.23‒12.55 Mb),displayed diverse allelic variations and they were not related to the FL478 type.In this region,tolerant lines like Kuttimanja,IET-13713I and Tulasimog have new alleles.As a result,these lines may be suitable candidates for novel genomic regions governing rice salinity tolerance.Salt-tolerance ability of Kuttimanja,Tulasimog and IET-13713I was validated in two years in three salinity stress environments.These promising lines can be used in breeding programs to broaden the genetic base of salinity tolerance in rice,and it may help to dissect key genomic regions responsible for salinity tolerance.展开更多
Objective Y-Chromosomal short tandem repeat polymorphism(Y-STR)analysis plays an indispensable role in the identification of male individuals,population genetics,and biogeographic research.While profiles of many popul...Objective Y-Chromosomal short tandem repeat polymorphism(Y-STR)analysis plays an indispensable role in the identification of male individuals,population genetics,and biogeographic research.While profiles of many populations based on Y-STR markers in human genomes are ample,haplotype data for the Wuwei Han are still scarce.Methods In this study,2180 unrelated Wuwei Han male individuals residing in Gansu Province,China were collected and genotyped using the novel Microreader™40Y Plus ID system.Phylogenetic relationship reconstructions,multidimensional scaling(MDS),and heatmap analysis were performed based on the genetic distance(Rst)values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database(YHRD).Results A total of 2129 unique haplotypes were obtained,and the haplotype diversity(HD)and discrimination capacity(DC)for the Wuwei Han were 0.9999 and 0.9931,respectively.Conclusion Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians,especially the geographically close Han populations.Overall,this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.展开更多
BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese po...BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese population.AIM To explored associations of two SNPs and haplotypes in the lncRNA NONHSAT102891 promoter region with depression susceptibility in Chinese population.METHODS This this case-control association study was approved by the Ethics Committee of Chengdu Medical College(approval number:201815).Patient diagnosis was based on DSM-IV criteria.We selected a total of 480 patients with depression and 329 healthy controls with no history of psychopathology,and performed genotyping of two SNPs by extracting peripheral venous blood samples from the subjects.The function of the two lncRNA NONHSAT102891 promoter G/C and A/T haplotypes was detected by dual-luciferase reporter assays of human embryonic kidney 293T transfected cells.RESULTS Stratified analysis of clinical and genotypic characteristics of our cohort showed that the degree of mild depressive episodes associated with the rs6230 TC/CC genotype increased by 1.59 times[TC/CC vs TT:odds ratio(OR)=1.59,95%confidence interval(CI):1.08-2.35,P=0.019].The haploid analysis revealed linkage disequilibrium between rs3792747 and rs6230,and the double SNP CG haplotype was more common in the control group compared to case group,indicating that this haplotype significantly reduced the risk of depression(C/G vs T/A:OR=0.42,95%CI:0.21-0.83,P=0.01).There was no significant difference in the dual-luciferase reporter activity of the G/C and A/T haplotypes compared with the control group(P>0.05),indicating that the double SNP haplotype has no transcrip-tional activity.CONCLUSION The rs3792747 and rs6230 CG haplotypes of the lncRNA NONHSA T102891 promoter may be related to a reduced risk of depression in the Han Chinese population.展开更多
The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by l...The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by low predictive potential and inability to predict which patients are at risk of developing metastatic disease. The aim of this study is to investigate the exon 4 of the KLK2 gene of subjects for changes in its nucleotide sequences (SNPs) and determine the correlation of these changes with serum PSA in an Igbo population of Nigeria. One hundred male subjects aged 40 years and above, who gave their consent, were used for the study. Their PSA determinations were done using ELISA technique while genetic studies were carried out using real-time PCR. tPSA, fPSA, and % fPSA of the subjects ranged between 0.8% - 18.30%, 0.10% - 1.60% and 0.0% - 0.7% respectively. Of the 100 subjects, 28 subjects had tPSA levels above 4.0 ng/ml with a mean of 7.10 (±3.30) ng/ml. Those with tPSA less than 4 ng/ml had a mean of 1.87 (±0.85) ng/m. 15 subjects showed SNPs with a mean tPSA of 6.87 (±4.82) ng/ml while the remaining 85 subjects without SNPs had a mean of 1.86 (±0.80) ng/ml. Results from direct DNA sequencing showed 11 SNPs. Ten subjects are curated in SNP database while one is uncurated. The Chi-square test showed significant association (p = 0.00) between tPSA levels and SNPs mutation (X<sup>2</sup> = 17.35, p = 0.00). A Kruskal-Wallis test demonstrated that the positional arrangement of the SNP mutations had no effect on PSA-total or free-values (H (10) = 10.92, p = 0.28;H (10) = 10.07, p = 0.38 respectively). Two SNPs: rs6072 and rs74478031 were associated with elevated PSA levels (p < 0.05). Their presence, therefore, has the potential to serve, in conjunction with raised PSA, as biomarkers of prostate cancer in the study population.展开更多
AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping wa...AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.展开更多
Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachmen...Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachment,wheat is increasingly subjected to environmental stress.Moreover,expanding urbanization increasingly encroaches upon prime agricultural land in countries like China,and alternative cropping areas must be found.Some of these areas have moderate constraining factors,such as salinity.Therefore,it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress.In this study,a panel of 307 wheat accessions,including local landraces,exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since1940,were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance.Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940 s.However,improvements in salinity tolerance during modern breeding are not as obvious as that of yield.To broaden genetic diversity for increasing salt tolerance,there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.展开更多
AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic seq...AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic sequences of the NR3C1 gene in 181 IBD patients, determined the single nucleotide polymorphisms, and predicted the NR3C1 haplotypes. Furthermore, we investigated whether certain NR3C1 haplotypes are significantly associated with steroid therapy outcomes. RESULTS: We detected 13 NR3C1 variants, which led to the formation of 17 different haplotypes with a certainty of > 95% in 173 individuals. The three most commonly occurring haplotypes were included in the association analysis of the influence of haplotype on steroid therapy outcome or IBD activity. None of the NR3C1 haplotypes showed statistically signifi cant association with glucocorticoid therapy success. CONCLUSION: NR3C1 haplotypes are not related to steroid therapy outcome.展开更多
The authors want to changed the web link of the software platform in this Briefing.Page 97,section 'INTRODUCTION',the web link of SHEsis is changed from http://www.nhgg.org/analysis tohttp://analysis.bio-x.
The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2...The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.展开更多
Objectire To disclose the relevancy of idiopathic membranous nephropathy (IMN) to HLA haplotype in Shanghai region population. Methods Analysis of HLA genotype and haplotype was carried out in 33 IMN patients and 71 c...Objectire To disclose the relevancy of idiopathic membranous nephropathy (IMN) to HLA haplotype in Shanghai region population. Methods Analysis of HLA genotype and haplotype was carried out in 33 IMN patients and 71 controls in Shanghai using PCR - SSO. Rcsults The normal haplotypes of controls were DR9- DQA1 * 0301, DR4 - DQA1 *0301, DR12- DQB1 * 0301 and DR9- DQB1 * 0303. The haplotype frequency (Hf) of DR2- DQA1 * 0101 was the highest in IMN group (Hf=12.86), presenting significant linkage disequilibrium. The dofference between two groups was significant (P<0.05). Conclusion It was concluded that the susceptibility of IMN in Shanghai population was associated with specific HLA haplotype.展开更多
Objective To investigate HLA-A,-B and -DRB1 allele and HLA-A-B-DRB1 haplotype frequencies in Mongolia ethnic group. Methods HLA-A, -B, -DRB1 allele and haplotype in the Mongolia ethnic group were investigated based on...Objective To investigate HLA-A,-B and -DRB1 allele and HLA-A-B-DRB1 haplotype frequencies in Mongolia ethnic group. Methods HLA-A, -B, -DRB1 allele and haplotype in the Mongolia ethnic group were investigated based on 93 individuals by PCR- sequence-based typing (SBT) method. Results Twenty-one alleles were detected for HLA-A, 44 for HLA-B, and 26 for HLA-DRB1. The most frequent alleles were HLA-A*2402(0.2097), HLA-B*1302(0.0699), and HLA-DRB1*0701(0.1237). The most common HLA-A-B-DRB1 haplotype were A*3001-B*1302-DRB1*0701, A*0101-B*3701-DRB1*1001, followed by the A*0201-B*4601-DRB1*0901, A*2402-B*4801-DRB1*1101, A*2402-B*5201-DRB1*1501, A*3201-B*3503-DRB1*1301, and A*3303-B*5801-DRB1*0301, which were also presented in Chinese populations. Conclusion The data can be used in forensic and paternity tests to estimate the frequency of a DNA profile or anthropologic research. The characteristics of the distribution of HLA alleles revealed that Mongolia ethnic group is characterized by northern Mongolian Chinese.展开更多
Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between ...Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between SNPs of the MDR1 gene (C1236T, G2677T/A, C3435T) and IM response in chronic myeloid leukemia (CML) patients. Method: A retrospective case-control study was conducted on 48 patients with CML undergoing IM therapy. All patients were genotyped using PCR-RFLP method. Results: The genotype and allele frequencies of C1236T and C3435T were not significantly different between CML patients responders and non-responders to IM (p > 0.05). The frequencies of 2677T allele and 2677TT genotype were significantly increased in CML patients IM responders which as compared with IM non-responders (50% vs 26.9%, p = 0.013 and 27.3% vs 3.8%, p = 0.029 respectively). Whereas the 2677AA genotype and CAC haplotype were found only in CML patients IM non-responders (15.4%). Conclusion: Pretreatment genotyping of G2677A/T appears to be useful for predicting IM resistance, which may allow the best choice of drug treatment for CML patients.展开更多
Pomoxis nigromaculatus, more commonly referred to as black crappie is indigenous to fresh water streams and lakes in the eastern United States and supports an important recreational fishery. We examined the genetic po...Pomoxis nigromaculatus, more commonly referred to as black crappie is indigenous to fresh water streams and lakes in the eastern United States and supports an important recreational fishery. We examined the genetic population structure of black crappie inhabiting three Georgian Lakes, Lake Sidney Lanier, Lake Seminole and Hartwell Lake. DNA sequencing of 229 fish samples, utilizing the DNA barcode marker cytochrome oxidase subunit I (COI) revealed 27 polymorphic sites which defined nine haplotypes. Only haplotype 2 was shared between all sample sites with six other haplotypes being unique for individual lakes, for an overall haplotype diversity of 0.734. Tajima’s D and Fu’s tests were implemented to assess departures from neutral expectations. Fst pairwise comparisons were statistically significant among all populations of black crappie evaluated in this study.展开更多
In this work, we study predicting the effect of non-synonymous SNPs on several cancers. We trained classifiers on both sequential and structural features extracted from the affected genes and assessed the predictions ...In this work, we study predicting the effect of non-synonymous SNPs on several cancers. We trained classifiers on both sequential and structural features extracted from the affected genes and assessed the predictions made by the trained classifiers using cross validation. Specifically, we investigated how the prediction performance can be improved by connecting SNPs in the context of haplotype and interacting sites of proteins encoded by affected genes. We found that accuracy was consistently enhanced by combining sequential and structural features, with increase ranging from a few percentage points up to more than 20 percentage points. The results for putting SNPs in the context of interacting sites were less consistent. Compared to individual SNPs, these that appear together in haplotype showed stronger correlation with one another and with the phenotype, and therefore led to significant improvement inprediction performance, with ROC score increased from 0.81 to 0.95. Although some similar effect has been expected for connecting SNPs to interacting sites in proteins, the performance actually got worse. This decrease in prediction accuracy may be caused by the small data set being used in the study, as many affected proteins in the study do not have known interacting sites.展开更多
For case-parents data, the information from offspring can be used to reduce the uncertainty of parents’ haplotype. In this article we develop likelihood ratio test to compare haplotype frequencies in transmitted and ...For case-parents data, the information from offspring can be used to reduce the uncertainty of parents’ haplotype. In this article we develop likelihood ratio test to compare haplotype frequencies in transmitted and non-transmitted group. The maximum likelihood estimate of the haplotype frequencies for the family data is obtained via expectation-maximization (EM) algorithm. Our proposed method can handle the uncertainty of haplotypes and missing data. The simulations show that the method is more powerful to test association between haplotype and traits than TRANSMIT. We also demonstrated the method to detect the association between Megsin gene and immunoglobulin A nephropathy.展开更多
The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individua...The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individuals in the end result. In some cases, there is excessive bone atrophy, which complicates the dental restorative treatment. The alveolar ridge receives the mechanical load continuously from the periodontal ligament connected to the teeth and it diminishes dramatically as a consequence of dental extraction;thus it is believed the continuing pattern of the alveolar bone resorption is related to this change. The reduced partial pressure of oxygen is the most prominent event from the reduced mechanical load. Vascular Endothelial Growth Factor (VEGF), regulated by HIF-1, reported close association with angiogenesis and bone turn over, where partial oxygen pressure has changed. Therefore the genetic association between Single Nucleotide Polymorphsim (SNP) of VEGF gene and RRR was investigated. 120 subjects (70.93 ± 9.28 years) which were treated at Dental clinic of Yonsei University with edentulous mandible were recruited. Mandibular bone height was measured following the protocol of the American College of Prosthodontists. Three variants, rs1570360, rs25648, and rs3025039 in VEGF from previous study, were used as tag-SNPs and genotyping for the study. Student’s t-test and ANOVA were used for statistical analysis. There was a notable association with rs1570360 (P = 0.051) in dominant group and haplotype A-C-C showed a statistically significant association with RRR in dominant group (P = 0.042). Results of this study may be useful in developing novel genetic diagnostic tests and identifying Koreans susceptible to developing severe RRR after dental extraction.展开更多
Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorph...Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorphic sites was also conducted, a few identified haplotypes were novel while the remainder was previously reported, haplotype1222212 was the most frequent haplotype in the study group and a strong linkage disequilibrium between two polymorphic restriction sites in these β thalassemia patients was uncovered.展开更多
基金This work was funded by the National Key Research and Development Program of China(2023YFF1000404)the Shenzhen Basic Research and Development Key Program of China(JCYJ20200109150713553)Hainan Key Research and Development in Modern Agriculture of China(ZDYF2021Y128).
文摘Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-wide association analysis to identify the EPN4 gene,which is allelic to NARROW LEAF1(NAL1).Overexpression lines containing the Teqing allele(TQ)of EPN4 had significantly increased EPN.NIL-EPN4^(TQ) in japonica(geng)cultivar Lemont(LT)exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT.Haplotype analysis indicated that accessions with EPN4-1 had medium EPN,medium grain number,and medium grain weight,but had the highest grain yield among seven haplotypes,indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield.Furthermore,accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations.Therefore,pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.
文摘Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been assessed yet. Therefore the objective of this study is to identify in Abidjan the HbS haplotypes that modulate HU treatment responses. Methods: In a cross-sectional descriptive and analytical study, children aged 5 to 15 years with SCD, and carrying the hemoglobin phenotypes SSFA2 and SFA2, were recruited into a HU treatment cohort. Various parameters on the haplotypes and the outcomes of the treatment were analyzed. Results: Thirty nine children with SCD were included. The phenotypic profile of the cohort was 86.6% of SSFA2 and 15.4% of SFA2. Three haplotypes were found, the Benin haplotype, the Senegal haplotype, and an atypical one. The participants belonged to three genotypes, Benin/atypical (64.1%), Benin/Senegal (33.3%) and Senegal/Senegal (2.6%). Overall, HU treatment was successful in all haplotypes with 12 out of 39 patients failing treatment after 12 months in the Benin haplotype group. The association between HU treatment success and the Benin haplotype was found in terms of the decrease in the number of white blood cells and the students missing class. Conclusion: The study revealed that inferring haplotype based on the phenotypic profile could be inaccurate. The proportion of atypical haplotype that were not previously described in Côte d’Ivoire was high. All the haplotypes seemed to be associated with HU treatment success but some patients with Benin haplotype did not respond well.
基金the Department of Science and Technology,Government of India(Grant No.CRG/2020/003078).
文摘Rice is sensitive to salinity stress at both the seedling and reproductive stages.The present study used 145 rice genotypes comprising of 100 landraces and 45 advanced breeding lines collected from different regions of India.These genotypes were evaluated in hydroponics under control[electrical conductivity(ECe)~1.2 dS/m]and saline(ECe~10.0 dS/m)environments along with susceptible(IR29)and tolerant(FL478)checks.The stress susceptibility index for eight morphophysiological traits was estimated.Analysis of variance showed significant differences among the genotypes for all the parameters studied in control,stress and relative stress conditions.We identified 3 landraces(Kuttimanja,Tulasimog and IET-13713I)as tolerant and 14 lines as moderately tolerant to salt stress.Strong correlations in the morphological(root and shoot lengths)and physiological traits(shoot Na^(+),Ca^(2+)and Mg^(2+)contents,and Na^(+)/K^(+)ratio)were observed under all the conditions.The hierarchical cluster analysis grouped the genotypes into five clusters,among which cluster Ⅱ comprised salt-tolerant lines.Haplotyping of Saltol region using 11 simple sequence repeat markers on 17 saline tolerant and moderately tolerant lines was conducted.Markers AP3206F,RM10793 and RM3412b,located close to SKC1 gene(11.23‒12.55 Mb),displayed diverse allelic variations and they were not related to the FL478 type.In this region,tolerant lines like Kuttimanja,IET-13713I and Tulasimog have new alleles.As a result,these lines may be suitable candidates for novel genomic regions governing rice salinity tolerance.Salt-tolerance ability of Kuttimanja,Tulasimog and IET-13713I was validated in two years in three salinity stress environments.These promising lines can be used in breeding programs to broaden the genetic base of salinity tolerance in rice,and it may help to dissect key genomic regions responsible for salinity tolerance.
基金supported by grants from the Shaanxi Basic Research Program of Natural Science(No.2021JQ-392)the International Cooperation Project of Shaanxi Province(No.2021KW-47).
文摘Objective Y-Chromosomal short tandem repeat polymorphism(Y-STR)analysis plays an indispensable role in the identification of male individuals,population genetics,and biogeographic research.While profiles of many populations based on Y-STR markers in human genomes are ample,haplotype data for the Wuwei Han are still scarce.Methods In this study,2180 unrelated Wuwei Han male individuals residing in Gansu Province,China were collected and genotyped using the novel Microreader™40Y Plus ID system.Phylogenetic relationship reconstructions,multidimensional scaling(MDS),and heatmap analysis were performed based on the genetic distance(Rst)values between our studied population and other populations of the Ymax module in the Y-STR Haplotype Reference Database(YHRD).Results A total of 2129 unique haplotypes were obtained,and the haplotype diversity(HD)and discrimination capacity(DC)for the Wuwei Han were 0.9999 and 0.9931,respectively.Conclusion Our results demonstrate that the Wuwei Han population had intimate genetic relationships with East Asians,especially the geographically close Han populations.Overall,this Y-Chromosomal assay gives valuable information about paternal lineages in male individual tracking and genealogical database construction.
基金Supported by National Natural Science Foundation of China,No.81901379Chengdu Medical College Graduate Research Innovation Fund Project,No.YCX2023-01-03National Undergraduate Training Program for Innovation and Entrepreneurship,No.202113705034.
文摘BACKGROUND Our previous study reported that the single-nucleotide polymorphism(SNP)rs155979 GC in the promoter region of long-chain non-coding RNA(lncRNA)NONHSAT102891 affects depression susceptibility in a Chinese population.AIM To explored associations of two SNPs and haplotypes in the lncRNA NONHSAT102891 promoter region with depression susceptibility in Chinese population.METHODS This this case-control association study was approved by the Ethics Committee of Chengdu Medical College(approval number:201815).Patient diagnosis was based on DSM-IV criteria.We selected a total of 480 patients with depression and 329 healthy controls with no history of psychopathology,and performed genotyping of two SNPs by extracting peripheral venous blood samples from the subjects.The function of the two lncRNA NONHSAT102891 promoter G/C and A/T haplotypes was detected by dual-luciferase reporter assays of human embryonic kidney 293T transfected cells.RESULTS Stratified analysis of clinical and genotypic characteristics of our cohort showed that the degree of mild depressive episodes associated with the rs6230 TC/CC genotype increased by 1.59 times[TC/CC vs TT:odds ratio(OR)=1.59,95%confidence interval(CI):1.08-2.35,P=0.019].The haploid analysis revealed linkage disequilibrium between rs3792747 and rs6230,and the double SNP CG haplotype was more common in the control group compared to case group,indicating that this haplotype significantly reduced the risk of depression(C/G vs T/A:OR=0.42,95%CI:0.21-0.83,P=0.01).There was no significant difference in the dual-luciferase reporter activity of the G/C and A/T haplotypes compared with the control group(P>0.05),indicating that the double SNP haplotype has no transcrip-tional activity.CONCLUSION The rs3792747 and rs6230 CG haplotypes of the lncRNA NONHSA T102891 promoter may be related to a reduced risk of depression in the Han Chinese population.
文摘The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by low predictive potential and inability to predict which patients are at risk of developing metastatic disease. The aim of this study is to investigate the exon 4 of the KLK2 gene of subjects for changes in its nucleotide sequences (SNPs) and determine the correlation of these changes with serum PSA in an Igbo population of Nigeria. One hundred male subjects aged 40 years and above, who gave their consent, were used for the study. Their PSA determinations were done using ELISA technique while genetic studies were carried out using real-time PCR. tPSA, fPSA, and % fPSA of the subjects ranged between 0.8% - 18.30%, 0.10% - 1.60% and 0.0% - 0.7% respectively. Of the 100 subjects, 28 subjects had tPSA levels above 4.0 ng/ml with a mean of 7.10 (±3.30) ng/ml. Those with tPSA less than 4 ng/ml had a mean of 1.87 (±0.85) ng/m. 15 subjects showed SNPs with a mean tPSA of 6.87 (±4.82) ng/ml while the remaining 85 subjects without SNPs had a mean of 1.86 (±0.80) ng/ml. Results from direct DNA sequencing showed 11 SNPs. Ten subjects are curated in SNP database while one is uncurated. The Chi-square test showed significant association (p = 0.00) between tPSA levels and SNPs mutation (X<sup>2</sup> = 17.35, p = 0.00). A Kruskal-Wallis test demonstrated that the positional arrangement of the SNP mutations had no effect on PSA-total or free-values (H (10) = 10.92, p = 0.28;H (10) = 10.07, p = 0.38 respectively). Two SNPs: rs6072 and rs74478031 were associated with elevated PSA levels (p < 0.05). Their presence, therefore, has the potential to serve, in conjunction with raised PSA, as biomarkers of prostate cancer in the study population.
基金Supported by The National R and D Program for Cancer ControlMinistry of Health and Welfare+1 种基金South KoreaNo.1120330
文摘AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.
基金financially supported by the National Youth Foundation of China(31901494,31601306,and 31901869)the National Natural Science Foundation of China(31971890)+1 种基金supported by Young Elite Scientists Sponsorship Program of China Association for Science and Technology(2017QNRC001)the Natural Science Fund of Jiangsu Province,China(BK20161092)。
文摘Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachment,wheat is increasingly subjected to environmental stress.Moreover,expanding urbanization increasingly encroaches upon prime agricultural land in countries like China,and alternative cropping areas must be found.Some of these areas have moderate constraining factors,such as salinity.Therefore,it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress.In this study,a panel of 307 wheat accessions,including local landraces,exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since1940,were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance.Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940 s.However,improvements in salinity tolerance during modern breeding are not as obvious as that of yield.To broaden genetic diversity for increasing salt tolerance,there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.
基金Supported by The Swiss IBD Cohort Study (SNF Grant 33CSC0-108792)the Swiss National Science Foundation (Grant 32-120463/1)+2 种基金the Zurich University Research Priority Pro-gramme "Integrative Human Physiology" (ZIHP)the Center of Clinical Research at the University Hospital Zurichthe Novartis Foundation for Biomedical Research
文摘AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic sequences of the NR3C1 gene in 181 IBD patients, determined the single nucleotide polymorphisms, and predicted the NR3C1 haplotypes. Furthermore, we investigated whether certain NR3C1 haplotypes are significantly associated with steroid therapy outcomes. RESULTS: We detected 13 NR3C1 variants, which led to the formation of 17 different haplotypes with a certainty of > 95% in 173 individuals. The three most commonly occurring haplotypes were included in the association analysis of the influence of haplotype on steroid therapy outcome or IBD activity. None of the NR3C1 haplotypes showed statistically signifi cant association with glucocorticoid therapy success. CONCLUSION: NR3C1 haplotypes are not related to steroid therapy outcome.
文摘The authors want to changed the web link of the software platform in this Briefing.Page 97,section 'INTRODUCTION',the web link of SHEsis is changed from http://www.nhgg.org/analysis tohttp://analysis.bio-x.
基金financially the National Natural Science Foundation of China(31871611 and31971890)the National Science Foundation for Young Scientistsin China(31901494 and 31901869)+1 种基金International Cooperation and Exchange of the National Natural Science Foundation of China(31961143019)the Integrated Extension Project of Agricultural Science and Technology Innovation in Shaanxi Province(NYKJ-2021-YL(XN)15)。
文摘The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.
文摘Objectire To disclose the relevancy of idiopathic membranous nephropathy (IMN) to HLA haplotype in Shanghai region population. Methods Analysis of HLA genotype and haplotype was carried out in 33 IMN patients and 71 controls in Shanghai using PCR - SSO. Rcsults The normal haplotypes of controls were DR9- DQA1 * 0301, DR4 - DQA1 *0301, DR12- DQB1 * 0301 and DR9- DQB1 * 0303. The haplotype frequency (Hf) of DR2- DQA1 * 0101 was the highest in IMN group (Hf=12.86), presenting significant linkage disequilibrium. The dofference between two groups was significant (P<0.05). Conclusion It was concluded that the susceptibility of IMN in Shanghai population was associated with specific HLA haplotype.
基金This work was supported by the National Natural Science Foundation of China (No.39970401)
文摘Objective To investigate HLA-A,-B and -DRB1 allele and HLA-A-B-DRB1 haplotype frequencies in Mongolia ethnic group. Methods HLA-A, -B, -DRB1 allele and haplotype in the Mongolia ethnic group were investigated based on 93 individuals by PCR- sequence-based typing (SBT) method. Results Twenty-one alleles were detected for HLA-A, 44 for HLA-B, and 26 for HLA-DRB1. The most frequent alleles were HLA-A*2402(0.2097), HLA-B*1302(0.0699), and HLA-DRB1*0701(0.1237). The most common HLA-A-B-DRB1 haplotype were A*3001-B*1302-DRB1*0701, A*0101-B*3701-DRB1*1001, followed by the A*0201-B*4601-DRB1*0901, A*2402-B*4801-DRB1*1101, A*2402-B*5201-DRB1*1501, A*3201-B*3503-DRB1*1301, and A*3303-B*5801-DRB1*0301, which were also presented in Chinese populations. Conclusion The data can be used in forensic and paternity tests to estimate the frequency of a DNA profile or anthropologic research. The characteristics of the distribution of HLA alleles revealed that Mongolia ethnic group is characterized by northern Mongolian Chinese.
文摘Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between SNPs of the MDR1 gene (C1236T, G2677T/A, C3435T) and IM response in chronic myeloid leukemia (CML) patients. Method: A retrospective case-control study was conducted on 48 patients with CML undergoing IM therapy. All patients were genotyped using PCR-RFLP method. Results: The genotype and allele frequencies of C1236T and C3435T were not significantly different between CML patients responders and non-responders to IM (p > 0.05). The frequencies of 2677T allele and 2677TT genotype were significantly increased in CML patients IM responders which as compared with IM non-responders (50% vs 26.9%, p = 0.013 and 27.3% vs 3.8%, p = 0.029 respectively). Whereas the 2677AA genotype and CAC haplotype were found only in CML patients IM non-responders (15.4%). Conclusion: Pretreatment genotyping of G2677A/T appears to be useful for predicting IM resistance, which may allow the best choice of drug treatment for CML patients.
文摘Pomoxis nigromaculatus, more commonly referred to as black crappie is indigenous to fresh water streams and lakes in the eastern United States and supports an important recreational fishery. We examined the genetic population structure of black crappie inhabiting three Georgian Lakes, Lake Sidney Lanier, Lake Seminole and Hartwell Lake. DNA sequencing of 229 fish samples, utilizing the DNA barcode marker cytochrome oxidase subunit I (COI) revealed 27 polymorphic sites which defined nine haplotypes. Only haplotype 2 was shared between all sample sites with six other haplotypes being unique for individual lakes, for an overall haplotype diversity of 0.734. Tajima’s D and Fu’s tests were implemented to assess departures from neutral expectations. Fst pairwise comparisons were statistically significant among all populations of black crappie evaluated in this study.
文摘In this work, we study predicting the effect of non-synonymous SNPs on several cancers. We trained classifiers on both sequential and structural features extracted from the affected genes and assessed the predictions made by the trained classifiers using cross validation. Specifically, we investigated how the prediction performance can be improved by connecting SNPs in the context of haplotype and interacting sites of proteins encoded by affected genes. We found that accuracy was consistently enhanced by combining sequential and structural features, with increase ranging from a few percentage points up to more than 20 percentage points. The results for putting SNPs in the context of interacting sites were less consistent. Compared to individual SNPs, these that appear together in haplotype showed stronger correlation with one another and with the phenotype, and therefore led to significant improvement inprediction performance, with ROC score increased from 0.81 to 0.95. Although some similar effect has been expected for connecting SNPs to interacting sites in proteins, the performance actually got worse. This decrease in prediction accuracy may be caused by the small data set being used in the study, as many affected proteins in the study do not have known interacting sites.
文摘For case-parents data, the information from offspring can be used to reduce the uncertainty of parents’ haplotype. In this article we develop likelihood ratio test to compare haplotype frequencies in transmitted and non-transmitted group. The maximum likelihood estimate of the haplotype frequencies for the family data is obtained via expectation-maximization (EM) algorithm. Our proposed method can handle the uncertainty of haplotypes and missing data. The simulations show that the method is more powerful to test association between haplotype and traits than TRANSMIT. We also demonstrated the method to detect the association between Megsin gene and immunoglobulin A nephropathy.
文摘The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individuals in the end result. In some cases, there is excessive bone atrophy, which complicates the dental restorative treatment. The alveolar ridge receives the mechanical load continuously from the periodontal ligament connected to the teeth and it diminishes dramatically as a consequence of dental extraction;thus it is believed the continuing pattern of the alveolar bone resorption is related to this change. The reduced partial pressure of oxygen is the most prominent event from the reduced mechanical load. Vascular Endothelial Growth Factor (VEGF), regulated by HIF-1, reported close association with angiogenesis and bone turn over, where partial oxygen pressure has changed. Therefore the genetic association between Single Nucleotide Polymorphsim (SNP) of VEGF gene and RRR was investigated. 120 subjects (70.93 ± 9.28 years) which were treated at Dental clinic of Yonsei University with edentulous mandible were recruited. Mandibular bone height was measured following the protocol of the American College of Prosthodontists. Three variants, rs1570360, rs25648, and rs3025039 in VEGF from previous study, were used as tag-SNPs and genotyping for the study. Student’s t-test and ANOVA were used for statistical analysis. There was a notable association with rs1570360 (P = 0.051) in dominant group and haplotype A-C-C showed a statistically significant association with RRR in dominant group (P = 0.042). Results of this study may be useful in developing novel genetic diagnostic tests and identifying Koreans susceptible to developing severe RRR after dental extraction.
文摘Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorphic sites was also conducted, a few identified haplotypes were novel while the remainder was previously reported, haplotype1222212 was the most frequent haplotype in the study group and a strong linkage disequilibrium between two polymorphic restriction sites in these β thalassemia patients was uncovered.
