There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of geno...There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.展开更多
A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technolog...A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the devel- opment of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for dif- ferent objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.展开更多
Hepatocellular carcinoma(HCC) is the fourth cause of cancer related mortality, and its incidence is rapidly increasing. Viral hepatitis, alcohol abuse, and exposure to hepatotoxins are major risk factors, but nonalcoh...Hepatocellular carcinoma(HCC) is the fourth cause of cancer related mortality, and its incidence is rapidly increasing. Viral hepatitis, alcohol abuse, and exposure to hepatotoxins are major risk factors, but nonalcoholic fatty liver disease(NAFLD) associated with obesity, insulin resistance, and type 2 diabetes, is an increasingly recognized trigger, especially in developed countries. Older age, severity of insulin resistance and diabetes, and iron overload have been reported to predispose to HCC in this context. Remarkably, HCCs have been reported in non-cirrhotic livers in a higher proportion of cases in NAFLD patients than in other etiologies. Inherited factors have also been implicated to explain the different individual susceptibility to develop HCC, and their role seems magnified in fatty liver, where only a minority of affected subjects progresses to cancer. In particular, the common I148 M variant of the PNPLA3 gene influencing hepatic lipid metabolism influences HCC risk independently of its effect on the progression of liver fibrosis. Recently, rare loss-of-function mutations in Apolipoprotein B resulting in very low density lipoproteins hepatic retention and in Telomerase reverse transcriptase influencing cellular senescence have also been linked to HCC in NAFLD. Indeed, hepatic stellate cells senescence has been suggested to bridge tissue aging with alterations of the intestinal microbiota in the pathogenesis of obesity-related HCC. A deeper understanding of the mechanisms mediating hepatic carcinogenesis during insulin resistance, and the identification of its genetic determinants will hopefully provide new diagnostic and therapeutic tools.展开更多
Background Atopy is a state of allergy to common antigens and is founded on an immune disturbance of exuberant Th2 activity and IgE production. There is also epidemiologieal and experimental evidence that exposure to ...Background Atopy is a state of allergy to common antigens and is founded on an immune disturbance of exuberant Th2 activity and IgE production. There is also epidemiologieal and experimental evidence that exposure to myeobacteria has the potential to suppress the development of asthma or atopy. Since Thl and Th2 immune mechanisms are significantly antagonistic, it is hypothesized that myeobaeterial exposure may moderate atopie disease by modification of immune responses. Methods One hundred and twenty mild to moderate persistent asthmatics accompanied with allergic rhinitis were randomly divided into four groups with one injection every other day for 18 times for group A with 1 ml of normal saline, B with 0.5 mg of Bacillus Calmette-Guérin polysaccharide nucleotide (BCG-PSN) and C with 1 mg of BCG-PSN, 36 times for group D with 0. 5 mg of BCG-PSN. Markers for the severity of asthma and rhinitis including the amount of inhaled corticosteriod, bronchodilator and oral H1 blocker-loratidine being used to obtain optimal symptomatic control, symptom scores of asthma and allergic rhinitis, peak expiratory flow (PEF), histamine provocative dose that produces at least a 20% change in forced expiratory volume with in 1 second (PD20-FEV1 ), blood IgE levels as well as dermatophagoides pteronysinus (DP) and dermatophagoides farinae (DF) skin prick test were measured every visit for 6 months. Results There were no differences for symptom scores of asthma, daily use of bronchodilator, PEF, PD20- FEV1, blood IgE as well as DF and DP skin prick test among the four groups. Score for allergic rhinitis decreased significantly in groups B, C and D on day 36 and 72 as compared with group A ( P 〈 0.05 ). Score for allergic rhinitis increased after day 72 in group B and C while it was significantly lower in group D ( P 〈 0.05 ). The patients in group D used less amount of inhaled beclomethosone than other groups ( P 〈 0.05 ) from day 72 after the treatment to day 180. Oral loratadine consumption i展开更多
本文采用高效液相色谱和氨基酸自动分析仪测定了工业化加工过程中盐水鸭中核苷酸及其降解产物以及游离氨基酸含量的变化,并采用滋味活性值和等鲜浓度来评价上述滋味物质的呈味作用和鲜味强度。结果表明,复卤和煮制工艺对风味核苷酸和游...本文采用高效液相色谱和氨基酸自动分析仪测定了工业化加工过程中盐水鸭中核苷酸及其降解产物以及游离氨基酸含量的变化,并采用滋味活性值和等鲜浓度来评价上述滋味物质的呈味作用和鲜味强度。结果表明,复卤和煮制工艺对风味核苷酸和游离氨基酸的形成过程影响最为显著。盐水鸭中的核苷酸类物质以5'-肌苷酸(5'-IMP)和肌苷(I)为主,占总量的47.33%;主要的游离氨基酸为Tau(212.37mg·100g-1)、Glu(96.66mg·100g-1)和Ala(95.52mg·100g-1)。5'-IMP和Glu的滋味活性值大于1,对盐水鸭的滋味有重要的贡献。盐水鸭的等鲜浓度为3.89 g MSG·100g-1,说明盐水鸭有强烈的鲜味强度。展开更多
Background Genetic factors are believed to play a role in the individual susceptibility to chronic obstructive pulmonary disease (COPD). A single nucleotide polymorphism (SNP) of tumour necrosis factor-α (TNF-α) has...Background Genetic factors are believed to play a role in the individual susceptibility to chronic obstructive pulmonary disease (COPD). A single nucleotide polymorphism (SNP) of tumour necrosis factor-α (TNF-α) has been reported but inconsistent results may arise from different populations and phenotypes of COPD. There are only a few published studies of interleukin-13 (IL-13) SNPs on COPD. The SNPs of TNF-α and IL-13 have not been studied in the Chinese population. This research was conducted to study the frequencies of IL-13 gene promoter 1055 (IL-13-1055) and TNF-α gene-308 polymorphisms in the patients with COPD and to investigate the effect of those genetic polymorphisms on COPD in the Chinese population.Methods A cohort of COPD patients and age matched controls were recruited from an inpatient hospital service in Beijing. Venous blood was obtained and genomic DNA was extracted from peripheral blood monocytes using standard method. Genomic DNA was used as a template for amplification by polymerase chain reaction (PCR) to determine the polymorphism at -1055 in the IL-13 gene promoter region. PCR restriction fragment length polymorphism (RFLP) was used to determine polymorphisms in the TNF-α gene-308 position. The products were investigated by sequence analysis also. Results One hundred and eleven COPD patients and 97 controls were studied. Seventy-five cases were current smokers in COPD patients and 36 were current smokers in controls. The frequencies of TT genotype in the IL-13 gene promoter region were 11.7% (13/111) in the COPD group and 13.4% (13/97) in the controls (P=0.713). However, the OR value of TT genotype was significantly increased to 6.4 (95% CI 1.62-25.39) in the smokers with COPD. TT genotype was also positively related to family history of COPD, OR=7.7 (95% CI 1.37-43.80). The frequencies of A allele in the TNF-α gene were 5.9% in COPD and 3.1% in controls (P=0.131). The OR value of A allele was 5.0 (95% CI 1.011 to 25.059) in smokers with COPD. Conclusions There is no significant diff展开更多
Background Ossification of the posterior longitudinal ligament (OPLL) has a strong genetic background. Previous studies have shown that bone morphogenetic protein-2 (BMP2) and BMP2 mRNA are expressed in ossifying ...Background Ossification of the posterior longitudinal ligament (OPLL) has a strong genetic background. Previous studies have shown that bone morphogenetic protein-2 (BMP2) and BMP2 mRNA are expressed in ossifying matrix and chondrocytes adjacent to cartilaginous areas of OPLL tissues and mesenchymal cells with fibroblastic features in the immediate vicinity of the cartilaginous areas. It is suggested that BMP2 plays different roles in the different stages of development of OPLL. However, it remains unknown which factors induce ligament cells to produce BMP2. Methods OPLL patients (n=-192) and non-OPLL controls (n=304) were studied. Radiographs of the cervical spine were analyzed for extent of OPLL. We investigated whether single nucleotide polymorphisms of exons 3(-726) T/C and 3(-583) NG in the BMP2 gene are statistically associated with genetic susceptibility to OPLL in Chinese Han subjects. Results There was no statistical difference between the occurrence of exons 3(-726) T/C and 3(-583) NG and the occurrence of OPLL in the cervical spine. However, there was a significant association between occurrence of exon 3(-726) T/C polymorphism and occurrence of OPLL in males of cases and controls in the cervical spine. In addition, no significant association was found between the exons 3(-726) T/C and 3(-583) A/G with number of ossified cervical vertebrae in OPLL patients. Conclusions Exon 3(-583) A/G polymorphism in BMP2 gene is not associated with the occurrence and the extent of OPLL in the cervical spine. Chinese Han male patients with TC and CC genotypes in exon 3(-726) T/C have genetic susceptibility to OPLL but not to more extensive OPLL in the cervical spine.展开更多
Aim: To analyze the distribution of the single nucleotide polymorphism (SNP) C677T in the methylenetetrahydrofolate reductase (MTHFR) gene in 355 infertile Chinese patients with idiopathic azoospermia or severe o...Aim: To analyze the distribution of the single nucleotide polymorphism (SNP) C677T in the methylenetetrahydrofolate reductase (MTHFR) gene in 355 infertile Chinese patients with idiopathic azoospermia or severe oligozoospermia and 252 fertile Chinese men as controls to explore the possible association of the SNP and male infertility. Methods: Using the polymerase chain reaction (PCR)-restriction fragment length polymorphism technique, the allele and genotype distribution of SNP C677T in the MTHFR gene were investigated in both patients and controls. Results: The frequencies of allele T (40.9% vs 30.4%, P = 0.002, odds ration [OR] = 1.58, 95% confidence interval [CI]: 1.24-2.02) and mutant homozygote (TT) (18.3% vs. 11.5%, P = 0.023, OR = 1.72, 95% CI: 1.07-2.76) as well as carrier with allele (TT + CT) (63.4% vs. 49.2%, P = 0.0005, OR = 1.79, 95% CI: 1.29-2.48) in infertile patients were significantly higher than those in controls. After patient stratification, the significant differences in distribution of the SNP between each patient subgroup and control group still remained. Conclusion: Our findings indicate that there is an association of SNP C677T in the MTHFR gene with male infertility, suggesting that this polymorphism might be a genetic risk factor for male infertility in Chinese men.展开更多
基金This study was supported by the National Key Research and Development Program of China (2016YFD0101802 and 2016YFE0108600) and National Natural Science Foundation of China (31550110212).
文摘There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of (a) rapid development in gene discovery of important traits, (b) deepened understanding of quantitative traits through new analytical models and population designs, (c) integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and (d) improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
基金grants from the National High Technology Research and Development Program of China,the National Program on Key Basic Research Project of China,the National Natural Science Foundation of China,Guangdong Innovative Research Team Program,the Ministry of Agriculture of China
文摘A high-density single nucleotide polymorphism (SNP) array is critically important for geneticists and molecu- lar breeders. With the accumulation of huge amounts of genomic re-sequencing data and available technologies for accurate SNP detection, it is possible to design high-density and high-quality rice SNP arrays. Here we report the devel- opment of a high-density rice SNP array and its utility. SNP probes were designed by screening more than 10 000 000 SNP loci extracted from the re-sequencing data of 801 rice varieties and an array named RiceSNP50 was produced on the Illumina Infinium platform. The array contained 51 478 evenly distributed markers, 68% of which were within genic regions. Several hundred rice plants with parent/F1 relationships were used to generate a high-quality cluster file for accurate SNP calling. Application tests showed that this array had high genotyping accuracy, and could be used for dif- ferent objectives. For example, a core collection of elite rice varieties was clustered with fine resolution. Genome-wide association studies (GWAS) analysis correctly identified a characterized QTL. Further, this array was successfully used for variety verification and trait introgression. As an accurate high-throughput genotyping tool, RiceSNP50 will play an important role in both functional genomics studies and molecular breeding.
文摘Hepatocellular carcinoma(HCC) is the fourth cause of cancer related mortality, and its incidence is rapidly increasing. Viral hepatitis, alcohol abuse, and exposure to hepatotoxins are major risk factors, but nonalcoholic fatty liver disease(NAFLD) associated with obesity, insulin resistance, and type 2 diabetes, is an increasingly recognized trigger, especially in developed countries. Older age, severity of insulin resistance and diabetes, and iron overload have been reported to predispose to HCC in this context. Remarkably, HCCs have been reported in non-cirrhotic livers in a higher proportion of cases in NAFLD patients than in other etiologies. Inherited factors have also been implicated to explain the different individual susceptibility to develop HCC, and their role seems magnified in fatty liver, where only a minority of affected subjects progresses to cancer. In particular, the common I148 M variant of the PNPLA3 gene influencing hepatic lipid metabolism influences HCC risk independently of its effect on the progression of liver fibrosis. Recently, rare loss-of-function mutations in Apolipoprotein B resulting in very low density lipoproteins hepatic retention and in Telomerase reverse transcriptase influencing cellular senescence have also been linked to HCC in NAFLD. Indeed, hepatic stellate cells senescence has been suggested to bridge tissue aging with alterations of the intestinal microbiota in the pathogenesis of obesity-related HCC. A deeper understanding of the mechanisms mediating hepatic carcinogenesis during insulin resistance, and the identification of its genetic determinants will hopefully provide new diagnostic and therapeutic tools.
文摘Background Atopy is a state of allergy to common antigens and is founded on an immune disturbance of exuberant Th2 activity and IgE production. There is also epidemiologieal and experimental evidence that exposure to myeobacteria has the potential to suppress the development of asthma or atopy. Since Thl and Th2 immune mechanisms are significantly antagonistic, it is hypothesized that myeobaeterial exposure may moderate atopie disease by modification of immune responses. Methods One hundred and twenty mild to moderate persistent asthmatics accompanied with allergic rhinitis were randomly divided into four groups with one injection every other day for 18 times for group A with 1 ml of normal saline, B with 0.5 mg of Bacillus Calmette-Guérin polysaccharide nucleotide (BCG-PSN) and C with 1 mg of BCG-PSN, 36 times for group D with 0. 5 mg of BCG-PSN. Markers for the severity of asthma and rhinitis including the amount of inhaled corticosteriod, bronchodilator and oral H1 blocker-loratidine being used to obtain optimal symptomatic control, symptom scores of asthma and allergic rhinitis, peak expiratory flow (PEF), histamine provocative dose that produces at least a 20% change in forced expiratory volume with in 1 second (PD20-FEV1 ), blood IgE levels as well as dermatophagoides pteronysinus (DP) and dermatophagoides farinae (DF) skin prick test were measured every visit for 6 months. Results There were no differences for symptom scores of asthma, daily use of bronchodilator, PEF, PD20- FEV1, blood IgE as well as DF and DP skin prick test among the four groups. Score for allergic rhinitis decreased significantly in groups B, C and D on day 36 and 72 as compared with group A ( P 〈 0.05 ). Score for allergic rhinitis increased after day 72 in group B and C while it was significantly lower in group D ( P 〈 0.05 ). The patients in group D used less amount of inhaled beclomethosone than other groups ( P 〈 0.05 ) from day 72 after the treatment to day 180. Oral loratadine consumption i
文摘本文采用高效液相色谱和氨基酸自动分析仪测定了工业化加工过程中盐水鸭中核苷酸及其降解产物以及游离氨基酸含量的变化,并采用滋味活性值和等鲜浓度来评价上述滋味物质的呈味作用和鲜味强度。结果表明,复卤和煮制工艺对风味核苷酸和游离氨基酸的形成过程影响最为显著。盐水鸭中的核苷酸类物质以5'-肌苷酸(5'-IMP)和肌苷(I)为主,占总量的47.33%;主要的游离氨基酸为Tau(212.37mg·100g-1)、Glu(96.66mg·100g-1)和Ala(95.52mg·100g-1)。5'-IMP和Glu的滋味活性值大于1,对盐水鸭的滋味有重要的贡献。盐水鸭的等鲜浓度为3.89 g MSG·100g-1,说明盐水鸭有强烈的鲜味强度。
文摘Background Genetic factors are believed to play a role in the individual susceptibility to chronic obstructive pulmonary disease (COPD). A single nucleotide polymorphism (SNP) of tumour necrosis factor-α (TNF-α) has been reported but inconsistent results may arise from different populations and phenotypes of COPD. There are only a few published studies of interleukin-13 (IL-13) SNPs on COPD. The SNPs of TNF-α and IL-13 have not been studied in the Chinese population. This research was conducted to study the frequencies of IL-13 gene promoter 1055 (IL-13-1055) and TNF-α gene-308 polymorphisms in the patients with COPD and to investigate the effect of those genetic polymorphisms on COPD in the Chinese population.Methods A cohort of COPD patients and age matched controls were recruited from an inpatient hospital service in Beijing. Venous blood was obtained and genomic DNA was extracted from peripheral blood monocytes using standard method. Genomic DNA was used as a template for amplification by polymerase chain reaction (PCR) to determine the polymorphism at -1055 in the IL-13 gene promoter region. PCR restriction fragment length polymorphism (RFLP) was used to determine polymorphisms in the TNF-α gene-308 position. The products were investigated by sequence analysis also. Results One hundred and eleven COPD patients and 97 controls were studied. Seventy-five cases were current smokers in COPD patients and 36 were current smokers in controls. The frequencies of TT genotype in the IL-13 gene promoter region were 11.7% (13/111) in the COPD group and 13.4% (13/97) in the controls (P=0.713). However, the OR value of TT genotype was significantly increased to 6.4 (95% CI 1.62-25.39) in the smokers with COPD. TT genotype was also positively related to family history of COPD, OR=7.7 (95% CI 1.37-43.80). The frequencies of A allele in the TNF-α gene were 5.9% in COPD and 3.1% in controls (P=0.131). The OR value of A allele was 5.0 (95% CI 1.011 to 25.059) in smokers with COPD. Conclusions There is no significant diff
文摘Background Ossification of the posterior longitudinal ligament (OPLL) has a strong genetic background. Previous studies have shown that bone morphogenetic protein-2 (BMP2) and BMP2 mRNA are expressed in ossifying matrix and chondrocytes adjacent to cartilaginous areas of OPLL tissues and mesenchymal cells with fibroblastic features in the immediate vicinity of the cartilaginous areas. It is suggested that BMP2 plays different roles in the different stages of development of OPLL. However, it remains unknown which factors induce ligament cells to produce BMP2. Methods OPLL patients (n=-192) and non-OPLL controls (n=304) were studied. Radiographs of the cervical spine were analyzed for extent of OPLL. We investigated whether single nucleotide polymorphisms of exons 3(-726) T/C and 3(-583) NG in the BMP2 gene are statistically associated with genetic susceptibility to OPLL in Chinese Han subjects. Results There was no statistical difference between the occurrence of exons 3(-726) T/C and 3(-583) NG and the occurrence of OPLL in the cervical spine. However, there was a significant association between occurrence of exon 3(-726) T/C polymorphism and occurrence of OPLL in males of cases and controls in the cervical spine. In addition, no significant association was found between the exons 3(-726) T/C and 3(-583) A/G with number of ossified cervical vertebrae in OPLL patients. Conclusions Exon 3(-583) A/G polymorphism in BMP2 gene is not associated with the occurrence and the extent of OPLL in the cervical spine. Chinese Han male patients with TC and CC genotypes in exon 3(-726) T/C have genetic susceptibility to OPLL but not to more extensive OPLL in the cervical spine.
基金Acknowledgment This work was supported by the National High Tech- nology Research and Development Program of China (Grants 2004AA216090 and 2002BA711A08), National Basic Research Program of China (Grant 2004Cb518805), the Natural National Science Foundation of China (Grant 30470960) and the China Medical Board of New York.
文摘Aim: To analyze the distribution of the single nucleotide polymorphism (SNP) C677T in the methylenetetrahydrofolate reductase (MTHFR) gene in 355 infertile Chinese patients with idiopathic azoospermia or severe oligozoospermia and 252 fertile Chinese men as controls to explore the possible association of the SNP and male infertility. Methods: Using the polymerase chain reaction (PCR)-restriction fragment length polymorphism technique, the allele and genotype distribution of SNP C677T in the MTHFR gene were investigated in both patients and controls. Results: The frequencies of allele T (40.9% vs 30.4%, P = 0.002, odds ration [OR] = 1.58, 95% confidence interval [CI]: 1.24-2.02) and mutant homozygote (TT) (18.3% vs. 11.5%, P = 0.023, OR = 1.72, 95% CI: 1.07-2.76) as well as carrier with allele (TT + CT) (63.4% vs. 49.2%, P = 0.0005, OR = 1.79, 95% CI: 1.29-2.48) in infertile patients were significantly higher than those in controls. After patient stratification, the significant differences in distribution of the SNP between each patient subgroup and control group still remained. Conclusion: Our findings indicate that there is an association of SNP C677T in the MTHFR gene with male infertility, suggesting that this polymorphism might be a genetic risk factor for male infertility in Chinese men.