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
Inflammasomes are multiprotein intracellular complexes which are responsible for the activation of inflammatory responses. Among various subtypes of inflammasomes, NLRP3 has been a subject of intensive investigation. ...Inflammasomes are multiprotein intracellular complexes which are responsible for the activation of inflammatory responses. Among various subtypes of inflammasomes, NLRP3 has been a subject of intensive investigation. NLRP3 is considered to be a sensor of microbial and other danger signals and plays a crucial role in mucosal immune responses, promoting the maturation of proinflammatory cytokines interleukin 1β(IL-1β) and IL-18. NLRP3 inflammasome has been associated with a variety of inflammatory and autoimmune conditions, including inflammatory bowel diseases(IBD). The role of NLRP3 in IBD is not yet fully elucidated as it seems to demonstrate both pathogenic and protective effects. Studies have shown a relationship between genetic variants and mutations in NLRP3 gene with IBD pathogenesis. A complex interaction between the NLRP3 inflammasome and the mucosal immune response has been reported. Activation of the inflammasome is a key function mediated by the innate immune response and in parallel the signaling through IL-1β and IL-18 is implicated in adaptive immunity. Further research is needed to delineate the precise mechanisms of NLRP3 function in regulating immune responses. Targeting NLRP3 inflammasome and its downstream signaling will provide new insights into the development of future therapeutic strategies.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
目的分析湘雅医院血脂异常人群中ApoE和(SLCO1B1)基因型频率分布特征,探究ApoE和SLCO1B1基因型与各项血脂指标的相关性,为防治动脉粥样硬化性疾病提供依据。方法收集湘雅医院2016年6月~2017年4月共87例血脂异常人群三酰甘油(triglycerid...目的分析湘雅医院血脂异常人群中ApoE和(SLCO1B1)基因型频率分布特征,探究ApoE和SLCO1B1基因型与各项血脂指标的相关性,为防治动脉粥样硬化性疾病提供依据。方法收集湘雅医院2016年6月~2017年4月共87例血脂异常人群三酰甘油(triglyceride,TG)、总胆固醇(total cholesterol,TC)、低密度脂蛋白胆固醇(low density lipoprotein cholesterol,LDL-C)、高密度脂蛋白胆固醇(high density lipoprotein cholesterol,HDL-C)数据,采用PCR荧光探针法检测87例血脂异常人群的ApoE和SLCO1B1基因型,分析基因频率分布特征并比较各基因型间各项血脂指标的差异。结果87例血脂异常人群ApoE各基因型频率为:E2/E2型1.15%,E2/E3型13.79%,E2/E4型1.15%,E3/E3型56.32%,E3/E4型26.44%和E4/E4型1.15%,各等位基因频率分布以E3占比最高,为76.44%,E2与E4分别为8.62%和14.94%。E4表型组TC和LDL-C浓度大于E2,E3组,3组表型TG,TC,LDL-C,HDL-C浓度水平差异无统计学意义。SLCO1B1各基因型频率为:*1a/*1a型6.90%,*1a/*1b型36.78%,*1a/*15型13.79%,*1b/*1b型26.44%和*1b/*15型16.09%,各单体型频率分布以*1b占比最高,为52.87%,*1a与*15分别为32.18%和14.94%,未检测到*5型。SLCO1B1各组TG,TC,LDL-C和HDL-C浓度水平差异无统计学意义。结论 ApoE基因型频率分布不均,其多态性与血脂水平可能存在相关性;SLCO1B1基因频率分布存在种族差异性,其多态性与血脂水平不相关。临床医师可以根据ApoE和SLCO1B1基因型合理选择用药剂量,以防治冠状动脉粥样硬化性疾病。展开更多
Integration of the genetic and metabolic fingerprinting can provide a new approach to differentiate similar Traditional Chinese Medical （TCM） materials. Two leguminous plants, Mojia Huangqi and Menggu Huangqi, are i...Integration of the genetic and metabolic fingerprinting can provide a new approach to differentiate similar Traditional Chinese Medical （TCM） materials. Two leguminous plants, Mojia Huangqi and Menggu Huangqi, are important medical herbs and share great similarities in morphology, chemical constituent, and genomic DNA sequence. The taxonomy of Mojia Huangqi and Menggu Huangqi has been debated for more than 50 years and discrimination of TCM materials directly affects the pharmacological and clinical effects. AFLP based genetic fingerprinting and GC-TOF/MS-based meta- bolic fingerprinting were used to successfully discriminate the two species. The results of AFLP supported the opinion that Menggu Huangqi was a variant of Mojia Huangqi. The metabolic fingerprinting showed growth locations have greater impacts on the metabolite composition and quantity than the genotypes （cultivated versus wild） in Menggu Huangqi. The difference of some soluble sugars, fatty acids, proline, and polyamine reflected plant adaptation to different growth environments. Using multivariate and univariate statistical analysis, three AFLP markers and eight metabolites were identified as candidate DNA and metabolic markers to distinguish the two herb materials. The correlation network between AFLP markers and metabolites revealed a complex correlation network, which indicated the special metabolic pathways and the regulation networks of Huangqi.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Inflammasomes are multiprotein intracellular complexes which are responsible for the activation of inflammatory responses. Among various subtypes of inflammasomes, NLRP3 has been a subject of intensive investigation. NLRP3 is considered to be a sensor of microbial and other danger signals and plays a crucial role in mucosal immune responses, promoting the maturation of proinflammatory cytokines interleukin 1β(IL-1β) and IL-18. NLRP3 inflammasome has been associated with a variety of inflammatory and autoimmune conditions, including inflammatory bowel diseases(IBD). The role of NLRP3 in IBD is not yet fully elucidated as it seems to demonstrate both pathogenic and protective effects. Studies have shown a relationship between genetic variants and mutations in NLRP3 gene with IBD pathogenesis. A complex interaction between the NLRP3 inflammasome and the mucosal immune response has been reported. Activation of the inflammasome is a key function mediated by the innate immune response and in parallel the signaling through IL-1β and IL-18 is implicated in adaptive immunity. Further research is needed to delineate the precise mechanisms of NLRP3 function in regulating immune responses. Targeting NLRP3 inflammasome and its downstream signaling will provide new insights into the development of future therapeutic strategies.
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.
文摘目的分析湘雅医院血脂异常人群中ApoE和(SLCO1B1)基因型频率分布特征,探究ApoE和SLCO1B1基因型与各项血脂指标的相关性,为防治动脉粥样硬化性疾病提供依据。方法收集湘雅医院2016年6月~2017年4月共87例血脂异常人群三酰甘油(triglyceride,TG)、总胆固醇(total cholesterol,TC)、低密度脂蛋白胆固醇(low density lipoprotein cholesterol,LDL-C)、高密度脂蛋白胆固醇(high density lipoprotein cholesterol,HDL-C)数据,采用PCR荧光探针法检测87例血脂异常人群的ApoE和SLCO1B1基因型,分析基因频率分布特征并比较各基因型间各项血脂指标的差异。结果87例血脂异常人群ApoE各基因型频率为:E2/E2型1.15%,E2/E3型13.79%,E2/E4型1.15%,E3/E3型56.32%,E3/E4型26.44%和E4/E4型1.15%,各等位基因频率分布以E3占比最高,为76.44%,E2与E4分别为8.62%和14.94%。E4表型组TC和LDL-C浓度大于E2,E3组,3组表型TG,TC,LDL-C,HDL-C浓度水平差异无统计学意义。SLCO1B1各基因型频率为:*1a/*1a型6.90%,*1a/*1b型36.78%,*1a/*15型13.79%,*1b/*1b型26.44%和*1b/*15型16.09%,各单体型频率分布以*1b占比最高,为52.87%,*1a与*15分别为32.18%和14.94%,未检测到*5型。SLCO1B1各组TG,TC,LDL-C和HDL-C浓度水平差异无统计学意义。结论 ApoE基因型频率分布不均,其多态性与血脂水平可能存在相关性;SLCO1B1基因频率分布存在种族差异性,其多态性与血脂水平不相关。临床医师可以根据ApoE和SLCO1B1基因型合理选择用药剂量,以防治冠状动脉粥样硬化性疾病。
文摘Integration of the genetic and metabolic fingerprinting can provide a new approach to differentiate similar Traditional Chinese Medical （TCM） materials. Two leguminous plants, Mojia Huangqi and Menggu Huangqi, are important medical herbs and share great similarities in morphology, chemical constituent, and genomic DNA sequence. The taxonomy of Mojia Huangqi and Menggu Huangqi has been debated for more than 50 years and discrimination of TCM materials directly affects the pharmacological and clinical effects. AFLP based genetic fingerprinting and GC-TOF/MS-based meta- bolic fingerprinting were used to successfully discriminate the two species. The results of AFLP supported the opinion that Menggu Huangqi was a variant of Mojia Huangqi. The metabolic fingerprinting showed growth locations have greater impacts on the metabolite composition and quantity than the genotypes （cultivated versus wild） in Menggu Huangqi. The difference of some soluble sugars, fatty acids, proline, and polyamine reflected plant adaptation to different growth environments. Using multivariate and univariate statistical analysis, three AFLP markers and eight metabolites were identified as candidate DNA and metabolic markers to distinguish the two herb materials. The correlation network between AFLP markers and metabolites revealed a complex correlation network, which indicated the special metabolic pathways and the regulation networks of Huangqi.
