With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genet...With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.展开更多
Objective:To investigate the effects of -2242,-1892 and -1837 single nucleotide polymorphisms(SNPs) on toll-like receptor 4(TLR4) promoter activity.Methods:Polymerase chain reaction(PCR) and site direct mutation techn...Objective:To investigate the effects of -2242,-1892 and -1837 single nucleotide polymorphisms(SNPs) on toll-like receptor 4(TLR4) promoter activity.Methods:Polymerase chain reaction(PCR) and site direct mutation technology were used to construct TLR4 basic promoter and -2242C,-1892A and -1837G mutate promoter plasmids.Dual-Luciferase Reporter assay system was used to detect the activity of constructed promoter following human embryonic kidney(HEK) 293 cells were transiently cotransfected with the constructed plasmids and the control plasmid pRL-CMV.Results:In HEK293 cells,the activity of -2242C mutate promoter was higher than -2242T promoter,and there was no significant difference when both -1892A and -1837G mutate promoter compared with -1892G and -1837A promoter,respectively.Conclusion:It is implied that -2242T→C base variation can enhance the activity of TLR4 promoter,while -1892 and -1837 SNPs have no effect on TLR4 promoter activity.展开更多
为发掘鮸鱼的EST-cSNP位点,以测序获得的鮸鱼脾脏4 609条高质量表达序列标签(expressed sequence tags,EST)序列为源序列,利用Vector NTI 11.0软件拼接出707条重叠群(contig)序列,检测到209个可信度高的编码区单核苷酸多态性(coding-reg...为发掘鮸鱼的EST-cSNP位点,以测序获得的鮸鱼脾脏4 609条高质量表达序列标签(expressed sequence tags,EST)序列为源序列,利用Vector NTI 11.0软件拼接出707条重叠群(contig)序列,检测到209个可信度高的编码区单核苷酸多态性(coding-region single nucleotide polymorphism,cSNP)位点;SNP位点数在包含SNP序列中的发生概率为0.743%,在209个SNP位点中包含114个碱基转换位点、74个碱基颠换位点和21个插入缺失位点,转换与颠换比为1.54;对所鉴定的SNP位点的相关序列进行基因注释表明,这些序列包括一批与免疫抗逆相关的基因,例如主要组织相容性复合体、免疫球蛋白、T细胞受体以及各类蛋白酶等.说明所发掘的SNP将有助于促进鮸鱼的分子遗传学及分子辅助育种研究.展开更多
文摘With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.
基金Supported by the Major State Basic Research Development Program of China (2005CB522602)the National Funds for Outstanding Youth Scientists (30325040)
文摘Objective:To investigate the effects of -2242,-1892 and -1837 single nucleotide polymorphisms(SNPs) on toll-like receptor 4(TLR4) promoter activity.Methods:Polymerase chain reaction(PCR) and site direct mutation technology were used to construct TLR4 basic promoter and -2242C,-1892A and -1837G mutate promoter plasmids.Dual-Luciferase Reporter assay system was used to detect the activity of constructed promoter following human embryonic kidney(HEK) 293 cells were transiently cotransfected with the constructed plasmids and the control plasmid pRL-CMV.Results:In HEK293 cells,the activity of -2242C mutate promoter was higher than -2242T promoter,and there was no significant difference when both -1892A and -1837G mutate promoter compared with -1892G and -1837A promoter,respectively.Conclusion:It is implied that -2242T→C base variation can enhance the activity of TLR4 promoter,while -1892 and -1837 SNPs have no effect on TLR4 promoter activity.
文摘为发掘鮸鱼的EST-cSNP位点,以测序获得的鮸鱼脾脏4 609条高质量表达序列标签(expressed sequence tags,EST)序列为源序列,利用Vector NTI 11.0软件拼接出707条重叠群(contig)序列,检测到209个可信度高的编码区单核苷酸多态性(coding-region single nucleotide polymorphism,cSNP)位点;SNP位点数在包含SNP序列中的发生概率为0.743%,在209个SNP位点中包含114个碱基转换位点、74个碱基颠换位点和21个插入缺失位点,转换与颠换比为1.54;对所鉴定的SNP位点的相关序列进行基因注释表明,这些序列包括一批与免疫抗逆相关的基因,例如主要组织相容性复合体、免疫球蛋白、T细胞受体以及各类蛋白酶等.说明所发掘的SNP将有助于促进鮸鱼的分子遗传学及分子辅助育种研究.
