The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron re...The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.展开更多
Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objec...Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.展开更多
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
This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association stu...This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.展开更多
Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken ...Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken with restricton fragment length polymorphisms. The associations of the SNPs with the total egg production （NE）, average days of continual laying （ADCL）, and number of double-yolked eggs （DYE） traits were analyzed. The frequency of restriction enzyme A/a alleles in the population was for GnRHR 0.69 （Bpu1102 Ⅰ A） and 0.31 （Bpu1102 Ⅰ a） and for NPY 0.46 （Dra Ⅰ B） and 0.54 （Dra Ⅰ b）. Trait data from a total of 120 hens, which were purebred introduced from Hainan Province, China from one generation were recorded. Two significant effects of genes＇ marker were found： for GnRHR and number of eggs （dominant; t= 2.67, df= 116） and NPY and number of eggs （additive; t= 1.97, df= 116）. The current research supports the effects of GnRHR and NPY genes on egg-laying traits of chickens.展开更多
Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic link...Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.展开更多
Type 2 diabetes(T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex ...Type 2 diabetes(T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex heterogeneous metabolic phenotype in different ethnic and racial groups remains challenging. Despite recent success, the functional role of the T2D susceptibility variants implicated by genome-wide association studies(GWAS) remains largely unknown. Genetic dissection of transcript abundance or expression quantitative trait(eQTL) analysis unravels the genomic architecture of regulatory variants. Availability of eQTL information from tissues relevant for glucose homeostasis in humans opens a new avenue to prioritize GWASimplicated variants that may be involved in triggering a causal chain of events leading to T2D. In this article, we review the progress made in the field of eQTL research and knowledge gained from those studies in understanding transcription regulatory mechanisms in human subjects. We highlight several novel approaches that can integrate eQTL analysis with multiple layers of biological information to identify ethnic-specific causal variants and gene-environment interactions relevant to T2D pathogenesis. Finally, we discuss how the eQTL analysis mediated search for "missing heritability" may lead us to novel biological and molecular mechanisms involved in susceptibility to T2D.展开更多
The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate ...The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate the oyster growth traits and the associations with bHLH genes variations,we analyzed the gene polymorphisms-traits association in a wild population,and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis.After screening the single nucleotide polymorphisms(SNPs)in three candidate genes of the bHLH family(88 bHLH genes in two wild oyster populations in total),we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene.This allele is a non-synonymous mutation(Phe/Leu)with an extremely significant association with shell width(P<0.01)and allele G is beneficial to shell width.This SNP on the CgLoblHLH4 gene might have a potential value as a genetic marker of growth traits that could be used in breeding in C.gigas in the future.展开更多
Myostatin( MSTN) is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1(MSTN-...Myostatin( MSTN) is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1(MSTN-1) in two commercial hatchery populations of Ancheryth r oculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms(SNPs) and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change(Val to Ile) at position 180. Association analyses based on 300 individuals revealed that the g.1129T>C SNP locus was significantly associated with total length(TL), body length(BL), body height(BH) and body weight(BW) in 6-and 18-month-old populations, while the g.1289G>A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.1129T>C and g.1289G>A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.展开更多
为研究影响肉鸡屠宰性状选育的主要遗传因素,试验采用全基因组关联分析(Genome-wide association study,GWAS)挖掘与屠宰性状相关的单核苷酸多态性(Single nucleotide polymorphism,SNP)位点和候选基因。以264只金陵花鸡终端父系公鸡为...为研究影响肉鸡屠宰性状选育的主要遗传因素,试验采用全基因组关联分析(Genome-wide association study,GWAS)挖掘与屠宰性状相关的单核苷酸多态性(Single nucleotide polymorphism,SNP)位点和候选基因。以264只金陵花鸡终端父系公鸡为试验材料,采集血液提取DNA,使用全基因组重测序技术获取个体基因型数据,使用PLINK 1.90软件对基因型数据进行质量控制。对宰前体重、屠体重、半净膛重、全净膛重4个性状进行屠宰测定,使用EXCEL和R语言进行正态分布检验和相关性分析。使用GEMMA软件进行GWAS分析,定位出显著的SNP位点。使用SPSS软件分析屠宰性状的有利基因型。结果显示:屠宰性状均符合正态分布,相关度在0.96以上。定位到4个显著的SNP位点,注释到一个基因为RAB6A。1和3号染色体显著位点TT为有利基因型,19号染色体上显著位点CC为有利基因型。研究提示:应根据挖掘到的显著SNPs和候选基因进行屠宰性状的选择,加强肉鸡屠宰性状分子育种的理论基础以提高屠宰加工型肉鸡的选择进展。展开更多
基金Supported by the National Basic Research Program of China(973Program)(No.2010CB126304)the Special Fund for Agro-scientific Research in the Public Interest(No.200903046)the Project from the Ministry of Science and Technology of China(No.2006DKA30470017)
文摘The growth hormone gene (GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G A) that was negatively correlated with body height and positively correlated with standard length/body height (P 0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T C). The CD genotype had a significantly positive correlation with both weight and total length (P 0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.
文摘Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.
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Project supported by Ovita Limited, Dunedin, New Zealand
文摘This paper presents a quick, easy to implement and versatile way of using stochastic simulations to investigate the power and design of using single nucleotide polymorphism (SNP) arrays for genome-wide association studies in farm animals. It illustrates the methodology by discussing a small example where 6 experimental designs are considered to analyse the same resource consisting of 6006 animals with pedigree and phenotypic records: (1) genotyping the 30 most widely used sires in the population and all of their progeny (515 animals in total), (2) genotyping the 100 most widely used sires in the population and all of their progeny (1102 animals in total), genotyping respectively (3) 515 and (4) 1102 animals selected randomly or genotyping respectively (5) 515 and (6) 1102 animals from the tails of the phenotypic distribution. Given the resource at hand, designs where the extreme animals are genotyped perform the best, followed by designs selecting animals at random. Designs where sires and their progeny are genotyped perform the worst, as even genotyping the 100 most widely used sires and their progeny is not as powerful of genotyping 515 extreme animals.
文摘Single nucleotide polymorphisms （SNP） of chicken gonadotropin-releasing hormone receptor （GnRHR） and neuropeptide Y （NPY） were selected to identify the genotypes of Wenchang （Chinese indigenous breed） chicken with restricton fragment length polymorphisms. The associations of the SNPs with the total egg production （NE）, average days of continual laying （ADCL）, and number of double-yolked eggs （DYE） traits were analyzed. The frequency of restriction enzyme A/a alleles in the population was for GnRHR 0.69 （Bpu1102 Ⅰ A） and 0.31 （Bpu1102 Ⅰ a） and for NPY 0.46 （Dra Ⅰ B） and 0.54 （Dra Ⅰ b）. Trait data from a total of 120 hens, which were purebred introduced from Hainan Province, China from one generation were recorded. Two significant effects of genes＇ marker were found： for GnRHR and number of eggs （dominant; t= 2.67, df= 116） and NPY and number of eggs （additive; t= 1.97, df= 116）. The current research supports the effects of GnRHR and NPY genes on egg-laying traits of chickens.
基金supported by the Agricultural Science and Technology Innovation Program (ASTIP-TRIC01)
文摘Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.
基金Supported by National Institutes of Health(NIH/NIDDK),Nos.R01 DK090111 and DK039311
文摘Type 2 diabetes(T2D) is a common metabolic disorder which is caused by multiple genetic perturbations affecting different biological pathways. Identifying genetic factors modulating the susceptibility of this complex heterogeneous metabolic phenotype in different ethnic and racial groups remains challenging. Despite recent success, the functional role of the T2D susceptibility variants implicated by genome-wide association studies(GWAS) remains largely unknown. Genetic dissection of transcript abundance or expression quantitative trait(eQTL) analysis unravels the genomic architecture of regulatory variants. Availability of eQTL information from tissues relevant for glucose homeostasis in humans opens a new avenue to prioritize GWASimplicated variants that may be involved in triggering a causal chain of events leading to T2D. In this article, we review the progress made in the field of eQTL research and knowledge gained from those studies in understanding transcription regulatory mechanisms in human subjects. We highlight several novel approaches that can integrate eQTL analysis with multiple layers of biological information to identify ethnic-specific causal variants and gene-environment interactions relevant to T2D pathogenesis. Finally, we discuss how the eQTL analysis mediated search for "missing heritability" may lead us to novel biological and molecular mechanisms involved in susceptibility to T2D.
基金Supported by the National Key R&D Program of China(No.2018YFD0901400)National Natural Science Foundation of China(No.31672678)+1 种基金Ningbo Municipal Science and Technology International Cooperation Research Projects(No.2016D10017)the Zhejiang Provincial Major Program of Science and Technology(No.2016C02055-9)。
文摘The basic helix-loop-helix(bHLH)genes encode a large superfamily of transcription factors in the Pacific oyster(Crassostrea gigas),and play a very important role in regulation of growth and development.To investigate the oyster growth traits and the associations with bHLH genes variations,we analyzed the gene polymorphisms-traits association in a wild population,and confirmed the results in another independent wild population by targeted gene re-sequencing and SNPshot analysis.After screening the single nucleotide polymorphisms(SNPs)in three candidate genes of the bHLH family(88 bHLH genes in two wild oyster populations in total),we identified the allele CgLoblHLH4-T/G located in the exon of the CgLoblHLH4 gene.This allele is a non-synonymous mutation(Phe/Leu)with an extremely significant association with shell width(P<0.01)and allele G is beneficial to shell width.This SNP on the CgLoblHLH4 gene might have a potential value as a genetic marker of growth traits that could be used in breeding in C.gigas in the future.
基金Supported by the National Science Foundation for Young Scientists of China(No.31402296)the National Science Foundation for Post-Doctoral Scientists of China(No.2014M562077)the Wuhan Chenguang Project for Young Scholars(No.201372304010832)
文摘Myostatin( MSTN) is a member of the transforming growth factor-β gene superfamily that negatively regulates skeletal muscle development and growth. In the present study, partial genomic fragments of Myostatin-1(MSTN-1) in two commercial hatchery populations of Ancheryth r oculter nigrocauda, an economically important freshwater fish, were screened for single nucleotide polymorphisms(SNPs) and then genotyped by direct sequencing of PCR products. Five SNPs were identified in intron 1 and exon 2, including a non-synonymous mutation causing an amino acid change(Val to Ile) at position 180. Association analyses based on 300 individuals revealed that the g.1129T>C SNP locus was significantly associated with total length(TL), body length(BL), body height(BH) and body weight(BW) in 6-and 18-month-old populations, while the g.1289G>A locus was significantly associated with BH and BW in the 6-month-old population. Haplotype analyses revealed that fish with the genotype combinations TC/TC or TC/GA showed better growth performance. Our results suggest that g.1129T>C and g.1289G>A have positive effects on growth traits and may be candidate gene markers for marker-assisted selection in A. nigrocauda.
文摘目的探讨冠心病人长非编码RNA ANRIL tag SNPs与QT间期的关系。方法对628例冠心病患者进行临床检测,记录标准12导联心电图,计算校正的QT间期(QTc);QTc男性<450 ms、女性<460 ms设为对照组,QTc男性≥450 ms、女性≥460 ms设为延长组。采用Fluidigm芯片(192.24)对ANRIL tag SNPs进行分型。结果QTc正常者为510人,占调查人群的81.21%;QTc延长者为118人,占调查人群的18.79%。单因素分析发现QTc延长与年龄(P<0.001)、尿酸(P=0.036)、冠状动脉狭窄严重程度(P=0.024)以及ANRIL多态性(rs944796,rs10965244,rs10965245)等相关;Logistic回归校正其他因素后,rs10965245仍与男性QTc延长相关。结论冠心病人群ANRIL基因多态性与冠心病患者获得性QT间期延长明显相关。
