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基于KASP(kompetitive allele specific PCR)技术平台,开发并验证可用于烟草核心种质基因分型的SNP(single nucleotide polymorphism)标记和对应检测引物,为烟草种质基因型鉴定评价、遗传多样性分析、核心种质筛选等提供技术和数据支持。利用Python和Perl脚本程序对覆盖烟草全基因组的1 179 154个SNP位点进行KASP引物设计和筛选,并通过试验验证其准确度和可用性。结果共有217 621个SNP位点完成了对应KASP引物设计,选择1 378个SNP位点进行试验验证,明确了732个可作为SNP标记,并确定48个SNP标记作为烟草种质资源基因分型的核心标记。这48个核心标记在烟草24条染色体上平均分布,平均PIC为0.36,平均MAF为0.39。利用确定的48个核心SNP标记,可以将各供试种质特别是将当前主栽烟草品种基因型进行区分,且标记具有极高的可靠性。 相似文献
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油棕属棕榈科多年生木本油料作物,果实含油量高达50%,且单位面积产油量高,享有"世界油王"美誉。油棕果实由外果皮、中果皮、内果皮(种壳)、种子四个部分组成,产油部分主要是中果皮和种子,其中种壳厚度是影响果实含油量的重要因素。SHELL基因控制种壳厚度,是一类MADS-box同源基因,SHELL基因在厚壳种和无壳种中的变异主要是第一个外显子上的两个SNP位点。该研究根据两个SNP位点进行特异标记开发,根据已知的油棕SHELL基因的序列,设计了4对SNP引物。4对SNP引物以2个SNP位点设计,每个SNP位点设计2对SNP标记,并均在引物3'端第二位引入强错配碱基。以2份薄壳种油棕材料和2份厚壳种油棕材料DNA为模板,扩增筛选油棕SHELL基因SNP引物。通过PCR扩增发现,设计的SHELL基因特异SNP标记EgSh(N)-f/EgSh(SNP)-2r能够鉴别油棕厚壳种和薄壳种。再用24株油棕树进行特异性验证,发现该标记能较准确地判断油棕的厚薄壳。该研究结果表明SNP标记EgSh(N)-f/EgSh(SNP)-2r可用来进行油棕种质资源早期分子鉴定,为高产油棕品种选育提供了技术支撑。 相似文献
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《植物遗传资源学报》2018,(6)
植物中广泛分布着单核苷酸多态性(SNP)位点。在此基础上发展而来的SNP标记因其具有高分辨率和共显性等优点,已成为当前作物遗传研究重要的分子工具。本研究拟建立基于高分辨率熔解曲线(HRM)技术的SNP分子标记,从而实现对栽培稻和野生稻的高效基因分型,为今后水稻的基因挖掘、品种鉴定以及分子育种等提供可靠、快捷的技术工具。利用水稻全基因组9 K SNP芯片对栽培稻品种黄华占和野生稻Y605进行扫描,寻找两者之间的SNP位点,并将其开发成基于HRM技术的特异分子标记。然后,利用这些分子标记对亲本黄华占、野生稻Y605以及两者的BC3回交群体进行分子检测,以验证其有效性。水稻9 K基因芯片在黄华占与野生稻Y605之间总共找到了4198个SNP位点,它们在12条染色体上较均匀分布。在水稻第1号染色体上随机挑选出5个SNP位点开发成基于HRM技术的特异分子标记。利用这些标记对黄华占与野生稻Y605的BC3F1和BC3F2群体进行检测分析,发现它们都能准确区分亲本的纯合与杂合基因型。并且,在回交后代的第1号染色体ZY1-1~ZY1-4标记区间检测到野生稻片段插入。水稻全基因组9 K SNP芯片可以很好地应用于水稻SNP标记的开发。开发的SNP特异标记能准确、高效地对栽培稻和野生稻进行基因分型。进一步完成基于HRM技术的水稻全基因组SNP标记的开发,可为今后野生稻的分子遗传研究、有利基因挖掘和育种应用提供高效的分子检测手段。 相似文献
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《生物技术通报》2019,(11)
地黄(Rehmannia glutinosa)是一种具有较高药用价值和经济价值的植物。准确的品种鉴定对地黄种质管理和育种至关重要,使用SNP分子标记来鉴定地黄种质和构建指纹图谱对地黄分子标记育种提供了新方法。利用地黄转录组数据和SRA数据库中的3个地黄转录组数据比对,寻找候选SNP,用PCR技术扩增和序列分析研究28个地黄品种候选SNP变异。从地黄转录组数据中获得了102 075条Unigenes,其中共有SNP位点35 339个,发生频率为0.51/kb;从中随机选取40个候选SNP位点,设计引物39对,用PCR和序列分析从中筛选出7对好的SNP引物,包含8个多态性好的SNP位点;利用最终筛选出的8个SNP位点构建地黄指纹图谱,可以将17个不同地黄种质区分开,可用于地黄种间和种内品种的鉴定。 相似文献
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【目的】家蚕Bombyx mori非滞育红卵突变体Re-nd是唯一在非滞育状态下卵色呈现鲜红色的突变品种。本研究通过基因连锁分析和定位克隆的方法确定Re-nd的突变基因所在的染色体及紧密连锁位置,为后续Re-nd的功能研究及应用奠定基础。【方法】以家蚕卵色突变体Re-nd和野生型大造进行杂交,配制基因连锁分析群体材料和定位克隆群体材料;针对家蚕全染色体进行SNP标记开发,利用BC1代群体材料进行基因连锁分析,确定Re-nd的突变基因所在的染色体;针对定位的Re nd的突变基因所在染色体进行SNP标记开发,利用BC1群体材料对Re-nd的突变基因进行定位克隆。【结果】基因连锁分析结果显示Re-nd的突变表型与第6号染色体上的SNP标记完全连锁;初步定位克隆结果显示Re-nd的突变基因位于SNP标记SNP7和SNP17之间,物理距离4.04 Mb;以SNP7和SNP17之间筛选出的6个SNP标记和25个重组个体进行精细定位克隆,结果显示Re-nd的突变基因所在的区域位于SNP10和SNP12两个SNP标记之间的nscaf2853上,物理距离949.3 kb左右。【结论】将Re-nd的突变基因定位于第6号染色体的2个SNP标记SNP10和SNP12之间,物理距离约949.3 kb。本研究为后续Re-nd突变基因的精细定位及功能应用研究奠定了基础。 相似文献
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《Journal of receptor and signal transduction research》2013,33(6):513-526
AbstractThe renin–angiotensin–aldosterone system (RAAS) plays a key role in the regulation of blood pressure (BP). Mutations on the genes that encode components of the RAAS have played a significant role in genetic susceptibility to hypertension and have been intensively scrutinized. The identification of such probably causal mutations not only provides insight into the RAAS but may also serve as antihypertensive therapeutic targets and diagnostic markers. The methods for analyzing the SNPs from the huge dataset of SNPs, containing both functional and neutral SNPs is challenging by the experimental approach on every SNPs to determine their biological significance. To explore the functional significance of genetic mutation (SNPs), we adopted combined sequence and sequence-structure-based SNP analysis algorithm. Out of 3864 SNPs reported in dbSNP, we found 108 missense SNPs in the coding region and remaining in the non-coding region. In this study, we are reporting only those SNPs in coding region to be deleterious when three or more tools are predicted to be deleterious and which have high RMSD from the native structure. Based on these analyses, we have identified two SNPs of REN gene, eight SNPs of AGT gene, three SNPs of ACE gene, two SNPs of AT1R gene, three SNPs of CYP11B2 gene and three SNPs of CMA1 gene in the coding region were found to be deleterious. Further this type of study will be helpful in reducing the cost and time for identification of potential SNP and also helpful in selecting potential SNP for experimental study out of SNP pool. 相似文献
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Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress 总被引:2,自引:0,他引:2
Rostoks N Mudie S Cardle L Russell J Ramsay L Booth A Svensson JT Wanamaker SI Walia H Rodriguez EM Hedley PE Liu H Morris J Close TJ Marshall DF Waugh R 《Molecular genetics and genomics : MGG》2005,274(5):515-527
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Hsin-Chou Yang Yu-Jen Liang Yi-Lin Wu Chia-Min Chung Kuang-Mao Chiang Hung-Yun Ho Chih-Tai Ting Tsung-Hsien Lin Sheng-Hsiung Sheu Wei-Chuan Tsai Jyh-Hong Chen Hsin-Bang Leu Wei-Hsian Yin Ting-Yu Chiu Chin-Iuan Chen Cathy S. J. Fann Jer-Yuarn Wu Teng-Nan Lin Shing-Jong Lin Yuan-Tsong Chen Jaw-Wen Chen Wen-Harn Pan 《PloS one》2009,4(5)
Young-onset hypertension has a stronger genetic component than late-onset counterpart; thus, the identification of genes related to its susceptibility is a critical issue for the prevention and management of this disease. We carried out a two-stage association scan to map young-onset hypertension susceptibility genes. The first-stage analysis, a genome-wide association study, analyzed 175 matched case-control pairs; the second-stage analysis, a confirmatory association study, verified the results at the first stage based on a total of 1,008 patients and 1,008 controls. Single-locus association tests, multilocus association tests and pair-wise gene-gene interaction tests were performed to identify young-onset hypertension susceptibility genes. After considering stringent adjustments of multiple testing, gene annotation and single-nucleotide polymorphism (SNP) quality, four SNPs from two SNP triplets with strong association signals (−log10(p)>7) and 13 SNPs from 8 interactive SNP pairs with strong interactive signals (−log10(p)>8) were carefully re-examined. The confirmatory study verified the association for a SNP quartet 219 kb and 495 kb downstream of LOC344371 (a hypothetical gene) and RASGRP3 on chromosome 2p22.3, respectively. The latter has been implicated in the abnormal vascular responsiveness to endothelin-1 and angiotensin II in diabetic-hypertensive rats. Intrinsic synergy involving IMPG1 on chromosome 6q14.2-q15 was also verified. IMPG1 encodes interphotoreceptor matrix proteoglycan 1 which has cation binding capacity. The genes are novel hypertension targets identified in this first genome-wide hypertension association study of the Han Chinese population. 相似文献
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The 3111 C/T single nucleotide polymorphism (SNP) in the CLOCK gene and the 825C/T SNP in the G-protein β3 subunit gene (GNB3) have been reported to influence diurnal preference. This study has attempted to characterize the association between the CLOCK gene and GNB3 polymorphisms and diurnal preference in healthy Korean college students. All subjects completed the 13-item Composite Scale for Morningness (CSM). The interaction between the 3111 C/T SNP in the CLOCK gene and the 825 C/T SNP in the GNB3 gene significantly influenced diurnal preference, according to the CSM Performance subscore (F=10.94, p=0.001). However, when the different polymorphisms of the two genes were analyzed independently, no direct correlations with diurnal preference were detected. The CLOCK gene 3111 C/T SNP and GNB3 gene 825 C/T SNP were found to manifest a gene-gene interaction that affects diurnal preference. 相似文献
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Shojaee S Sina F Banihosseini SS Kazemi MH Kalhor R Shahidi GA Fakhrai-Rad H Ronaghi M Elahi E 《American journal of human genetics》2008,82(6):1375-1384
Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome. 相似文献
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Matthew A Brown 《Arthritis research & therapy》2009,11(5):254-6
The advent of high-throughput SNP genotyping methods has advanced research into the genetics of common complex genetic diseases
such as ankylosing spondylitis (AS) rapidly in recent times. The identification of associations with the genes IL23R and ERAP1 have been robustly replicated, and advances have been made in studies of the major histocompatibility complex genetics of
AS, and of KIR gene variants and the disease. The findings are already being translated into increased understanding of the immunological
pathways involved in AS, and raising novel potential therapies. The current studies in AS remain underpowered, and no full
genomewide association study has yet been reported in AS; such studies are likely to add to the significant advances that
have already been made. 相似文献
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Katherine A. Dick Krueger Shoji Tsuji Yoko Fukuda Yuji Takahashi Jun Goto Jun Mitsui Hiroyuki Ishiura Joline C. Dalton Michael B. Miller John W. Day Laura P. W. Ranum 《PloS one》2009,4(5)
The identification of genes for monogenic disorders has proven to be highly effective for understanding disease mechanisms, pathways and gene function in humans. Nevertheless, while thousands of Mendelian disorders have not yet been mapped there has been a trend away from studying single-gene disorders. In part, this is due to the fact that many of the remaining single-gene families are not large enough to map the disease locus to a single site in the genome. New tools and approaches are needed to allow researchers to effectively tap into this genetic gold-mine. Towards this goal, we have used haploid cell lines to experimentally validate the use of high-density single nucleotide polymorphism (SNP) arrays to define genome-wide haplotypes and candidate regions, using a small amyotrophic lateral sclerosis (ALS) family as a prototype. Specifically, we used haploid-cell lines to determine if high-density SNP arrays accurately predict haplotypes across entire chromosomes and show that haplotype information significantly enhances the genetic information in small families. Panels of haploid-cell lines were generated and a 5 centimorgan (cM) short tandem repeat polymorphism (STRP) genome scan was performed. Experimentally derived haplotypes for entire chromosomes were used to directly identify regions of the genome identical-by-descent in 5 affected individuals. Comparisons between experimentally determined and in silico haplotypes predicted from SNP arrays demonstrate that SNP analysis of diploid DNA accurately predicted chromosomal haplotypes. These methods precisely identified 12 candidate intervals, which are shared by all 5 affected individuals. Our study illustrates how genetic information can be maximized using readily available tools as a first step in mapping single-gene disorders in small families. 相似文献
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Heon‐Jeong Lee Jong‐Woo Paik Seung‐Gul Kang Se‐Won Lim 《Chronobiology international》2013,30(4):589-597
The 3111 C/T single nucleotide polymorphism (SNP) in the CLOCK gene and the 825C/T SNP in the G‐protein β3 subunit gene (GNB3) have been reported to influence diurnal preference. This study has attempted to characterize the association between the CLOCK gene and GNB3 polymorphisms and diurnal preference in healthy Korean college students. All subjects completed the 13‐item Composite Scale for Morningness (CSM). The interaction between the 3111 C/T SNP in the CLOCK gene and the 825 C/T SNP in the GNB3 gene significantly influenced diurnal preference, according to the CSM Performance subscore (F=10.94, p=0.001). However, when the different polymorphisms of the two genes were analyzed independently, no direct correlations with diurnal preference were detected. The CLOCK gene 3111 C/T SNP and GNB3 gene 825 C/T SNP were found to manifest a gene‐gene interaction that affects diurnal preference. 相似文献
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The European black poplar (Populus nigra L.) has been used as a
germplasm resource for the breeding of new poplar varieties around the world. The
identification and screening of its high nitrogen use efficiency genotypes could
enable the breeding of new resource-efficient poplar varieties. The accessions were
screened using MALDI-TOF MS genotyping technology for ammonium
transporter (AMT) and nitrate transporters (NRT) genes against phenotypic data for
seedling height and ground diameter traits, in both low and high nitrogen
environments. Allele re-sequencing of seven genes related to root development
was carried out using the minisequencing method. By cluster analysis, 101
accessions of black poplar were divided into 4 populations, and it was concluded
that Central Europe is the origin of the evolution of low-nitrogen and highefficiency
populations of European black poplar. Association study between SNP
typing and seedling height and ground diameter traits showed that there were
significant correlations between four SNP loci and growth traits under the
contrasting N levels. We found that SNP3 and SNP4 in the PttAMT1;3 gene were
significantly associated with seedling height traits, and that SNP2 and SNP7 in the
PttAMT1;2 and PttAMT1;5 genes, respectively, were significantly associated with
ground diameter traits. Thus, considerable allelic diversity is present within the
candidate genes studied and can be utilized to develop functional markers to select
for poplars with improved growth under N stress conditions. 相似文献