双向等位基因特异性PCR与限制性片段长度多态性基因分型方法比较

目的:比较双向等位基因特异性PCR(Bi-PASA)法与聚合酶链式反应-限制性片段长度多态性(RFLP)法对EZH2基因单核苷酸多态性(SNPs)位点rs887569基因分型结果有无差异,并用Bi-PASA法对EZH2基因rs17171119位点基因分型后分析与结直肠癌(CRC)易感性的相关性。方法:提取96名CRC患者与100名体检健康者的外周血DNA,分别用Bi-PASA法与聚合PCR-RFLP法检测EZH2基因单核苷酸多态性(SNPs)位点rs887569基因型,对两种分型结果进行比较;使用Bi-PASA法对EZH2基因rs17171119位点进行基因分型后用病例-对照方法分析该SNPs在中国人群中的分布。结果:Bi-PASA与PCR-RFLP对EZH2基因rs887569位点基因分型的准确率分别为99.5%和100%;EZH2基因的rs17171119 SNPs位点多态性与结直肠癌易感性无显著相关性(P=0.938,OR=0.846,95%CI:0.586-1.221)。结论:Bi-PASA是一种简单有效检测SNPs的方法,分型结果较为可靠;rs17171119 SNPs位点多态性与结直肠癌易感性无关,但本结论还有待更大样本量基因分型的验证。     

β_2-AR基因5’-调控区-654位与-1429位单核苷酸多态性与新疆哈萨克族原发性高血压关系的研究

目的:检测β2-肾上腺素能受体(β2-AR)基因5’-调控区部分序列单核苷酸多态性(SNPs),并探讨这些SNPs与新疆哈萨克族原发性高血压的关系。方法:应用MALDI-TOFMS方法测定β2-AR基因5’-调控区-654位与-1429位单核苷酸多态性确定SNP类型,并进行基因分型。结果:β2-AR基因5’-调控区-654位与-1429位单核苷酸多态性分别为-654位G→A、-1429位T→A碱基变异。2种SNPs基因型频率在正常人群分布符合Hardy-Weinberg平衡。其中-654位SNPs基因型GG、GA、AA频率在正常血压和高血压人群间的分布没有显著性差异(x2=1.26,df=2,P>0.05),位于-1429bp处SNPs基因型在2组人群中分布差异无显著性(x2=1.85,df=2,P>0.05)。结论:β2-AR基因-654位与-1429位SNPs可能仅为基因多态性标志。     

β2-AR基因5’-调控区-654位与-1429位单核苷酸多态性与新疆哈萨克族原发性高血压关系的研究

目的：检测β2-肾上腺素能受体（β2-AR）基因5’-调控区部分序列单核苷酸多态性（SNPs）,并探讨这些SNPs与新疆哈萨克族原发性高血压的关系。方法：应用MALDI-TOFMS方法测定β2-AR基因5’-调控区-654位与-1429位单核苷酸多态性确定SNP类型,并进行基因分型。结果：β2-AR基因5’-调控区-654位与-1429位单核苷酸多态性分别为-654位G→A、-1429位T→A碱基变异。2种SNPs基因型频率在正常人群分布符合Hardy-Weinberg平衡。其中-654位SNPs基因型GG、GA、AA频率在正常血压和高血压人群间的分布没有显著性差异（x2=1.26,df=2,P〉0.05）,位于-1429bp处SNPs基因型在2组人群中分布差异无显著性（x^2=1.85,df=2,P〉0.05）。结论：β2-AR基因-654位与-1429位SNPs可能仅为基因多态性标志。     

微测序技术分析人类单核苷酸多态性

单核苷酸多态性 (singlenucleotidepolymorphism)是指染色体基因组水平上单个核苷酸变异引起的DNA序列多态性 ,即一种二等位基因标记。目前推断在基因组中至少有 30万个SNP[1 ] 。随着分子遗传学的发展 ,疾病研究从对单基因疾病的研究转向探讨多基因疾病 (如心血管疾病、神经系统疾病、各种肿瘤等 )的相关因素。因此 ,需要在人类基因组中找到一种数目众多、分布广泛且相对稳定的遗传标记 ,单核苷酸多态性正代表了这样一种标记。因此SNPs已成为继第一代限制性片段多态性标记 ,第二代微卫星多态性标记后具有重要研究价值的第三代基因遗传…     

NBS1基因SNPs与中国汉族人群原发性肝癌的遗传易感性

为分析DNA损伤修复相关基因NBS1单核苷酸多态性(SNPs)与原发性肝癌遗传易感性的关系,并对高分辨率单链构象多态性(SSCP)检测技术在SNPs分型中的适用性进行评估,本研究对来自中国汉族人群的327例原发性肝癌以及295例阴性对照中NBS1基因常见SNPs的稀有等位基因频率进行检测和分析．此外,对NBS1基因6个常见SNPs分别选择部分样本同时进行直接序列测定,以比较2种方法的检测效果．119例原发性肝癌以及95例肝硬化/慢性肝炎组织标本的SSCP分析结果表明,6个常见NBS1基因SNPs位点(102G>A, 320+208G/A, 553G>C, 1197T>C, 2016A>G和2071-30A>T)中,SNP 1197T>C的稀有等位基因频率为68.1%,显著高于肝硬化/慢性肝炎对照的57.9% (P = 0.0298)．对该SNP位点另外采用208份肝细胞癌和200份健康人群血液标本进一步分析, 肝细胞癌SNP 1197T>C的稀有等位基因频率为66.8%,显著高于健康人群对照的58.8% (P = 0.0170)．其他5个SNPs的稀有等位基因频率在原发性肝癌与肝硬化/慢性肝炎之间均无显著性差异．高分辨率SSCP分析法与直接序列测定法对所选样本的SNPs基因分型结果完全一致,而且直接测序法对PCR扩增产物质量的要求相对高分辨率SSCP分析更高．研究表明,中国汉族人群NBS1基因SNP 1197T>C可能与原发性肝癌的发生相关,高分辨率SSCP技术准确度与直接测序法相当,且操作更加简便易行,非常适用于大量样本多个已知SNPs的基因分型．     

多药耐药基因分型芯片的制备及优化

目的:建立多药耐药基因(mdr1)分型芯片,以检测患者的单核苷酸多态性(SNPs)。方法:设计并合成探针和引物,制备芯片;构建野生型和突变型质粒,以其为模板经PCR仪扩增后,与芯片上的探针杂交,并用扫描仪分析结果。结果:构建了野生型和突变型质粒,与芯片杂交能很好地区分基因型;优化了制备条件,建立了分型标准。结论:该基因芯片是一种快速特异的基因分型方法。     

SNPs在水生动物遗传多样性分析的应用

Lander于1996年提出的单核苷酸多态性(single nucleotide polymorphisms,SNPs)被认为是第三代理想的遗传标记.SNPs是基因组水平上由单个碱基变异引起的DNA序列多态性,广泛应用于生物的遗传多样性研究.本文就SNPs定义、特性,及其在水生动物遗传多样性分析的应用进行综述.     

六个核基因片段在中国颗粒野生稻中的单核苷酸多态性及其在群体遗传学研究中的应用

为了筛选可用于亚洲栽培稻的重要野生近缘物种颗粒野生稻群体遗传结构研究的有效SNPs标记,本研究共选取Osgstf3、OsNAC6、BADH、XCP2、EMF2和ERCC4 6个重要水稻功能基因,检测了来自中国云南和海南12份颗粒野生稻代表样品中的单核苷酸多态性,结果发现Osgstf3、OsNAC6、BADH和XCP2的单核苷酸多态性接近于零,但在EMF2和ERCC4内含子区中检测到较低的核苷酸变异。利用EMF2和ERCC4片段对来自云南的3个天然群体和来自海南的2个天然群体共52个个体进行了群体遗传学研究,发现该物种具有高水平的遗传分化和低水平的遗传变异的独特群体遗传结构;这种剧烈的遗传分化不仅来自云南和海南两个地区之间,而且还来自地区内居群间,说明该野生稻生长的热带、亚热带森林生境的破坏导致了碎裂的居群间基因流强烈受阻。     

MDR1基因多态性及其临床相关性研究进展

体内外研究证明,人体中P—gP在药物的吸收、分布、代谢和排泄（ADME）过程中发挥了非常重要的作用。多药耐药基因MDR1（ABCB1）是P-gP的编码基因。药物基因组学和遗传药理学研究发现在不同个体中MDR1基因多态性与P—gP表达和功能的改变密切相关,而且这些多态位点存在基因型分布和等位基因频率的种族差异性。近几年,已陆续发现在MDR1基因中有50处单核苷酸多态性（SNPs）和3处插入与缺失多态性。随后,大量文献报道某些位点的SNPs如C3435T会使个体患病的易感性增加。因此人们相信,深入研究MDR1基因多态性与P—gP的生理和生化方面的相关性将对个体医疗有着非常深远的意义。文章总结了国外最新的研究进展并结合本实验室的工作着重讨论了4个方面：1）P—gP对药代动力学性质的影响：2）MDR1基因多态性及其对遗传药理学性质的影响;3）MDR1^C3435T的单核苷酸多态性与P-gP表达和功能之间的相关性：4）MDR1基因多态性与人类某些疾病之间的相关性。     

贵州地方山羊ADIPOQ基因外显子1和3多态性研究

为分析山羊ADIPOQ基因的多态性,筛选出对山羊繁殖性状有显著影响的SNPs位点,本研究以黔北麻羊和贵州黑山羊为试验对象,构建池DNA,采用PCR产物直接测序法对2个品种山羊该基因的外显子1和3进行单核苷酸多态性检测,估算各SNPs等位基因频率,并利用在线软件预测不同基因型的m RNA二级结构。结果显示,4对引物扩增片段均存在多态性,共发现5个单碱基突变,分别位于内含子1中的C109G,外显子3中的A730G、G1055A、A1691T和A2244G。利用生物信息学软件对外显子3中的A1691T、A2244G进行分析,结果表明2个SNPs位点均导致编码的m RNA二级结构发生改变。表明ADIPOQ基因在黔北麻羊和贵州黑山羊群体中存在较高的遗传多样性,ADIPOQ位点有望丰富两个山羊品种繁殖性状的研究内容。     

Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.).

We searched the genomes of eight rice cultivars (Oryza sativa L. ssp. japonica and ssp. indica) and a wild rice accession (Oryza rufipogon Griffith) for nucleotide polymorphisms, and identified 7805 polymorphic loci, including single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), in predicted intergenic regions. Polymorphisms are useful as DNA markers for genetic analysis or positional cloning with segregating populations of crosses. Pairwise comparison between cultivars and a neighbor-joining tree calculated from SNPs agreed very well with relationships between rice strains predicted from pedigree data or calculated with other DNA markers such as p-SINE1 and simple sequence repeats (SSRs), suggesting that whole-genome SNP information can be used for analysis of evolutionary relationships. Using multiple SNPs to identify alleles, we drew a map to illustrate the alleles shared among the eight cultivars and the accession. The map revealed that most of the genome is mono- or di-allelic among japonica cultivars, whereas alleles well conserved among modern japonica paddy rice cultivars were often shared with indica cultivars or wild rice, suggesting that the genome structure of modern cultivars is composed of chromosomal segments from various genetic backgrounds. Use of allele-sharing analysis and association analysis were also tested and are discussed.     

Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers.

We searched for SNPs in 417 regions distributed throughout the genome of three Oryza sativa ssp. japonica cultivars, two indica cultivars, and a wild rice (O. rufipogon). We found 2800 SNPs in approximately 250,000 aligned bases for an average of one SNP every 89 bp, or one SNP every 232 bp between two randomly selected strains. Graphic representation of the frequency of SNPs along each chromosome showed uneven distribution of polymorphism-rich and -poor regions, but little obvious association with the centromere or telomere. The 94 SNPs that we found between the closely related cultivars 'Nipponbare' and 'Koshihikari' can be converted into molecular markers. Our establishment of 213 co-dominant SNP markers distributed throughout the genome illustrates the immense potential of SNPs as molecular markers not only for genome research, but also for molecular breeding of rice.     

Development of genome-wide DNA polymorphism database for map-based cloning of rice genes

DNA polymorphism is the basis to develop molecular markers that are widely used in genetic mapping today. A genome-wide rice (Oryza sativa) DNA polymorphism database has been constructed in this work using the genomes of Nipponbare, a cultivar of japonica, and 93-11, a cultivar of indica. This database contains 1,703,176 single nucleotide polymorphisms (SNPs) and 479,406 Insertion/Deletions (InDels), approximately one SNP every 268 bp and one InDel every 953 bp in rice genome. Both SNPs and InDels in the database were experimentally validated. Of 109 randomly selected SNPs, 107 SNPs (98.2%) are accurate. PCR analysis indicated that 90% (97 of 108) of InDels in the database could be used as molecular markers, and 68% to 89% of the 97 InDel markers have polymorphisms between other indica cultivars (Guang-lu-ai 4 and Long-te-pu B) and japonica cultivars (Zhong-hua 11 and 9522). This suggests that this database can be used not only for Nipponbare and 93-11, but also for other japonica and indica cultivars. While validating InDel polymorphisms in the database, a set of InDel markers with each chromosome 3 to 5 marker was developed. These markers are inexpensive and easy to use, and can be used for any combination of japonica and indica cultivars used in this work. This rice DNA polymorphism database will be a valuable resource and important tool for map-based cloning of rice gene, as well as in other various research on rice (http://shenghuan.shnu.edu.cn/ricemarker).     

Characterisation of single nucleotide polymorphisms in sugarcane ESTs

Commercial sugarcane cultivars (Saccharum spp. hybrids) are both polyploid and aneuploid with chromosome numbers in excess of 100; these chromosomes can be assigned to 8 homology groups. To determine the utility of single nucleotide polymorphisms (SNPs) as a means of improving our understanding of the complex sugarcane genome, we developed markers to a suite of SNPs identified in a list of sugarcane ESTs. Analysis of 69 EST contigs showed a median of 9 SNPs per EST and an average of 1 SNP per 50 bp of coding sequence. The quantitative presence of each base at 58 SNP loci within 19 contiguous sequence sets was accurately and reliably determined for 9 sugarcane genotypes, including both commercial cultivars and ancestral species, through the use of quantitative light emission technology in pyrophosphate sequencing. Across the 9 genotypes tested, 47 SNP loci were polymorphic and 11 monomorphic. Base frequency at individual SNP loci was found to vary approximately twofold between Australian sugarcane cultivars and more widely between cultivars and wild species. Base quantity was shown to segregate as expected in the IJ76-514 × Q165 sugarcane mapping population, indicating that SNPs that occur on one or two sugarcane chromosomes have the potential to be mapped. The use of SNP base frequencies from five of the developed markers was able to clearly distinguish all genotypes in the population. The use of SNP base frequencies from a further six markers within an EST contig was able to help establish the likely copy number of the locus in two genotypes tested. This is the first instance of a technology that has been able to provide an insight into the copy number of a specific gene locus in hybrid sugarcane. The identification of specific and numerous haplotypes/alleles present in a genotype by pyrophosphate sequencing or alternative techniques ultimately will provide the basis for identifying associations between specific alleles and phenotype and between allele dosage and phenotype in sugarcane.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Discovery of genome-wide DNA polymorphisms in a landrace cultivar of Japonica rice by whole-genome sequencing

Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7% of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the methodology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi (http://www.nodai-genome.org/oryza_sativa_en.html).     

Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars

Background

High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield.

Results

An informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta.

Conclusions

Introgression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-346) contains supplementary material, which is available to authorized users.     

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community.     

SNPs in ecological and conservation studies: a test in the Scandinavian wolf population

Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.     

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus

Oilseed rape (Brassica napus) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.