SNP及其在肉牛育种中的应用进展

单核苷酸多态性(Single nucleotide polymorphism,SNP)作为第三代分子标记,具有位点丰富、代表性强和遗传稳定等特点,已成为分子标记研究领域的焦点。本研究综述了SNP特点、检测方法及其在肉牛生长发育性状、繁殖性状、胴体与肉质性状的应用,作为分子标记辅助选择的候选基因,加快肉牛育种进程。     

棉花单核苷酸多态性标记研究进展

单核苷酸多态性标记已在农作物研究中得到广泛应用并取得重大进展。为了便利棉花SNP(Single nucleotide polymorphism)标记的研究和应用,介绍了利用基因芯片、简化基因组测序、重测序等在棉花中开发SNP标记的方法 ,综述了SNP标记在棉花遗传图谱构建、数量位点的定位和分子标记辅助育种、基因组测序以及系统进化等研究中的应用。并对异源四倍体棉花中SNP标记开发时,同源序列位点和部分同源序列位点上的SNP标记辨别问题进行了系统探讨,对其快捷的开发、检测方式和在数量基因定位中的应用前景进行了展望。     

基于SNP标记的关联分析在玉米耐旱研究中的应用

单核苷酸多态性(Single nucleotide polymotphisin,SNP)标记的发展促进了关联分析对植物复杂数量性状的遗传研究.研究证明:多数SNP变异与基因功能密切相关,通过关联分析可以发掘这些功能型位点变异并应用于作物遗传育种.因此,本文综述了近些年来在玉米上利用SNP标记进行关联分析的研究进展,展望了其在耐旱分子育种和遗传网络解析方面的应用前景.     

后基因组时代下作物的SNP分型方法

单核苷酸多态性(single nucleotide polymorphisms,SNPs)是生物体最普遍的一种多态差异,在植物功能基因组研究和作物遗传改良方面有着广泛的应用。利用全基因组水平SNP标记谱进行遗传变异的研究、群体结构分析、关联性分析、作物分子设计育种,以及对大规模SNP数据进行验证、评估等,都迫切需要发展和利用各种不同的SNP分型手段实现。本文综述了目前常用的一些SNP分型方法,简要介绍了检测原理及操作流程,并对后基因组时代下作物的高通量SNP数据的分析进行了讨论。     

单核苷酸多态性在水稻遗传育种中的应用

单核苷酸多态性(SNP)是最新发展起来的继限制性片段多态性(RFLP)、微卫星标记(SSR)后的新一代分子标记,具有分布不均匀、丰度高、检测易实现自动化的特点。SNPs日益成为功能基因组学和分子标记辅助选择等领域研究的主要手段。本文主要介绍SNPs在水稻基因组中的分布、特点、检测及其在遗传育种中的应用。     

采用基于高分辨率熔解曲线技术的SNP标记定位徐州142无絮的短绒控制基因

【目的】定位徐州142无絮(XZ142w)突变体的短绒控制基因n2。【方法】以陆地棉(Gossypium hirsutum L.)徐州142(XZ142)×XZ142w的F2群体为研究对象,利用108个简单重复序列(Simple sequence repeat,SSR)标记对n2进行初步定位,再根据2个亲本材料中有单核苷酸多态性(Single nucleotide polymorphic,SNP)的差异基因设计50对SNP引物,用高分辨率熔解曲线(High resolution melting,HRM)技术从中筛选在亲本间有多态性的SNP引物,并用于后代的基因分型。【结果】利用108个SSR标记将n2初步定位在26号染色体的20.2c M的遗传区间内;用HRM技术筛选到9对亲本间有多态性的SNP引物,成功实现基因分型;并结合以SSR构建的连锁图谱,将n2的遗传区间缩小为19.5 c M,n2与最近的SNP标记Cricaas20158遗传距离为5.5 c M,且遗传图谱上的标记与四倍体陆地棉测序物理图谱基本一致。【结论】HRM技术可用于棉花中的SNP检测和n2基因的定位。     

遗传标记的单核苷酸多态性和插入-删除以及玉米指纹重叠群在遗传图上的定位

单核苷酸多态性（SNPs）和插入-删除标记（InDels）日益成为主要作物的重要遗传标记。本研究中，我们想证明这两种标记在将指纹重叠群定位到遗传图谱上的实用性。为了得到SNP和InDcl标记，我们扩增了12个玉米品系中与3000个单基因相对应的基因组区域，其中194个单基因（6．4％）在琼脂凝胶上表现出B73和Mo17间的大小多态性InDels。     

遗传标记及其在园艺植物研究中的应用

评述了形态学标记（morphological markers）、细胞学标记(cytological markers)、生化标记(biochemical markers)、DNA分子标记(DNA molecular markers)等技术的发展现状,着重介绍了近年来DNA指纹图谱技术,即限制性片段长度多态性(Restriction Fragment Length Polymorphism,RFLP)、随机扩增片段长度多态性 (Random Amplified Polymophismic DNA,RAPD)、简单重复序列 (simple sequence repeats,SSR)、扩增片段长度多态性(Amplified Fragment Length Polymorphism,AFLP)、单核苷酸多态性 (single nucleotide polymorphism,SNP) 等标记技术的特点及其在园艺植物品种的分类鉴定、纯度的分析检测及品种间亲缘关系等研究中的应用。     

植物SNP数据库及转化CAPS的方法

单核苷酸多态性(SNP)在植物基因组中广泛存在,基于SNP的分子标记也正越来越广泛地应用到植物基因定位、图位克隆及分子标记辅助育种等方面。模式植物拟南芥和水稻的全基因组序列测定已经完成,拟南芥有两种生态型完成了全序列测定,水稻有两个品种完成了全序列测定。许多植物有来自不同品种或不同组织器官或生长发育阶段的大量的EST序列。这些序列是植物SNP开发的重要资源。利用生物信息学手段对全基因组序列或EST序列进行分析已经形成了许多SNP位点数据库,这些数据库的建立为基于SNP的基因功能研究及分子标记开发提供了宝贵的资源。本文对植物SNP位点开发涉及的数据库资源及已经形成的SNP位点数据库进行了总结,并讨论了将SNP位点转化成CAPS或dCAPS标记的方法和相应的工具软件。     

SNP检测方法的研究进展

作为近年来最有发展潜力的第三代分子标记,单核苷酸多态性(single nucleotide polymorphism,SNP)在遗传分析中得到了广泛应用。目前SNP的检测方法大致可以分为两大类:一大类是以单链构象多态性(SSCP)、变性梯度凝胶电泳(DDGE)、酶切扩增多态性序列(CAPS)、等位基因特异性PCR(allele-specific PCR,AS-PCR)等为代表的以凝胶电泳为基础的传统经典的检测方法。另一大类是以直接测序、DNA芯片、变性高效液相色谱(DHPLC)、质谱检测技术、高分辨率溶解曲线(HRM)等为代表的高通量、自动化程度较高的检测方法。本文综述了两大类SNP检测方法中主要检测技术的原理和应用,并分析在实际应用中各种检测技术的优缺点。     

四种天麻基于SLAF测序的SNP标记开发与分析

为了分析天麻种质资源的遗传多样性及其进化关系,开发特异性SNP(Singlenucleotidepolymorphism)标记位点。实验通过对4种不同种或不同产地的同种天麻共28个样品进行SLAF测序,首次在天麻种质资源中得到SLAF标签并开发SNP标记,通过De nove测序技术,构建SLAF文库,利用GATK和SAMTOOLS技术开发SNP标记。共获得75.95 M高质量的reads数据,471001个SLAF标签,其中多态性SLAF标签19675个,并开发出60238个群体SNP。对SNP标记的分析的结果表明,作为主要栽培种的天麻(W)由于长时间的人工培育,也许使得其遗传进化体系与其他的天麻种质资源存在较大差异。另外,所有样品中SNP标记的杂合率普遍高于20%,突出了天麻这一物种广泛的杂合性。而且,利用简化基因组测序技术SLAF-seq可以高效地、低成本地开发出大量的可用于群体遗传结构分析的SNP标记。     

基于基因重测序信息的大豆基因靶向CAPS标记开发

为了开发大豆基因靶向的功能分子标记,本研究采用生物信息学方法分析了大豆基因重测序数据,筛选出酶切位点突变的SNP位点,设计PCR引物163对,选用东北地区主栽品种绥农14的DNA为模板进行PCR扩增,其中139对引物获得大小为400~1 200 bp的特异片段。以大豆绥农14、合丰25、Acher、Evans、Peking、PI209332、固新野生大豆、科丰1号和南农1138-2的DNA为模板,采用筛选的139对引物进行PCR扩增,对扩增产物进行酶切分析,发现73对引物的PCR产物具有酶切多态性,开发出CAPS标记73个。通过功能注释分析发现,这73个CAPS标记靶向的基因主要参与细胞内亚细胞定位过程、蛋白质的结合与催化以及代谢过程等,与大豆重要农艺性状的形成相关,可以用于大豆品种的鉴定和分子系统进化的研究。     

Discovery and genotyping of high-throughput SNP markers for crown rust resistance gene Pc94 in cultivated oat

Crown rust caused by Puccinia coronata f. sp. avenae Eriks is a serious problem for oat production worldwide and pyramiding multiple resistance genes into new cultivars is a key objective of breeders. Many race specific resistance genes have been mapped and markers that are closely linked to them have been identified. However, the use of these markers in oat breeding practice has been limited due to the economics of marker assisted selection (MAS) deployment. Single nucleotide polymorphism (SNP) markers have been demonstrated to have a high-throughput capability with relatively low cost and numerous semi-automated SNP scoring platforms exist. Gene Pc94 has remained highly effective since it was first tested on the Canadian crown rust populations in 1993 and is one of the few effective genes available in Western Canada. In the present study, PCR products were amplified using primers derived from sequences of amplified fragment length polymorphism bands which have been shown to be linked to Pc94 . Genomic DNA from genotypes, with and without the Pc94 gene, were used as the PCR templates. By comparative sequence alignment amongst the PCR fragments, many putative SNP sites were identified. From these sites, four SNP sites were selected and validated by the single base extension method. One SNP site, Pc94 -SNP1a, was tested on two F_2:3 populations segregating for the resistance gene. The map distances between the SNP marker and Pc94 were 2.1 and 5.4 cM in the two different populations. Various oat cultivars and germplasm lines were also tested for a wider application of the SNP marker. Fluorescent technology and capillary electrophoresis allowed for the semi-automated, fairly high-throughput scoring of the SNP markers.     

植物功能基因单核苷酸多态性的研究进展

单核苷酸多态性(SNP)的挖掘和检测目前是一个被广泛关注的研究热点。为能够明晰功能基因SNP和中药材生理活性物质的形成及药材产地之间关系的研究思路,本研究简要归纳了次生代谢功能基因、抗逆性功能基因和农艺性状功能基因等SNP的研究及应用,并对功能基因SNP与植物地理分布关系的研究进行了总结分析。同时,认为借鉴遗传背景清晰的物种挖掘和开发SNP信息用来对其他药用植物开展研究、参照有效成分生源途径较明确的物种对其他药用植物进行相关代谢关键酶基因的探究性研究,是解决数量浩瀚而遗传背景有限的药用植物基因研究的不错的路径,此外提出优良农艺性状或特殊生理现象基因应该成为药用植物功能基因研究的关注点。     

Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis> L.)

Chickpea genetic mapping has been hampered by insufficient amplicon length polymorphism for sequence based markers. To develop an alternative source of polymorphic markers, we determined naturally abundant single nucleotide polymorphism (SNP) in coding and genomic regions between FLIP 84-92C (C. arietinum) and PI 599072 (C. reticulatum) and identified an inexpensive method to detect SNP for mapping. In coding sequences, 110 single base changes or substitutions (47% transitions and 53% transversions) and 18 indels were found; while 50 single base changes (68% transitions and 33% transversions) and eight indels were observed in genomic sequences. SNP frequency in coding and genomic regions was 1 in 66 bp and 1 in 71 bp, respectively. In order to effectively use this high frequency of polymorphism, we used Cleaved Amplified Polymorphic Site (CAPS) and derived CAPS (dCAPS) marker systems to identify a restriction site at SNP loci. In this study, we developed six CAPS and dCAPS markers and fine mapped QTL1, a region previously identified as important for ascochyta blight resistance. One of the CAPS markers from a BAC end was identified to account for 56% of the variation for ascochyta blight resistance in chickpea. Conversion of naturally abundant SNPs to CAPS and dCAPS for chickpea mapping, where absence of amplicon length polymorphism is a constraint, has potential to generate high-density maps necessary for map-based cloning and integration of physical and genetic maps.     

Clustering of amplified fragment length polymorphism markers in a linkage map of rye

Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI‐MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F₂ mapping population. Seventy‐one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM.