盐肤木基因组DNA提取方法改进及AFLP体系的建立

经过反复试验,摸索出一种提取高质量植物基因组DNA的方法:改良的4×CTAB法.以盐肤木叶片为实验材料,提取到高质量的基因组DNA,建立了酶切、连接、预扩增、选择性扩增的AFLP反应体系.通过两种引物组合"E+3/M+3"和"E+2/M+3"策略筛选出8对条带分辨率高、多态性好的引物组合,优化了盐肤木的AFLP银染反应...     

利用AFLP技术分析丹顶鹤的亲缘关系

建立了丹顶鹤(Grus japonensis)AFLP分析体系,经筛选,利用28对选择性扩增引物构建了5对丹顶鹤AFLP亲缘关系分析图谱,共得到1 114个扩增条带,其中多态性条带551条,多态性比例为49.5%。每个引物组合扩增的条带数为20～66条,其中,引物E4M1扩增的条带最多,为66条;引物E6M1扩增的条带数最少,为20条。经统计分析,计算了各样品间的相似性系数在0.71～0.88之间,得到5对丹顶鹤的遗传距离,并构建了UPGMA聚类图,结果1号与2号、3号与4号鹤的亲缘关系较近,其余3对鹤(自然配对)亲缘关系较远。表明丹顶鹤具有识别亲缘关系的行为机制,丰富了丹顶鹤繁殖行为机制的研究内容,并为深入研究建立合理的散养丹顶鹤繁育体系提出了建议。     

山茶属金花茶组金花茶系的AFLP分析

应用扩增片段长度多态性(AFLP)分子标记方法,对分布于我国的金花茶组金花茶系的35个样品进行了分析,样品包括了《中国植物志》收录的该类群的15种2变种、2个未收录的种和4个已归并但在分类处理上存在分歧的种。4对引物组合：E—ACG／M—CAG,E—ACG／M—CTG,E—AGG／M—CTG,E—AGG／M—CAT用于选择性扩增,其中EcoRI引物的5′端用荧光染料进行标记。这4个引物组合共得到298条扩增带,其中278条带是多态性的。计算了样品间的Nei和Li(1979)相似性系数,基于这一相似性系数应用UPGMA法进行聚类分析,得到了树状分枝图。分析结果表明：(1)贵州金花茶是一个好种;(2)支持将毛籽金花茶、陇瑞金花茶、弄岗金花茶和大样弄岗金花茶归并到淡黄金花茶的观点;(3)薄叶金花茶、小花金花茶、夏石金花茶和小瓣金花茶之间的亲缘关系较近。     

红豆杉种质资源遗传多样性的AFLP分析

目的：通过对5份红豆杉种质资源的AFLP分析,探求各种质间的遗传多样性。方法：采用扩增片段长度多态性（AFLP）标记,在DNA水平上进行遗传多样性研究,筛选了32对选择性扩增引物,将扩增出的条带作为原始矩阵,用NTSYS-PC软件计算并分析了红豆杉种质间的相似度,构建了遗传系统进化树。结果：（1）SDS法提取的红豆杉基因组DNA质量较佳,能够满足AFLP分析的要求;（2）从32对选择性扩增引物中,筛选出10对多态性较强、带型较好、分辨率较高的组合;（3）构建了红豆杉AFLP指纹图谱,将5个红豆杉种质全部区分开来;（4）通过构建进化树,把5个种质分成3类。结论：红豆杉种质资源有丰富的遗传多样性。     

裸燕麦AFLP反应体系的优化

影响裸燕麦AFLP反应的关键因素包括基因组DNA提取过程中氯仿-异戊醇的抽提次数,酶切时间,预扩增产物稀释倍数,选择性扩增中Mg2+、dNTP、引物浓度等.本研究对这些影响因素进行了优化,初步建立了适合裸燕麦的AFLP反应体系.并将该体系应用于引物筛选,在12份材料中,共筛选出20对条带清晰、多态性好的引物组合,为裸燕麦遗传多样性分析提供了基础.     

新疆核桃早实特性及RAPD分析

用RAPD技术进行新疆核桃早实特性的分子标记研究,用180个10-mer随机引物分别扩增早实和晚实近等基因池DNA,筛选出5个多态性引物,结果只有引物OPG15（5’-ACT GGG ACT C-3’）在早实近等基因池及其个体中能重复扩增出一条约710bp的特异片段OPG15 710,而晚实近等基因池及其个体中无此特异片段,将OPG15 710克隆于pUCm-T载体,筛选阳性克隆用限制性内切酶Pst1消化,表明克隆片段大小正确。实步分析认为,OPG15 710可能是与核桃早实特性相关的分子标记,该标记仍在研究之中,该研究将为进一步克隆早实基因,实现早实优质,探索早实机制奠定基础。     

蜡梅AFLP分子标记技术体系的建立

利用简易CTAB法、改良的CTAB法和SDS法提取蜡梅[Chimonanthus praecox(L.)Link]成熟叶和嫩叶的基因组,并进行了检测比较。结果显示,改良的CTAB法更适合蜡梅基因组DNA的提取,蜡梅叶片的年龄并不影响蜡梅基因组DNA的提取;同时利用AFLP分子标记技术,采用MseI-EcoR I酶切组合,从168对引物中筛选出10对带型分布均匀、多态性高且分辨能力强的引物,分别为:M23E46、M24E46、M25E46、M23E47、M24E47、M41E47、M41E94、M64E94、M64E66和M24E75,并确定了适用于蜡梅AFLP反应的最佳酶切连接、预扩和选扩体系,从而为今后利用AFLP分子标记技术研究蜡梅的品种分类和野生居群的遗传多样性分析打下坚实的基础。     

基于果蝇DNA甲基化的AFLP体系的建立及优化

以黑腹果蝇(Drosophila melanogaster)Canton-S品系为材料,采用改良SDS法提取高质量DNA,对连接、预扩增及选择性扩增进行分析,建立适用于果蝇基因组DNA甲基化多态性研究的AFLP优化体系:1)10μL连接体系加T4连接酶1 U,AluⅠ接头50 pmol,EcoR Ⅰ接头5 pmol,4℃反应12 h;2)25μL预扩增体系含Mg2+0.2 mmol/L,dNTPs 0.15 mmol/L,模板1.0μL,Taq DNA聚合酶2 U,E-00 50 ng,A-00 50 ng;3)25μL选择性扩增体系含Mg2+0.1 mmol/L,dNTPs 0.15 mmol/L,模板2.0μL,Taq DNA酶1.5 U、E+340 ng,A+3 40 ng.该体系稳定性高、重复性好,适用于果蝇基因组DNA甲基化多态性研究.     

13种石斛属植物遗传多样性的AFLP分析

采用AFLP技术对13种石斛属植物的遗传多样性进行了分析。选择性扩增引物组合E ACT/M CAC、E AAC/M CAC和E ACA/M CAC分别对这13种材料进行扩增,得到丰富的条带。在100-300bp共得到346条带,多态性带342条,多态性百分率为98.8%。聚类分析结果表明,在相似系数0.54处,可将13种材料分为Ⅰ、Ⅱ、Ⅲ类。Ⅰ类包括:串珠石斛、铁皮石斛、广东石斛、重唇石斛、晶帽石斛、细叶石斛、滇桂石斛、报春石斛、玫瑰石斛、球花石斛;Ⅱ类包括:鼓槌石斛;Ⅲ类包括:美花石斛(花,浅红)、美花石斛(花,淡白)。AFLP分析结果与传统分类学的结果基本一致,表明该标记技术对石斛属植物的遗传多样性和分类研究是可行的。     

部分两用桃品种(系)指纹图谱的建立

以近亲个体'顺10-16'、'青北10-7'和'贺春'为材料建立了两用桃AFLP研究体系,从64对引物组合中筛选出了E-AAT/M-ACT、E-AAT/M-CTG、E-ACA/M-CTG和E-ACA/M-CTT等4个多态性好、分辨率高的引物组合;应用该体系对'锦春'等23个两用桃品种(系)进行AFLP分析,结果共扩增出127条带,其中多态性带62条,多态性百分率48.8%,以其中特异性较高的23个多态性条带构建了这23个两用桃品系的指纹图谱,为两用桃品种鉴定及保护奠定了基础.     

Optimization of AFLP fingerprinting of organisms with a large-sized genome: a study on Alstroemeria spp.

 The recently introduced PCR-based DNA fingerprinting technique AFLP (amplified fragment length polymorphism) allows the selective amplification of subsets of genomic restriction fragments. AFLP has been used for multiple purposes such as the construction of linkage maps, marker saturation at specific genomic regions, analysis of genetic diversity and molecular phylogeny and cultivar identification. AFLP can be tailored by varying the number of selective nucleotides added to core primers and can allow accurate amplification, even in complex template mixtures generated from plant species with very large genomes. In this study Alstroemeria, a plant species with a very large genome, was tested for adapting the AFLP protocol. The results indicated that the estimated number of amplification products was close to the observed number when eight selective nucleotides were used but that seven selective nucleotides did not increase the number of amplification products fourfold. However, we found reproducibility in both +7 and +8 fingerprints. Various distributions of selective nucleotides over the various rounds of preamplifications were tested. Preamplification with four selective nucleotides followed by final amplification with eight selective nucleotides produced clear and reproducible AFLP patterns. The effects of GC content of primers and multiple preamplification steps were also discussed. Received: 16 March 1998 / Accepted: 14 July 1998     

The inheritance and chromosomal localization of AFLP markers in a non-inbred potato offspring

AFLP^TM is a new technique to generate large numbers of molecular markers for genetic mapping. The method involves the selective amplification of a limited number of DNA restriction fragments out of complex plant genomic DNA digests using PCR. With six primer combinations 264 segregating AFLP amplification products were identified in a diploid backcross population from non-inbred potato parents. The identity of an AFLP marker was specified by the primer combination of the amplification product and its size estimated in bases. The segregating AFLP amplification products were mapped by using a mapping population with 217 already known RFLP, isozyme and morphological trait loci. In general, the AFLP markers were randomly distributed over the genome, although a few clusters were observed. No indications were found that AFLP markers are present in other parts of the genome than those already covered by RFLP markers. Locus specificity of AFLP markers was demonstrated because equally sized amplification products segregating from both parental clones generally mapped to indistinguishable maternal and paternal map positions. Locus specificity of AFLP amplification products will allow to establish the chromosomal identity of linkage groups in future mapping studies.Since AFLP technology is a multi-locus detection system, it was not possible to identify the AFLP alleles which belong to a single AFLP locus. The consequences of a genetic analysis based on single alleles, rather than on loci with two or more alleles on mapping studies using progenies of non-inbred parents are discussed.     

Assessment of genetic diversity in 31 species of mangroves and their associates through RAPD and AFLP markers

Random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity in 31 species of mangroves and mangrove associates. Four AFLP primer combinations resulted in the amplification of 840 bands with an average of 210 bands per primer combination and 11 RAPD primers yielded 319 bands with an average of 29 bands per primer. The percentage of polymorphism detected was too high indicating the high degree of genetic variability in mangrove taxa both at inter- and intra-generic levels. In the dendrogram, species belonging to a particular family/ genus, taxa inhabiting similar habitats or having similar adaptations tended to be together. There were exceptions too; as many unrelated species of mangroves form clusters. The intrafamilial classification and inter-relationships of genera in the family Rhizophoraceae could be confirmed by molecular analysis. Both the markers RAPD and AFLP were found equally informative and useful for a better understanding of the genetic variability and genome relationships among mangroves and their associated species.     

ATG-anchored AFLP (ATG-AFLP) analysis in cotton

Amplified fragment length polymorphism (AFLP) marker system has had broad applications in biology. However, the anonymous AFLP markers are mainly amplified from non-coding regions, limiting their usefulness as a functional marker system. To take advantages of the traditional AFLP techniques, we propose substitution of a restriction enzyme that recognizes a restriction site containing ATG, called ATG-anchored AFLP (ATG-AFLP) analysis. In this study, we chose NsiI (recognizing ATGCAT) to replace EcoRI in combination with MseI to completely digest genomic DNA. One specific adaptor, one pre-selective primer and six selective amplification primers for the NsiI site were designed for ligation and PCR. Six NsiI and eight MseI primers generated a total of 1,780 ATG-AFLP fragments, of which 750 (42%) were polymorphic among four genotypes from two cultivated cotton species (Upland cotton, Gossypium hirsutum and Pima cotton, G. barbadense). The number of ATG-AFLP markers was sufficient to separate the four genotypes into two groups, consistent with their evolutionary and breeding history. Our results also showed that ATG-AFLP generated less number of total and polymorphic fragments per primer combination (2-3 vs. 4-5) than conventional AFLP within Upland cotton. Using a recombination inbred line (RIL) population, 62 polymorphic ATG-AFLP markers were mapped to 19 linkage groups with known chromosome anchored simple sequence repeat (SSR) markers. Of the nine ATG-AFLP fragments randomly chosen, three were found to be highly homologous to cotton cDNA sequences. An in-silico analysis of cotton and Arabidopsis cDNA confirmed that the ATG-anchored enzyme combination NsiI/MseI did generate more fragments than the EcoRI/MseI combination.     

糙皮侧耳(Pleurotus ostreatus)的AFLP指纹图谱分析

在对糙皮侧耳(Pleurotus ostreatus)的AFLP分析条件进行优化的基础上,利用该技术建立了14株产自不同地区的糙皮侧耳：DNA指纹图谱,并进行了数据分析。结果表明,在合成的14条引物的不同组合中,引物对E-3／M-3可以产生较多的DNA多态片段,E-AGC／M-CAT引物对的扩增效果最好,共获得184条DNA扩增带,其中多态性条带i101条,占54．89％。利用UPGMA法对所获数据进行聚类分析,计算得到糙皮侧耳菌株之间的遗传距离,发现不同品种间遗传距离差异较大,从0．192到0．754,说明糙皮侧耳的遗传多样性比较丰富。绘制的指纹分析树状图表明,14个糙皮侧耳菌株被分为6个组群,其中P17和杂3的相似性系数最高,达到了81．2％,而侧5与其他菌株的亲缘关系相对最远。     

三例小麦细胞质雄性不育系线粒体DNA的扩增片段长度多态性分析

细胞质雄性不育是小麦杂种优势利用的重要途径,为了鉴定3例小麦雄性不育系的细胞质类型,对其线粒体DNA(mtDNA)进行扩增片段长度多态性(Amplified fragment length polymorphism,AFLP)分析。文中利用差速离心法和不连续蔗糖密度梯度超速离心法提取纯化小麦线粒体。结果表明:通过该提取方法获得的mtDNA,其质量和纯度能够满足PCR反应和遗传学分析。在64对选扩引物中,筛选到了4对特异性引物,其中引物E1/M7在ms(Kots)-90-110不育系扩增出3条特异条带;引物E4/M2在ms(Ven)-90-110不育系扩增出2条特异条带;引物E7/M6在ms(S)-90-110不育系中扩增出2条特异条带;引物E6/M4在ms(Kots)-90-110不育系中扩增出2条特异条带。这些特异引物可以用来作为鉴定具有粘果山羊草Aegilops kotschyi、偏凸山羊草Ae.ventricosa、斯卑尔脱小麦Triticum spelta 3类不育细胞质型小麦雄性不育系的细胞质分子标记,为研究小麦细胞质雄性不育机理奠定了分子基础。     

斜带髭鲷高质量DNA提取及AFLP分析体系建立

目的:提取斜带髭鲷高质量基因组DNA并建立适用于AFLP分析的体系。方法:以斜带髭鲷(Hapalogenys nitens)为材料提取高质量基因组DNA,并进行AFLP扩增。对AFLP分析体系中几个关键环节(基因组双酶切、连接、预扩增及选择性扩增、变性聚丙烯酰胺凝胶电泳和银染)做了优化。结果:提取的斜带髭鲷全基因组DNA纯度高,无拖尾。采用9组选择性引物共检测出350个不同的扩增位点,其中多态位点为175个,多态性比例为49.58%。聚丙烯酰胺凝胶电泳图像染色均匀,条带清晰且无背景干扰。结论:该分析体系的建立为斜带髭鲷的群体遗传多态性、种质资源、遗传图谱、遗传育种等研究奠定基础。     

Conversion of AFLP markers associated with FHB resistance in wheat into STS markers with an extension-AFLP method.

Amplified fragment length polymorphism (AFLP) has proven a powerful tool for tagging genes or quantitative trait loci (QTLs) of interest in plants. However, conversion of AFLP markers into sequence-tagged site (STS) markers is technically challenging in wheat owing to the complicated nature of its genome. In this study, we developed an "extension-AFLP" method to convert AFLP markers associated with Fusarium head blight (FHB) resistance into STS markers. When an AFLP marker of interest was detected with an EcoRI+3-MseI+4-selective primer combination, the PCR product was used as a template for an additional selective amplification with four primer pairs, in which one additional selective base (either A, C, G, or T) was added to the 3' end of one of the two primers. The extended primer pair that produced the targeted band was further extended by adding each of the four selective nucleotide bases for the next round of selective amplification. Extension selective amplification was performed until the target bands became clear enough for subsequent cloning and sequencing. By using the extension-AFLP method, we successfully converted two AFLP markers located on chromosome 3BS and associated with FHB resistance into STS markers. Our results indicated that the extension-AFLP method is an efficient approach for converting AFLP markers into STS markers in wheat. The developed STS markers might be used for marker-assisted selection (MAS) for FHB resistance in wheat breeding programs.     

Molecular identification of AFLP fragments associated with elytra color variation of the Asian ladybird beetle,Harmonia axyridis (Coleoptera: Coccinellidae)

The Asian ladybird beetle, Harmonia axyridis shows polymorphism in elytra color patterns. However, it is uncertain whether these color patterns are regulated by genetic factors. This investigation used amplified fragment length polymorphism (AFLP) analysis to determine any genetic causes of the variability of color patterns. Using four individuals of each group, AFLP analysis produced 37 polymorphic bands. Among several polymorphic bands, six AFLP markers were associated with elytra color patterns after further analysis using six additional individuals of each group. These polymorphic sites were sequenced but did not match DNA sequence data deposited in GenBank. Based on the color-associated AFLP markers, SCAR primers were designed for PCR amplification of genomic DNA. These primers (SCAR 12 and SCAR 44) were used to analyze color-associated loci and/or alleles of H. axyridis DNA. SCAR 12 primers designed from a Spectabilis type-specific fragment (AFLP 12) amplified a specific band of 530 bp in four Spectabilis individuals, but not in the insects with other color patterns.