DNA分析技术及其在植物研究中的应用

从DNA/DNA杂交、RFLP分析、DNA的限制酶图谱和核苷酸序列分析、PCR技术、DNA指纹技术、RAPD分析等六个方面详细描述DNA分析技术在植物学研究中的应用 ,并讨论了DNA分析技术与植物系统学的关系。

DNA分子标记技术在环境污染物检测中的应用

DNA分子标记是DNA分子碱基序列变异的直接反映,利用分子标记物对污染物造成的生物体DNA损伤的检测和定量分析研究是可行的方法。文章主要综述了DNA加合物技术、随机扩增DNA多态性技术(RAPD)、扩增片段长度多态性技术(AFLP)、单细胞凝胶电泳技术(SCGE)及反转录聚合酶链式反应(RT-PCR)的原理及其在环境污染物检测中的应用。该方法具有快速、简便、特异性强的特点,在环境污染物早期诊断和评价方面具有重要意义,已广泛应用于遗传毒理学研究。

DNA指纹技术在污染土壤生态毒理诊断中的应用

生物标记物能在细胞或分子水平上指示暴露-效应关系,是进行污染土壤生态毒理诊断的主要技术手段之一。随着分子生物学技术的飞速发展,出现了一系列以聚合酶链式反应为基础的、在分子水平上检测污染物质导致的生物体DNA损伤的DNA指纹技术。DNA指纹技术的主要类型有:随机扩增多态性DNA(RAPD)、聚合酶链式反应-单链构象多态性(PCR-SSCP)、扩增片段长度多态性(AFLP)、任意引物聚合酶链式反应(AP-PCR)、差异显示反转录聚合酶链式反应(DDRT)、短DNA重复序列(SSR)及限制片段长度多态性(RFLP)等。这些技术与检测基因突变、染色体畸变和损伤为主的一系列经典研究方法如彗星分析、微核实验等相比具有简便、快速、灵敏等优点。本文着重介绍了随机扩增多态性DNA、聚合酶链式反应-单链构象多态性、扩增片段长度多态性3种重要的DNA指纹技术在污染土壤诊断中的应用。

DNA指纹图谱技术在土壤微生物多样性研究中的应用

土壤中的微生物多样性是十分丰富的,传统培养方法对土壤微生物多样性的研究有很大局限性。近年来,各种基于16S rDNA基因的指纹图谱分析技术取得了长足的进步,并广泛应用于土壤微生物多样性的研究。这些技术主要有变性梯度凝胶电泳(DGGE)/温度梯度凝胶电泳(TGGE)、单链构象多态性(SSCP)、随机引物扩增多态性DNA(RAPD)、限制性片段长度多态性(RFLP)和扩增核糖体DNA限制性分析(ARDRA)等。对这些技术近年来在土壤微生物多样性研究领域的应用予以简短综述,并初步探讨未来几年土壤微生物分子生态学发展的方向。

非营养缺陷型原生质体融合选育角蛋白酶生产菌

以两性霉素B抗性作为标记 ,通过单株灭活 ,进行栖土曲霉种内非营养缺陷型原生质体融合 .在 40 %的PEG(Mr=6 0 0 0 )促融下 ,融合频率为 1.6 2× 10 -5.连续传接 10代后 ,获得稳定的融合子 .对孢子体积、核DNA含量、生长速度进行了测定 ,并利用RAPD技术分析比较了亲本及融合子的基因组DNA指纹多态性 ,证明融合子为杂合二倍体 ,产角蛋白酶活力较亲本显著提高 .图 3表 4参 17

镉胁迫对蚕豆幼苗基因组DNA多态性的影响

采用随机扩增多态性DNA(RAPD)技术检测镉(Cd)胁迫对蚕豆幼苗根尖DNA多态性的影响。结果表明,不同浓度(2·5、5和15mg·L-1)镉处理7d后,蚕豆幼苗根伸长及根系中可溶性蛋白质含量均受到了抑制。选用12条寡核苷酸引物(10bp)对蚕豆幼苗根尖细胞中基因组DNA进行RAPD扩增,其中有6个引物产生特异性PCR产物。对照组蚕豆幼苗根尖基因组DNA的RAPD图谱中可分辨出86条RAPD谱带,其分子量为200~2520bp。处理组与对照组RAPD图谱之间存在明显差异,且与镉浓度之间存在剂量-效应关系。这些结果表明,镉影响蚕豆幼苗根尖细胞中基因组模板的稳定性,故利用RAPD技术获得的DNA多态性变化可作为检测镉遗传毒性效应的生物标记物。

桤木属宿主与弗兰克氏菌的共生关系研究

用RAPD-PCR方法对分布在云南省高黎贡山的尼泊尔桤木,分布在吉林长白山的色赤杨、西伯利亚赤杨和东北赤杨进行遗传多样性分析。结果发现分布在长白山的3种赤杨聚类关系较它们与尼泊尔桤木的关系更近,其中色赤杨和西伯利亚赤杨有更近的聚类关系,与它们对应共生的Frankia菌居群亲缘关系表现相似的特征;高黎贡山的尼泊尔桤木遗传多样性水平最高,其次是色赤杨和西伯利亚赤杨,东北赤杨最低。桤木属植物与对应共生的Frankia菌的遗传多样性水平也一致。这些结果暗示着桤木属宿主植物和其Frankia菌共生物之间存在共进化关系。东北3种宿主植物与Frankia菌之间存在于种下基因型类群的共生搭配,表明共生关系的建立过程中可能存在基因型上的选择。Alnus-Frankia共生固氮体系的建立可能是单起源的。

苔藓植物DNA提取方法研究

提取高质量的 DNA是对苔藓植物遗传多样性进行研究的基础。该文以苔藓植物为试材 ,用 5种方法 ,即快速提取法、改良 CTAB法、CTAB法、SDS法及高盐法 (第一种为自行设计 ,第二种是对原有方法的改进 )对苔藓植物 DNA提取方法进行了比较研究。结果表明 ,快速提取法和改良 CTAB法是 2种适合于苔藓植物 DNA提取的方法。这 2种方法提取的 DNA浓度和纯度均比较高 ,凝胶电泳显示无明显降解现象 ,适宜作为 PCR扩增的模板 ,并成功地进行了 RAPD扩增。

云南尼泊尔桤木遗传多样性研究

分别在云南省来凤山、高黎贡山、鸡足山、苍山和无量山,采集58个尼泊尔桤木Alnus nepalensis叶样品,提取总DNA,对它们进行RAPD-PCR分析。3个随机引物共扫描到DNA位点85个,其中多态性位点64个,样品内的多态性为75.30%;用非加权组法(UPGMA)聚类分析,建立尼泊尔桤木分子聚类树状图,以相似系数0.68为标准分为6类;用POPGENE软件分析Nei’s遗传多样性指数和Shannon遗传多样性指数。结果表明:云南尼泊尔桤木遗传多样性丰富,其中,鸡足山尼泊尔桤木居群多样性指数最高,无量山居群中,分布在南坡的尼泊尔桤木多样性指数高于分布于北坡的样品。尼泊尔桤木的分布及遗传结构与环境区域有密切的关系,区域特点是决定尼泊尔桤木遗传多样性水平的重要因子之一。该结果对于研究尼泊尔桤木遗传多样性以及它与共生固氮弗兰克氏菌Frankia的协同进化有一定的利用价值。

Identification of 27 Porphyra lines (Rhodophyta) by DNA fingerprinting and molecular markers

Twenty-seven Porphyra lines, including lines widely used in China, wild lines and lines introduced to China from abroad in recent years, were screened by random amplified polymorphic DNA (RAPD) technique with 120 operon primers. From the generated RAPD products, 11 bands that showed stable and repeatable RAPD patterns amplified by OPC-04, OPJ-18 and OPX-06, respectively were scored and used to develop the DNA fingerprints of the 27 Porphyra lines. Moreover, the DNA fingerprinting patterns were converted into computer language expressed with two digitals, 1 and 0, which represented the presence (numbered as 1) or absence (numbered as 0) of the corresponding band, respectively. Based on the above results, computerized DNA fingerprints were constructed in which each of the 27 Porphyra lines has its unique fingerprinting pattern and can be easily distinguished from others. Software named PGI (Porphyra germplasm identification) was designed for identification of the 27 Porphyra lines. In addition, seven specific RAPD markers from seven Porphyra lines were identified and two of them were successfully converted into SCAR (sequence characterized amplification region) markers. The developed DNA fingerprinting and specific molecular markers provide useful ways for the identification, classification and resource protection of the Porphyra lines.

Molecular biotechnology of marine algae in China

Molecular biotechnology of marine algae is referred to as the biotechnology on the identification, modification, production and utilization of marine algal molecules. It involves not only the manipulation of macromolecules such as DNA, RNA and proteins, but also deals with low molecular weight compounds such as secondary metabolites. In the last decade, molecular systematic researches to investigate the relationship and to examine the evolutionary divergence among Chinese marine algae have been carried out by Chinese scientists. For example, RAPD has been widely used in several laboratories to elucidate genetic variations of the reds, such as Porphyra, Gracilaria, Grateloupia and the greens such as Ulva and Enteromorpha. Some important data have been obtained. The study on molecular genetic markers for strain improvement is now in progress. In 1990s, genetic engineering of economic seaweeds such as Laminaria, Undaria, Porphyra, Gracilaria and Grateloupia has been studied in China. For Laminaria japonica, the successfully cultivated kelp in China, a model transformation system has been set up based on the application of plant genetic techniques and knowledge of the algal life history. Progress has been made recently in incorporating a vaccine gene into kelp genome. Evidence has been provided showing the expression of gene products as detectable vaccines. In the present paper, the progress of molecular biotechnological studies of marine algae in China, especially researches on elucidating and manipulating nucleic acids of marine algae, are reviewed.

Molecular phylogeny and species identification of pufferfish of the genus Takifugu (Tetraodontiformes, Tetraodontidae)

The phylogenetic relationships and species identification of pufferfishes of the genus Takifugu were examined by use of randomly amplified polymorphic DNA (RAPD) and sequencing of the amplified partial mitochondrial 16S ribosomal RNA genes. Amplifications with 200 ten-base primers under predetermined optimal reaction conditions yielded 1962 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances between 5 species of Takifugu and Lagocephalus spadiceus as the outgroup were calculated from the presence or absence of the amplified fragments. Approximately 572 bp of the 16S ribosonial RNA gene was amplified, using universal primers, and used to determine the genetic distance values. Topological phylogenic trees for the 5 species of Takifugu and outgroup were generated from neighbor-joining analysis based on the data set of RAPD analysis and sequences of mitochondrial 16S rDNA. The genetic distance between Takifugu rubripes and Takifugu pseudommus was almost the same as that between individuals within cacti species, but much smaller than that between T. rubripes, T. pseudommus, and the other species. The molecular data gathered from both analysis of mitochondria and nuclear DNA strongly indicated that T. rubripes and T. pseudommus should be regarded as the same species. A fragment of approximately 900 bp was amplified from the genome of all 26 T. pseudommus individuals examined and 4 individuals of intermediate varieties between T. rubripes and T. pseudommus. Of the 32 T. rubripes individuals, only 3 had the amplified fragment. These results suggest that this fragment may be useful in distinguishing between T. rubripes and T. pseudommus.

Screening of salt tolerant watercress variants on natural seawater contained medium

The responses of stem segments of watercress (Nasturtium officinale R. Br.) to 6-BA,NAA and 2,4-D were studied. MS medium supplemented with 2.0 mg/L 6-BA, 0.2 mg/L 2,4-D was used for callus initiation and maintenance. MS medium supplemented with 4.0 mg/L 6-BA was suitable for plant regeneration and MS medium without plant hormone supplement was used for rooting and plant propagation. For screening of salt tolerant calli, stem segments of watercress were plated onto callus initiation medium containing 1/3 natural seawater. Seventeen out of the 325 plated explants produced calli. The growth curves demonstrated that the growth rate of salt-tolerant calli on saline medium almost matched that of the control calli on normal medium. Some of the salt-tolerant calli were transferred to the normal regeneration medium or saline regeneration medium to induce plant regeneration. In the first case, buds and shoots were regenerated in the same way as those of control calli on normal regeneration medium. More than 1 000 regenerated shoots were obtained of which 83 regenerated shoots were cut and transferred to saline MS base medium. At first, all shoot growth was inhibited, but 40 days after the transfer, rapid-growing axillary shoots were observed on 16 of the original shoots but none on the control shoots on saline MS base medium. Moreover, green spots appeared on most calli 10 days after they were transferred to saline medium, however buds appeared only on 5 calli from the 30 transferred calli and at the end only 2 rapid-growing shoots were obtained from two calli. In total, 18 variant lines were obtained through. propagation of the salt-tolerant shoots on saline MS base medium. RAPD analysis was performed in 10 of the 18 salt-tolerant variant lines and DNA variation was detected in all the tested variant lines.

Identification and assessing the cultivars of Laminaria Lamx. (phaeophyceae) with molecular markers

Molecular markers were used to identify and assess cultivars of Laminaria Lamx. and to delineate their phylogenetic relationships. Random amplified polymorphic DNA (RAPD) analysis was used for detection. After screening, 11 primers were selected and they yielded 133 bands in all, of which approximately 99.2% were polymorphic. The genetic distances between gametophytes ranged from 0.412 to 0.956. Two clusters were formed with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the simple matching coefficient. All cultivars of Laminaria japonica Aresch. used for breeding in China fell into one cluster. L. japonica from Japan, L. saccharina (L.) Lam., and L. angustata Kjellm. formed the other cluster and showed higher genetic variation than L. japonica from China. Nuclear ribosomal DNA (rDNA) sequences, including internal transcribed spacers (ITS1 and ITS2) were studied and aligned. The nucleotides of the sequences ranged from 634 to 668, with a total of 692 positions including TTS1, ITS2, and the 5.8S coding region. The phylogenetic tree obtained by the neighbor-joining method favored, to some extent, the results revealed by RAPD analysis. The present study indicates that RAPD and ITS analyses could be used to identify and assess Laminaria germplasm and to distinguish some species and, even intraspecies, in Laminaria.

牙鲆群体遗传多样性及鲽形目鱼类分子系统学初步研究

本文以山东近海野生和养殖牙鲆Paralichthys olivaceus(T．& S.)为研究对象，采用同工酶电泳和随机扩增多态性DNA(RAPD)两种方法，进行了群体遗传学研究；另外，用PCR扩增了牙鲆、桂皮斑鲆Pseudorhombus cinnamomeus(T．& S.)、石鲽Kareius bicoloratus，Basilewsky和大菱鲆Psetta maxima 4种鲽形目鱼类mtDNA 16s rRNA基因区的部分片段，采用生物信息、学方法构建了鲽形目分子系统树。主要结果如下：1．首先建立了适于牙鲆同工酶分析的水平淀粉凝胶和垂直聚丙烯酰胺凝胶电泳系统；对获得的牙鲆15种同工酶基本酶谱进行了生化遗传分析，进而对自然和养殖群体的生化遗传结构进行了分析，共记录了29个基因座位，发现了9个多态座位。2．野生群体的生化遗传参数多态基因座位比例(31．O％)、等位基因平均数(1．38)和群体平均杂合度(0．0802)都明显高于养殖群体(24．1％，1．28，O．0788)；在野生群体中有9个多态基因座位，而养殖群体仅7个多态基因座位；其中，除了Cat和Idhp-1(仅养殖群体)(P < 0．05)有显著差异、Ldh-C(P < O．01)完全偏离Hardy-Weinberg定律外，其余多态座位基因频率均符合Hardy-Weinberg遗传平衡定律。野生和养殖群体的遗传相似性系数(I)为0．9877，它们的遗传距离(D)是0．0124；两群体间的遗传分化系数G_(st)为0．0681，D_m为0．01，表明总变异中的6．8％的遗传变异产生于群体间的基因差异。3．采用11个随机引物对20个野生个体和24个养殖个体进行了RAPD群体遗传多样性分析，分别扩增出88条和86条DNA带，片段大小在200-2500bp之间，平均每个引物扩增的带数是7．8-8．0。两个群体的多态座位比例分别是43．2％和34．9％，平均杂合度是0．2739和0．2255，而Shannon遗传多样性指数表明两群体的遗传变异中有88．12％的遗传变异来自种群内，只有11．88％的变异来自群体间。遗传分化指数G_(st)的结果也验证了Shannon遗传多样性指数的结果：总群体的遗传变异中约有12％是由两群体间的基因差异产生的。4．本文对牙鲆两个群体的同一批样品分别采用经典的同工酶方法和RAPD方法进行了较系统的比较分析。发现，RAPD所显示的多态性要比同工酶的高得多，因为大部分RAPD的变异是源于非编码区和重复DNA，可以遍布整个基因组，而同工酶仅是功能基因的产物，只表现编码区的变异。因此，自然选择在同工酶编码区的作用要多于RAPD标记。在遗传相似性系数(I)和遗传距离(D)上，RAPD的分析结果与同工酶的分析结果也是有差异的，用同工酶分析两个群体遗传距离只有0．0124，而用RAPD研究可达0．0508。遗传分化指数的差异也很大，同工酶为0．0681，RAPD为0．1237。5．RAPD和同工酶的分析结果是类似的，即自然群体的多态座位比例和平均杂合度要比养殖群体高，降低幅度在同工酶中界于1．7～22．3％之间，在RAPD中则界于15．9～19．2％之间。这充分证明了养殖群体的遗传多样性水平已有明显的丧失，值得我们注意。6．构建了鲽形目鱼类mtDNA 16S rRNA基因的分子系统树。通过分子克隆法将牙鲆、桂皮斑鲆、大菱鲆和石鲽mtDNA 16S rRNA目的基因片段连接到质粒载体上，经MegaBACE测序仪测序，分别获得了590、595、582和590bp序列，通过生物信息学方法对其进行了序列分析和核酸变异比较，结合NCBI上6种鲽形目鱼类的同源序列探讨了这4种鱼类在鲽形目中的遗传分化和分子系统进化，构建了系统树，其中，桂皮斑鲆的16S rRNA基因在系统树中的位置与物种形态资料的系统演化不相符，而其它三种很好地呈现了它们在鲽形目中的系统位置。同时，可以看出mtDNA 16S rRNA基因片段可以构建一个相对准确的树，特别是NJ树和ML树比较接近，更为客观一些。由比对序列获得的物种之间的遗传距离也基本可以反映种、属、科间的不同变异水平。