DNA fingerprinting of eukaryote genomes by synthetic oligodeoxyribonucleotide probes

An extreme level of DNA sequence polymorphism, the basis of DNA fingerprinting, was first demonstrated using genome derived cloned probes. Subsequently, it was shown that DNA fingerprinting can also be carried out using short synthetic oligodeoxyribonucleotide probes specific for simple repetitive sequences. Further, in addition to radioactively labeled probes, non-radioactive oligonucleotides generate equally informative hybridization patterns. We discuss the development in the area of DNA fingerprinting and its future scope with respect to plant, animal and the human DNA.     

DNA amplification fingerprinting: A strategy for genome analysis

A novel strategy to detect genetic differences among organisms, DNA amplification fingerprinting (DAF), uses a thermostable DNA polymerase directed by usually one short (≥5 bp) oligonucleotide primer of arbitrary sequence to amplify short segments of genomic DNA and generate a range of DNA extension products. These products can be analyzed by polyacrylamide gel electrophoresis and silver staining. DAF is rapid and sensitive and is independent of cloning and prior genetic characterization. Here we describe this new methodology, its application to plant genotyping, and its perspectives in DNA fingerprinting and genome mapping.     

DNA指纹图谱技术在动物行为学研究上的应用

ＤＮＡ指纹图谱技术于８０年代末在国外已被广泛应用于行为学尤其是动物繁殖行为学研究中,国内在此方面的应用尚少。综述了ＤＮＡ指纹图谱技术在动物行为学研究中的作用,介绍了ＤＮＡ指纹图谱的产生、实验操作方法、应用实例及其优缺点。     

Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data

DNA fingerprinting analysis such as amplified ribosomal DNA restriction analysis (ARDRA), repetitive extragenic palindromic PCR (rep-PCR), ribosomal intergenic spacer analysis (RISA), and denaturing gradient gel electrophoresis (DGGE) are frequently used in various fields of microbiology. The major difficulty in DNA fingerprinting data analysis is the alignment of multiple peak sets. We report here an R program for a clustering-based peak alignment algorithm, and its application to analyze various DNA fingerprinting data, such as ARDRA, rep-PCR, RISA, and DGGE data. The results obtained by our clustering algorithm and by BioNumerics software showed high similarity. Since several R packages have been established to statistically analyze various biological data, the distance matrix obtained by our R program can be used for subsequent statistical analyses, some of which were not previously performed but are useful in DNA fingerprinting studies.     

莲藕品种DNA指纹图谱的绘制

采用RAPD技术对14个莲藕品种进行遗传多态性分析,用5个Operon引物和80个SBS的RAPD引物进行筛选,从中选出来自SBS的RAPD-C13和RAPD-D15扩增出的8条多态性条带,绘制了14个品种的DNA指纹图谱,在该图谱中每个品种均有各自特异的DNA指纹。     

AFLP在分子生物学研究中的应用

扩增片段长度多态性（AFLP）可靠性强,多态检出率高,因而被认为是最有效的DNA指纹分析技术。AFLP已广泛应用于分类学、病理学、种群遗传学、DNA指纹分析的研究和建立数量性状基因图谱,成为最主要的遗传标记。介绍了AFLP的原理、影响因素及其在分子生物学研究中的应用。     

Fingerprinting of Mixed Bacterial Strains and BIOLOG Gram-Negative (GN) Substrate Communities by Enterobacterial Repetitive Intergenic Consensus Sequence-PCR (ERIC-PCR)

PCR-based genomic fingerprinting by use of enterobacterial repetitive intergenic consensus primers (ERIC-PCR) was evaluated for its use in fingerprinting DNA of mixed Gram-negative bacterial strains and BIOLOG Gram-negative (GN) microplate substrate communities. ERIC-PCR fingerprints of six different pure bacterial strains and a combined mixture of the strains were compared with fingerprints obtained by two more established methods: amplified ribosomal DNA restriction analysis (ARDRA) and random amplified polymorphic DNA analysis (RAPD-PCR). The ERIC-PCR fingerprint of the mixed strains was highly reproducible and was more species-specific and representative of the individual strain fingerprints than the ARDRA and RAPD-PCR fingerprints, respectively. ERIC-PCR fingerprinting of model and rhizosphere BIOLOG GN substrate communities also provided clearly distinguishable fingerprints. Results of this study suggest that ERIC-PCR represents a rapid and highly discriminating method for fingerprinting DNA of mixed Gram-negative bacterial strains and BIOLOG GN substrate communities. Received: 11 September 1998 / Accepted: 29 October 1998     

Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data

DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the locus affiliation of alleles is directly observable. Yet DNA fingerprinting has been proved to be a cost-effective method of detecting hypervariable polymorphisms in several organisms, where the traditional loci fail to detect enough variation for microevolutionary studies. In the present paper we demonstrate that the above-mentioned features of DNA fingerprinting data do not cause any serious problem when they are used in evolutionary studies. Bias-corrected estimators of Nei's standard and minimum genetic distances are derived, and, by an application of this theory to data on seven short tandem repeat loci in three major human populations, it is shown that these modified measures of genetic distances based on DNA fingerprint patterns are quite close to Nei's distances based on locus-specific allele frequencies. Empirical as well as theoretical support of the adequacy of such genetic distances from DNA fingerprinting data is also discussed, and it indicates that the technical limitations of DNA fingerprinting should not deter the use of the method for short-term evolutionary studies.      

DNA fingerprinting: a tool for determining genetic distances between strains of poultry

Summary DNA fingerprinting, a technique based on the detection of hypervariable minisatellite regions in DNA restriction fragments, was tested for its applicability to conduct population genetics in poultry. Using MspI digestion and phage M13 DNA as a probe, between 25 and 35 minisatellite-containing DNA fragments were observed per bird. Comparison of the banding pattern of offspring with their parents revealed that the bands were inherited as stable genetic traits. The variability of the DNA fingerprinting pattern was reduced in inbred strains. DNA fingerprints of chickens from five well-defined populations of known genetic relationships were analyzed and indices of genetic distances were computed. They correctly reflected the history of these strains, indicating that DNA fingerprinting may be a powerful tool to characterize genetic relationships between different breeding populations of the same species.     

Biotechnology in forensic medicine: new ways of fingerprinting

The impact of biotechnology on forensic science is reflected in the increasing use of recombinant DNA techniques to identify individuals. Different methods of identification are reviewed and include DNA fingerprinting and antibody fingerprinting.     

动物的双亲判别与DNA指纹图谱

在亲缘识别和婚配选择等动物行为学研究中,需要知道动物之间的亲缘关系。通过分析以往的各种双亲判别方法,如蛋白电泳和血清学技术等,其中DNA指纹图谱法被认为是目前最好的。这种方法已在许多种动物(狗、猫、小家鼠、家燕、蓠雀、天鹅等)和人的研究中得到应用。DNA指纹图谱方法的基本原理是这样,两个动物的DNA 片断具有完全相同的碱基排序的情形从理论上讲其可能性极小,所以每个个体(除同卵双生子外)的DNA经提取、酶切、凝胶电泳、RNA或DNA探针杂交和放射性自显影后所形成的条带分布应该是有区别的、具有个体的特异性,这些条带就是DNA指纹图谱。动物个体DNA 指纹图谱中的每一条带,除了偶然发生的基因突变, 都可以从父母双方、或父方、或母方找到。据此,本文介绍了如何使用DNA指纹图谱进行包括父方和母方亲代判别的方法,如条带比较法和相似性系数法。     

大豆灰斑病菌DNA指纹图谱初步分析

大豆灰斑病菌具有明显的生理分化现象,鉴定病菌生理小种对于培育和推广抗病品种具有重要意义。从大豆灰斑病菌一毒力较强菌株的DNA基因组文库中筛选出2个含重复顺序的克隆,并用其对16个菌株的基因组DNA进行了Southern分析,获得了基因组特异的指纹图谱,对指纹图谱和毒力间的关系进行了初步比较。     

A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars

 Commercial scale fingerprinting of potato cultivars is made difficult by the need for speed, reliability and the ability to distinguish between large numbers of genotypes. There are also problems in extrapolating the results of small experimental studies to predict the performance of techniques or primers for larger applications. The potential of ISSR-PCR for fingerprinting purposes was evaluated using four primers on 34 potato cultivars. The complex band profiles generated were reproducible between repeat PCRs, DNA extractions, electrophoreses and gel scorings. Two primers were each able to distinguish all cultivars. The combined use of any two of the four primers also allowed complete diagnosis. It is concluded that ISSR-PCR provides a quick, reliable and highly informative system for DNA fingerprinting that is amenable for routine applications. Two possible correlates of the ability of primers to distinguish between genotypes were then examined. Marker Index failed to correlate significantly with genotype diagnosis, but a strong and seemingly linear relationship was observed between Resolving Power of a primer and its ability to distinguish genotypes (r²=0.98). Resolving Power of one or a pair of primers was found to provide a moderately accurate estimate of the number of genotypes identified. Possible implications for future studies on DNA fingerprinting are discussed. Received: 7 May 1998 / Accepted: 15 July 1998     

Assessment of DNA fingerprinting for determining genetic diversity in sheep populations

Genomic DNA, prepared from 12 animals from four sheep flocks, was digested with either HaeIII or Hin fI and probed with three DNA fingerprinting probes. Mean DNA fingerprint band sharing and band frequency calculated for each flock were used to estimate genetic diversity. Each of the DNA fingerprinting systems showed the same trend in diversity within the sampled flocks, and greater diversity between the flocks than within the flocks. DNA fingerprinting therefore provides a useful measure of genetic diversity in sheep.     

Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications

Amplified fragment length polymorphism (AFLP) is a novel molecular fingerprinting technique that can be applied to DNAs of any source or complexity. Total genomic DNA is digested using two restriction enzymes. Double-stranded nucleotide adapters are ligated to the DNA fragments to serve as primer binding sites for PCR amplification. Primers complementary to the adapter and restriction site sequence, with additional nucleotides at the 3′-end, are used as selective agents to amplify a subset of ligated fragments. Polymorphisms are identified by the presence or absence of DNA fragments following analysis on polyacrylamide gels. This technique has been extensively used with plant DNA for the development of high-resolution genetic maps and for the positional cloning of genes of interest. However, its application is rapidly expanding in bacteria and higher eukaryotes for determining genetic relationships and for epidemiological typing. This review describes the AFLP procedure, and recent, novel applications in the molecular fingerprinting of DNA from both eukaryotic and prokaryotic organisms. Received 19 December 1997/ Accepted in revised form 3 June 1998     

武汉东湖浮游生物群落DNA多态性与富营养化

对武汉东湖不同程度富营养化湖区 ,即站 、站 与站 浮游生物进行了群落级 DNA多态性的 DNA指纹研究 ,并就其拓扑结构与富营养化特征参数之间关系进行了分析。实验结果如下 :(1)各站点总氮、总磷及叶绿素 a分别为 1.14 6～ 2 .2 35mg/ L、0 .0 13～ 0 .2 10 mg/ L 和 4 0 .2 5～ 10 9.2 2 μg/ L;(2 )所筛选的 5个随机引物共获得 2 9个扩增位点 ,其中多态位点占75 .9% ,各引物扩增谱带数在 2～ 6间。站 的扩增条带数最多、谱带多态率最高 (6 9.6 % )、特有带最多 ;(3)特定浮游生物类群的特异性 PCR扩增谱带为 1～ 6条不等 ,站间差别甚小。聚类及综合分析表明 :DNA指纹拓扑结构与浮游生物及特定浮游生物类群的物种多样性丰度相吻合 ,并与富营养化主要指示参数存在明显相关 ,即在一定范围内浮游生物群落 DNA多态性与富营养化程度呈反方向发展 ,而原生动物则表现出同向性发展趋势。因此 ,群落级 DNA指纹分析不仅能为生态学研究洞开一片新颖的视窗 ,并有可能孕育出一种简便而灵敏的水体富营养化危机预警系统     

DNA fingerprinting of Mycobacterium xenopi strains

Mycobacterium xenopi is an environmental bacterium that occasionally causes disease in humans. A method is described for DNA fingerprinting strains of this species. Seven of 10 strains from humans were clearly distinguishable from each other using DNA fingerprinting. This method will enable the investigation of possible environmental sources and human spread of disease due to this species.     

Probability of paternity in paternity testing using the DNA fingerprint procedure

For the purpose of applying DNA fingerprinting to paternity testing, we established a general formula to calculate the probability of paternity and evaluated the ability of DNA fingerprinting to determine paternity.     

The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture

In 1985, Alec Jeffreys reported the development of multilocus DNA fingerprinting by Southern blot-detection of hypervariable minisatellites or variable number of tandem repeat (VNTR) loci. This technology found immediate application to various forensic and scientific problems, including fisheries and aquaculture. By 1989, however, it was recognized by many researchers that inherent problems exist in the application of multilocus fingerprinting to large sample sizes as might occur in fisheries and aquaculture genetic studies. As such, individual VNTRs were cloned for single-locus DNA fingerprinting. Although single-locus fingerprinting ameliorates many of the problems associated with multilocus DNA fingerprinting, it suffers from the problem that electrophorectic anomalies of band migration within and between gels necessitates binning of alleles, thus underestimating genetic variability in a given population. Amplification of microsatellite loci by the polymerase chain reaction, however, solved many of the problems of Southern blot-based DNA fingerprinting. Moreover, microsatellites exhibit attributes that make them particularly suitable as genetic markers for numerous applications in aquaculture and fisheries research: (1) they are abundant in the genome; (2) they display varying levels of polymorphism; (3) alleles exhibit codominant Mendelian inheritance; (4) minute amounts of tissue are required for assay (e.g., dried scales or otoliths); (5) loci are conserved in related species; (6) potential for automated assay. Recent innovations in DNA fingerprinting technology developed over the past 5 years are discussed with special emphasis on microsatellites and their application to fisheries and aquaculture, e.g., behavioural and population genetics of wild species, and selection and breeding programmes for aquaculture broodstock.     

Use of DNA fingerprinting for human population genetic studies

DNA fingerprinting techniques have been used in population genetic studies on many different kinds of organisms. Here, we present new applications for multilocus DNA fingerprint probes in population studies and demonstrate the applicability of DNA fingerprinting to human population genetics, using M13 phage DNA as a probe. The new approach, which is based on a factor method of numerical coding of non-quantitative data (factor correspondence analysis-FCA), shows good agreement between population position, as indicated by the three principal factors, and ethnogenetic proximity.