DNA fingerprinting in cattle using the probe pV47

The multilocus probe pV47 detected an average of nine bands in cattle between 23 kb and 4 kb. Band sharing was estimated for three groups of unrelated animals. The first group comprised 20 individuals of 12 different breeds, the second group 10 individuals of the Swiss Simmental population and the third group 11 individuals of the Swiss Brown Swiss population. The band sharing probabilities were 33%, 42% and 58% respectively. The DNA fingerprints of 38 offspring with a total of 277 bands revealed no bands that could not be traced to the parents.     

DNA fingerprinting in roe deer using the digoxigenated probe (GTG)5

The digoxigenin-labelled oligonucleotide (GTG)₅ was used as a multilocus probe to detect hypervariable microsatellites in roe deer DNA digested with Hae III. The resulting fingerprints of 24 animals belonging to four subpopulations were characterized with regard to within-subpopulation as well as between-subpopulation similarity. The mean number of polymorphic fragments was 20 and the average band-sharing rate for unrelated animals 0.27. A mean probability of 91.5% for a fragment to be present in the heterozygous state was evaluated and the probabilities of identical band patterns in unrelated individuals were estimated to be in the range 1.3 times 10^-16 - 2.5 times 10^-18. Though band-sharing rates of animals belonging to different subpopulations (range 0.18-0.24) were lower than those of within-subpopulations, several measures of population subdivision and the genetic distance do not reveal a striking differentiation of the subpopulations studied.     

Isolation of a mouse DNA fragment with homology to a Drosophila ribosomal protein gene

A mouse genomic library in lambda Charon 4A was screened for putative ribosomal protein genes using a fragment of the gene encoding Drosophila ribosomal protein 49 as a hybridization probe under nonstringent hybridization conditions. A recombinant phage was selected and its restriction enzyme map determined. The major species of mouse poly(A)+ mRNA homologous to the putative gene is about 740 nucleotides long.     

Features of the DNA fingerprinting probe pITZ1

Stringently controlled plasmids generate DNA fingerprint patterns in mammals when used at low hybridization temperatures. In order to develop a probe for use in paternity testing in cattle we screened a bovine, partial genomic plasmid library with the PCR-amplified ori region of plasmid P1. Of eight isolated clones one generated strong band patterns at high stringency in various mammalian species (data not shown). Sequence analysis revealed an imperfect, compound dinucleotide repeat region, which was PCR-amplified and cloned into the plasmid vector pUC19. Fingerprint results generated by this probe (termed pITZ1) in cattle are compared with the results generated by VNTR-probe pV47, which itself was developed by screening a human chromosome 16 library with tandem repeats of bacteriophage M13. Probe pITZ1 is useful in conjunction with other VNTR-probes for DNA fingerprinting in cattle and donkey populations. The dinucleotide repeat region responsible for the band patterns generated with pITZ1 is close to an Alu -like sequence, which may be involved in eukaryotic replication mechanisms.     

DNA fingerprinting in horses using a simple (TG)n probe and its application to population comparisons

A synthetic polynucleotide (TG)_n was hybridized to equine DNA digested with HinfI and hypervariable hybridization patterns were obtained. Mendelian inheritance of these DNA fingerprinting patterns was confirmed by pedigree analysis. Estimates of the probabilities of identical band patterns in unrelated individuals of different breeds (Swedish Trotters, North Swedish Trotters, Thoroughbreds and Arabians) were in the range 1 times 10-⁴-7 times 10-⁶ The variability derived with the (TG)_n, probe in horses was higher than what we obtained with several other commmonly used probes for DNA fingerprinting. Individuals within breeds tended to be more similar to each other with regard to DNA fingerprint pattern than to individuals of other breeds. Moreover, a parsimony analysis made on the basis of the hybridization patterns gave clustering of individuals within breeds. The possibility of using hypervariable probes for the identification of breed-specific characters is discussed.     

Absence from the mouse genome of DNA sequences related to the globin gene family.

Radioactively labelled DNA, complementary to mouse α and β globin messenger RNA, was annealed with unlabelled mouse embryo DNA under conditions of both optimum and lowered stringency. Although an increase in saturation of unlabelled DNA fragments with complementary DNA molecules is produced by lowered stringency, the values obtained are within the range expected for the known globin chains.It is concluded that within the limits of our experimental conditions, there does not exist a large family of DNA sequences related to the globin genes.     

DNA fingerprinting of the mosquito pathogen Bacillus sphaericus with M13 DNA as a probe

Hypervariable nucleotide sequences were detected in Bacillus sphaericus by hybridization with radioactively labelled M13 DNA. Different serotypes could be distinguished by their hybridization profiles. The appearance of bands common for mosquito-pathogenic strains and their absence in an apathogenic strain opens the probability that M13 could hybridize to specific alleles, related to insect toxicity.     

Isolation of the human insulin-like growth factor I gene using a single synthetic DNA probe.

A single synthetic oligonucleotide was employed as hybridization probe to detect and enable isolation of the human insulin-like growth factor I (IGF-I) gene from a human genomic DNA library. The synthetic oligonucleotide probe coded for the B-chain of IGF-I and was designed for expression in Escherichia coli. Despite numerous interspersed mismatches, the synthetic probe hybridized specifically with seven recombinant lambda phage containing almost the entire B-chain region of the human IGF-I gene. The usefulness of this approach was further demonstrated by the detection of lambda phage containing human preproinsulin, using A and B chain synthetic oligonucleotides, 90 and 63 nucleotides in length, as hybridization probes. The nucleotide sequence of the human IGF-I exon suggests that IGF-I is synthesized as a larger precursor molecule.     

Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo

The dam DNA methyltransferase gene from Escherichia coli was introduced into Drosophila in order to probe chromatin structure in vivo. Expression of the gene caused no visible defects or developmental delay even at high levels of active methylase. About half of each target site was found to be methylated in vivo, apparently reflecting a general property of chromatin packaged in nucleosomes. Although site-specific differences were detected, most euchromatic and heterochromatic sites showed comparable degrees of methylation, at least at high methylase levels. Methylase accessibility of a lacZ reporter gene subject to position-effect variegation throughout development was only slightly reduced, consistent with studies of chromatin accessibility in vitro. Silencing of lacZ during development differed from silencing of an adjacent white eye pigment reporter gene in the adult, as though chromatin structure can undergo dynamic alterations during development.     

Discrimination between closely related Triticeae species using genomic DNA as a probe

Summary Labelled total genomic DNA was used as a probe in combination with blocking DNA to discriminate between taxonomically closely related species in the genera Hordeum and Secale. Discrimination was possible both by Southern hybridization to size-fractionated restriction enzyme digests of genomic DNA and by in situ hybridization to chromosome preparations. To distinguish between two species (e.g. H. vulgare and H. bulbosum), genomic DNA from one species was used as the labelled probe, while unlabelled DNA from the other species was applied at a much higher concentration as a block. The blocking DNA presumably hybridized to sequences in common between the block and the labelled probe, and between the block and DNA sequences on the membrane or chromosomes in situ. If so, mainly species-specific sequences would remain as sites for probe hybridization. These species-specific sequences are dispersed and represent a substantial proportion of the genome (unlike many cloned, species-specific sequences). Consequently, rapid nonradioactive methods detected probe hybridization sites satisfactorily. The method was able to confirm the parentage of hybrid plants. It has potentially wide application in plant breeding for the detection of alien DNA transfer, and it can be easily adapted to many species.     

Genetic variation detected by DNA fingerprinting with a rice minisatellite probe in Oryza sativa L.

A rice minisatellite probe detecting DNA fingerprints was used to assess genetic variation in cultivated rice (Oryza sativa L.). Fifty-seven cultivars of rice, including 40 closely related cultivars released in the US, were studied. Rice DNA fingerprinting revealed high levels of polymorphism among distantly related cultivars. The variability of fingerprinting pattern was reduced in the closely related cultivars. A genetic similarity index (S) was computed based on shared fragments between each pair of cultivars, and genetic distance (D) was used to construct the dendrograms depicting genetic relationships among rice cultivars. Cluster analysis of genetic distance tended to group rice cultivars into different units corresponding with their varietal types and breeding pedigrees. However, by comparison with the coefficients of parentage, the criterion of relatedness based on DNA fingerprints appeared to overestimate the genetic relationships between some of the closely related US cultivars. Although this may reduce the power of fingerprints for genetic analysis, we were able to demonstrate that DNA fingerprinting with minisatellite sequences is simpler and more sensitive than most other types of marker systems in detecting genetic variation in rice.This paper reports the results of research only. Mention of a proprietary product does not consititute an endorsement or a recommendation for its use by the USDA or the University of Missouri. Contribution from the US Department of Agriculture, Agricultural Research Service, Plant Genetics Research Unit, and the University of Missouri Agricultural Experiment Station Journal Series No. 12178.     

A novel probe for human DNA fingerprinting based on chi-like sequences.

A synthetic oligodeoxyribonucleotide (oligo) containing crossover initiating hotspot-like sequences was designed on the assumption that hypervariability is partly due to the presence of molecular signals which promote recombination. This oligo, when used as a probe for human DNA fingerprinting, generated individual-specific DNA band patterns. The probability of two unrelated individuals having the same DNA band pattern, using this probe, was estimated to be 1.9 x 10(-13).     

DNA homologies among Drosophila species and a related genus.

Deoxyribonucleic acids of members of the family Drosophilidae; e.g., D. melanogaster, D. robusta, D. pellewae, D, immigrans, D. mcclintockae, D. calloptera, C. procnemis and from a tissue culture cells of D. melanogaster have been compared with respect to base composition, heterogenecity, and nucleotide sequence homology. Considerable heterogeneity exists in DNA's from 3rd instar larvae and tissue culture cells. The DNA base composition of adult species ranges from 33-42 moles percent GC; in addition a polydAT component is apparent in larval DNA's. There are about 21 and 29 percent intragenomic homology in DNA's of D. melanogaster and D. immigrans, respectively. Relatively large differences were revealed in the nucleotide sequences of several species by DNA hybridization and thermal stability studies.     

Discrimination of Mycobacterium avium- Mycobacterium intracellulare strains by genomic DNA fingerprinting with a 16S rRNA gene probe

Abstract Ribotyping was investigated as a means of distinguishing ten different serotyped reference strains and seven epidemiologically unrelated isolates of Mycobacterium avium - Mycobacterium intracellulare using a labelled 16S rDNA probe. Thirteen restriction enzymes were screened towards an accurate discrimination of strins. Two selected restriction enzymes ( Sac I and Cla I) enabled us to classify the 17 strains into ten ribotypes with an index of discrimination of 0.897. Typeability and reproductibility of the method reached 100%. The patterns obtained exhibited polymorphism of RE fragments within and outside the 16S rRNA gene and may be useful for epidemiological studies.     

Individualization and estimation of relatedness in crocodilians by DNA fingerprinting with a Bkm-derived probe

Individual-specific DNA fingerprints of crocodilians were obtained by the use of Bkm-2(8) probe. Pedigree analyses of Crocodylus palustris, C. porosus and Caiman crocodilus revealed that the multiple bands (22–23 bands with Aludigest) thus obtained were inherited stably in a Mendelian fashion. Unique fingerprints permitted us to identify individuals, assign parentage, and reconstruct the DNA profile of a missing parent. Average band sharing between unrelated crocodiles was found to be 0.37. Band sharing between animals of known pedigrees increased predictably with relatedness and provided a basis for distinguishing relatives from non-relatives. Similar results obtained in other species/genera, using the same probe, suggest that this approach may be applicable to all species of crocodilians, and could facilitate genetic studies of wild and captive populations.     

DNA fingerprinting in horses using a simple (TG)n probe and its application to population comparisons

A synthetic polynucleotide (TG)n was hybridized to equine DNA digested with HinfI and hypervariable hybridization patterns were obtained. Mendelian inheritance of these DNA fingerprinting patterns was confirmed by pedigree analysis. Estimates of the probabilities of identical band patterns in unrelated individuals of different breeds (Swedish Trotters, North Swedish Trotters, Thoroughbreds and Arabians) were in the range 1 x 10(-4) - 7 x 10(-6). The variability derived with the (TG)n probe in horses was higher than what we obtained with several other commonly used probes for DNA fingerprinting. Individuals within breeds tended to be more similar to each other with regard to DNA fingerprint pattern than to individuals of other breeds. Moreover, a parsimony analysis made on the basis of the hybridization patterns gave clustering of individuals within breeds. The possibility of using hypervariable probes for the identification of breed-specific characters is discussed.