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.     

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.     

Polymorphism of untranscribed spacer rDNA as a molecular genetic marker in population studies of cattle]

Variable polymorphic patterns were detected using EcoRI-SalI fragment of bovine rDNA, including 3'-end of 28S rRNA gene with the adjacent portion of the transcribed spacer, as a probe for hybridization. Some features of these polymorphic patterns are similar to DNA fingerprints detected with the M13 probe. Bovine rDNA spacer polymorphism was used as a molecular genetic marker for population analysis of individual specific patterns of 4 cattle breeds with the help of the Jeffreys' method. It was supposed that the probability of identical fingerprints appearance could be the characteristics of heterogeneity of cattle populations. The observed length of polymorphic gragments ranged from 2000 to 6000 bp. The mean number of fragments per individual for all breeds was 15.05. The probability of identical patterns appearance was very high: from 1.18 x 10(-5) in ajshir's breed to 1.43 x 10(-7) in "white and black"s' breed. So, high probability seems to be dependent on the high allelic frequency and the way of breeding.     

Application of DNA fingerprints for cell-line individualization.

DNA fingerprints of 46 human cell lines were derived using minisatellite probes for hypervariable genetic loci. The incidence of 121 HaeIII DNA fragments among 33 cell lines derived from unrelated individuals was used to estimate allelic and genotypic frequencies for each fragment and for composite individual DNA fingerprints. We present a quantitative estimate of the extent of genetic difference between individuals, an estimate based on the percentage of restriction fragments at which they differ. The average percent difference (APD) among pairwise combinations from the population of 33 unrelated cell lines was 76.9%, compared with the APD in band sharing among cell lines derived from the same individual (less than or equal to 1.2%). Included in this survey were nine additional cell lines previously implicated as HeLa cell derivatives, and these lines were clearly confirmed as such by DNA fingerprints (APD less than or equal to 0.6%). On the basis of fragment frequencies in the tested cell line population, a simple genetic model was developed to estimate the frequencies of each DNA fingerprint in the population. The median incidence was 2.9 X 10(-17), and the range was 2.4 X 10(-21) to 6.6 X 10(-15). This value approximates the probability that a second cell line selected at random from unrelated individuals will match a given DNA fingerprint. Related calculations address the chance that any two DNA fingerprints would be identical among a large group of cell lines. This estimate is still very slight; for example, the chance of two or more common DNA fingerprints among 1 million distinct individuals is less than .001. The procedure provides a straightforward, easily interpreted, and statistically robust method for identification and individualization of human cells.     

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.     

Fingerprinting human chromosomes by polymerase chain reaction-mediated DNA amplification.

We describe here a method for DNA fingerprinting of human chromosomes by Alu-polymerase chain reaction (PCR) amplification of DNA from monochromosomal hybrids, following digestion with restriction endonucleases. DNA digestion with restriction enzymes prior to PCR amplification reduces the total number of amplified fragments. The number and pattern of bands of PCR products observed in an electrophoretic medium are chromosome specific and provide a "fingerprint signature" for individual human chromosomes. Using this approach, we have produced fingerprints for human chromosomes 2, 5, 7, 9, and 12. The applicability of this approach to chromosome identification was assessed by comparing the fingerprints obtained for two different hybrids containing chromosome 7. DNA fragments specific for the long and the short arms of human chromosome 12 have also been identified. In addition, Alu-PCR-generated DNA fragments, specific for different chromosomes, were used to probe Southern blots of a hybrid cell panel to identify human chromosomes present in hybrid cell lines. The chromosomal specificity of these probes permits the identification of intact as well as rearranged chromosomes composed of segments arising from more than one chromosome.     

Prediction of Heterosis from DNA Fingerprints in Chickens

To assess the value of DNA fingerprints for the prediction of heterosis in chickens, retrospective analyses of data from three crossbreeding experiments and DNA fingerprints (DFP) of parental strains were conducted using two minisatellite and one middle-repetitive DNA probes. DFP bands were assessed on pooled DNA samples of 10-15 individuals per parental genetic group. The number of DFP bands evaluated in the experiments ranged from 81 to 139. The probes varied in their predictive value, but predictability of heterosis generally increased with multiple probes. Highly significant correlations (0.68-0.87) between band sharing ratios (SH) and heterosis were found in 25 crosses of White Leghorns in the first egg production cycle for age at sexual maturity, egg production, and mature body weight: traits with heterosis of 10% or more of the means. Regressions of SH explained 78.4% of the variation in heterosis in age at sexual maturity, 60.2% in egg production and 46.4% in mature body weight. For ``broiler' traits with heterosis of <1%, none of the correlations, based on 13 crosses, were significant. It was concluded that multilocus probe DFP of pooled DNA samples show promise as predictors of heterosis.     

GENETIC VARIABILITY WITHIN A POPULATION AND BETWEEN DIPLOID/HAPLOID TISSUE OF MACROCYSTIS PYRIFERA (PHAEOPHYCEAE)1

Multi-locus DNA fingerprints using an M13 probe were obtained for eight individuals of giant kelp Macrocystis pyrifera (L.) C. Ag. collected from Monterey Bay, California. For each individual, DNA was extracted from a diploid blade and from ca. 10⁹ haploid spores that were released from four to Jive sporophylls. Viable or swimming spores from one individual were pooled and referred to as a spore group. A total of 34 bands (4–19 kb) was detected in DNA fingerprints from the eight blades and eight spore groups, with individual blade or spore groups exhibiting 7–18 bands (mean = 12.6). One band (4.5 kb) was present in all 16 samples. Eight bands were detected in 11–14 of the 16 samples. Similarity indices were calculated for all pairwise comparisons of fingerprint bands among all possible combinations of blades and spore groups. Mean similarity indices for the eight blades (0.51, SE = 0.032) and spore groups (0.56, SE = 0.031) were significantly lower than for the eight comparisons of the blade and spore groups from a single individual (0.86, SE = 0.052). The data indicate that DNA fingerprints can be used to measure genetic variation within populations of M. pyrifera because variation of DNA fingerprints associated with meiotic products (spores) of a given individual is small relative to variation observed among individuals within the population. Additionally, fingerprint variation between diploid vegetative tissue and haploid meiotic products may be a measure of genetic change due to recombination or DNA turnover mechanisms.     

The efficiency of multilocus DNA fingerprint probes for individualization and establishment of family relationships, determined from extensive casework.

The properties of human DNA fingerprints detected by multilocus minisatellite probes 33.6 and 33.15 have been investigated in 36 large sibships and in 1,702 Caucasian paternity cases involving the analysis of over 180,000 DNA fingerprint bands. The degree of overlap of minisatellite loci detected by these two probes is shown to be negligible (approximately 1%), and the resulting DNA fingerprints are therefore derived from independent sets of hypervariable loci. The level of allelism and linkage between different hypervariable DNA fragments scored with these probes is also low, implying substantial statistical independence of DNA fragments. Variation between the DNA fingerprints of different individuals indicates that the probability of chance identity is very low (much less than 10(-7) per probe). Empirical observations and theoretical considerations both indicate that genetic heterogeneity between subpopulations is unlikely to affect substantially the statistical evaluation of DNA fingerprints, at least among Caucasians. In paternity analysis, the proportion of nonmaternal DNA fragments in a child which cannot be attributed to the alleged father is shown to be an efficient statistic for distinguishing fathers from nonfathers, even in the presence of minisatellite mutation. Band-sharing estimates between a claimed parent and a child can also distinguish paternity from nonpaternity, though with less efficiency than comparison of a trio of mother, child, and alleged father.     

Assignment of RAPD marker probes designed from 12 linkage groups of Flammulina velutipes to CHEF-separated chromosomal DNAs

Electrophoretic karyotype analyses of Flammulina velutipes FSB and its monokaryotic progeny, omFSB1 and omFSB2, obtained from oidia were performed by contour-clamped homogeneous electric field (CHEF) gel electrophoresis. At least 11 chromosome-sized DNA bands (CB 1 through CB 11) for FSB, 6 bands for omFSB1, and 7 bands for omFSB2, respectively, were resolved on a CHEF gel. Southern hybridization analysis on CHEF-separated chromosomal DNA of FSB was carried out using RAPD marker probes prepared from each of the 12 linkage groups. The bands CB 1, 2, and 4 each hybridized to two or three probes for different linkage groups. The bands CB 5 and 6 both hybridized to a common probe. The bands CB 3, 7, 8, and 9 each hybridized to a single specific probe for different linkage groups. The two smallest bands (CB 10 and 11) did not hybridize with any probes.     

GENETIC VARIABILITY AND PARENTAGE IN MACROCYSTIS PYRZFERA (PHAEOPHYCEAE) USING MULTI-LOCUS DNA FINGERPRINTING1

Multi-locus DNA fingerprints using an M13 probe were obtained for two individuals of Macrocystis pyrifera (L.) C. Ag. collected from Monterey Bay, California, and their laboratory-reared offspring. DNA was extracted from each of two field-collected individuals (= parents), their self-fertilized diploid offspring (three and seven individuals), and one diploid individual resulting from spores of the two parents. A total of 20 bands (4–19 kb) was detected among all individuals, ranging from 7 to 14 bands for any one individual. Two bands were present in all individuals, and three bands were unique to one parent and its three progeny. Ten bands were observed in the out-crossed individual, of which three were inherited from one parent, two from the other parent, and five were present in both parents. Genetic similarity between each parent and their self-fertilized offspring was significantly higher than similarity between the two self-fertilized groups. The data show that multi-locus DNA fingerprints can be used to assess parentage in the giant kelp and that there is consistent agreement between genetic similarity and known genetic relatedness among parents and offspring.     

Power of exclusion for parentage verification and probability of match for identity in American Kennel Club breeds using 17 canine microsatellite markers

DNA analysis of microsatellite markers has become a common tool for verifying parentage in breed registries and identifying individual animals that are linked to a database or owner. Panels of markers have been developed in canines, but their utility across and within a wide range of breeds has not been reported. The American Kennel Club (AKC) authorized a study to determine the power to exclude non-parents and identify individuals using DNA genotypes of 17 microsatellite markers in two panels. Cheek swab samples were voluntarily collected at Parent Breed Club National Specialty dog shows and 9561 samples representing 108 breeds were collected, averaging 88.5 dogs per breed. The primary panel of 10 markers exceeded 99% power of exclusion for canine parentage verification of 61% of the breeds. In combination with the secondary panel of seven markers, 100% of the tested breeds exceeded 99% power of exclusion. The minimum probability match rate of the first panel was 3.6 x 10(-5) averaged across breeds, and with the addition of the second panel, the probability match rate was 3.2 x 10(-8); thus the probability of another random, unrelated dog with the same genotype is very low. The results of this analysis indicated that, on average, the primary panel meets the AKC's needs for routine parentage testing, but that a combination of 10-15 genetic markers from the two panels could yield a universal canine panel with enhanced processing efficiency, reliability and informativeness.     

A bacterial artificial chromosome based physical map of the Ustilago maydis genome.

Ustilago maydis, a basidiomycete, is a model organism among phytopathogenic fungi. A physical map of U. maydis strain 521 was developed from bacterial artificial chromosome (BAC) clones. BAC fingerprints used polyacrylamide gel electrophoresis to separate restriction fragments. Fragments were labeled at the HindIII site and co-digested with HaeIII to reduce fragments to 50-750 bp. Contiguous overlapping sets of clones (contigs) were assembled at nine stringencies (from P < or = 1 x 10(-6) to 1 x 10(-24)). Each assembly nucleated contigs with different percentages of bands overlapping between clones (from 20% to 97%). The number of clones per contig decreased linearly from 41 to 12 from P < or = 1 x 10(-7) to 1 x 10 (-12). The number of separate contigs increased from 56 to 150 over the same range. A hybridization-based physical map of the same BAC clones was compared with the fingerprint contigs built at P < or = 1 x 10(-7). The two methods provided consistent physical maps that were largely validated by genome sequence. The combined hybridization and fingerprint physical map provided a minimum tile path composed of 258 BAC clones (18-20 Mbp) distributed among 28 merged contigs. The genome of U. maydis was estimated to be 20.5 Mbp by pulsed-field gel electrophoresis and 24 Mbp by BAC fingerprints. There were 23 separate chromosomes inferred by both pulsed-field gel electrophoresis and fingerprint contigs. Only 11 of the tile path BAC clones contained recognizable centromere, telomere, and subtelomere repeats (high-copy DNA), suggesting that repeats caused some false merges. There were 247 tile path BAC clones that encompassed about 17.5 Mbp of low-copy DNA sequence. BAC clones are available for repeat and unique gene cluster analysis including tDNA-mediated transformation. Program FingerPrint Contigs maps aligned with each chromosome can be viewed at http://www.siu.edu/~meksem/ustilago_maydis/.     

大仓鼠DNA指纹谱探针的筛选

采用一种简便提取高质量DNA 的方法, 从大仓鼠肝脏组织中提取其总DNA , 分别以人工合成的微卫星核心序列(GTG)₅和(CA)₈做单一引物, 进行特异引物PCR 反应。电泳检测后回收15 条特异性片段。与被标记过的大仓鼠基因组DNA 反向杂交结果表明, 15 个片段中(GTG)_5-8 、(CA)_8-1b和(CA_{) 8-5b}产生了较强的阳性信号。我们依据3 个片段的测序结果设计适合DIG标记的探针, 该探针得到的大仓鼠不同地理种群个体的指纹图谱有较高的个体特异性和种群多态性, 而且与传统的来源于其它生物重复序列的探针如33.6 和33.15 形成的指纹图谱相比得到的变异适中, 便于统计。     

Are DNA profiles breed‐specific? A pilot study in pigs

In this study, DNA fingerprints from 32 unrelated domestic pigs were analysed and screened for breed-specificity. Three breed groups were analysed: Chinese Meishan, Large White and a collection of other European breeds. Ninety-three distinct and variable bands were used to estimate genetic distances between the animals. Between the groups these individual genetic distances substantially exceeded those within a group. Linear discriminant analysis showed that the 23 most common DNA fragments revealed sufficient breed-specificity as to assign each pig correctly to its breed or breed group. These findings, although based on a small sample, indicate that selective use of minisatellite variation in pigs appears to be a valuable novel approach toward the development of breed DNA profiles and the resolution of breed relationships.     

Viral abundance and genome size distribution in the sediment and water column of marine and freshwater ecosystems

The size distribution of viral DNA in natural samples was investigated in a number of marine, brackish and freshwater environments by means of pulsed field gel electrophoresis (PFGE). The method was modified to work with both water and sediment samples, with an estimated detection limit for individual virus genome size groups of 1-2 x 10(4) virus-like particles (VLP) mL(-1) water and 2-4 x 10(5) VLP cm(-3) sediment in the original samples. Variations in the composition and distribution of dominant virus genome sizes were analyzed within and between different habitats that covered a range in viral density from 0.4 x 10(7) VLP mL(-1) (sea water) to 300 x 10(7) VLP cm(-3) (lake sediment). The PFGE community fingerprints showed a number of cross-system similarities in the genome size distribution with a general dominance of genomes in the 30-48, 50-70 and 145-200 kb size fractions, and with many of the specific genome sizes detected in all the investigated habitats. However, large differences in community fingerprints were also observed between the investigated sites, and some virus genome sizes were found only in specific biotopes (e.g. lake water), in specific ecosystems (e.g. a particular lake) or even in specific microhabitats (e.g. a particular sediment stratum).     

Chimaeric and constitutive DNA fingerprints in the common marmoset (Callithrix jacchus)

Marmosets normally produce dizygotic twins sharing placental blood vessels and exchanging bone marrow cells. Each individual is therefore likely to be a blood chimaera. To date, marmosets had only been DNA fingerprinted using blood samples and probes 33.6 and 33.15, resulting in highly similar fingerprints among litter mates and little variation between other individuals, thereby limiting this method's use for individual identification and parentage testing. In this study, novel probes were applied to detect greater polymorphism and to produce individual-specific DNA fingerprints. As expected, blood DNA profiles of twins and triplets were virtually identical, confirming chimaerism in this tissue and identifying litter mates. Furthermore, these profiles were sufficiently variable to distinguish between sibs from different litters and between all other individuals. To produce individual-specific DNA fingerprints, the use of DNA extracted from tissues poor in leukocytes was essential. The findings demonstrate that, despite extensive blood chimaerism, marmoset colonies can be effectively DNA fingerprinted for indicidual identification, zygosity testing, and relationship studies.     

DNA fingerprints of sheep using an M13 probe

The bacteriophage M13 DNA was used to detect hypervariable minisatellites in several families of Booroola sheep as well as Merino and Suffolk sheep. Digestion of sheep DNA gave rise to three to eight fragments with different restriction enzymes demonstrating considerable polymorphism between the different breeds. The length of informative DNA fragments varied in size from 6 to 20kb. The DNA fingerprints generated were individual specific and allowed for differentiation between closely related animals. The pattern obtained with sheep DNA was different from that observed with humans and other vertebrates in the proportion of high molecular weight DNA fragments present. Pedigree analysis of DNA patterns of dams and their offspring for several sets of twins and triplets showed a clear distinction between individuals and failed to reveal the presence of monozygosity.