DNA fingerprinting in reptiles: Bkm hybridization patterns in Crocodilia and Chelonia

Genome ◽  
1991 ◽  
Vol 34 (3) ◽  
pp. 472-476 ◽  
Author(s):  
Suzanne Demas ◽  
Stephen Wachtel
Keyword(s):  
Endangered Species ◽  
Dna Fingerprinting ◽  
Population Studies ◽  
Wide Spectrum ◽  
Chelonia Mydas ◽  
W Chromosome ◽  
Dna Fingerprints ◽  
Tetranucleotide Repeat ◽  
Restriction Fragments ◽  
Potential Value

The simple tetranucleotide repeat GATA (GACA) occurs in all eukaryotes so far studied. In many species, the arrangement of these sequences varies considerably among individuals. Thus GATA (GACA) type probes produce DNA fingerprints when hybridized with restricted DNA from different individuals within a species. Banded krait minor (Bkm) satellite DNA (related to sequences originally recovered from the W chromosome of the banded krait and consisting essentially of a series of GATA repeats) is found in a wide spectrum of vertebrates and invertebrates. We used the Bkm 2(8) clone to evaluate the occurrence of this satellite in DNA from five species of Crocodilia and six species of Chelonia, including the sea turtles Chelonia mydas and Lepidochelys kempi. Well-resolved DNA fingerprints were obtained. Among the crocodilians, fewer restriction fragments were generated and fewer of the fragments were polymorphic, than among the chelonians, consistent with the view that the crocodilians are less divergent within species. The Bkm 2(8) clone can accordingly be used to advantage in individual, familial, and population studies, and perhaps in the evaluation of taxonomic relationships in these animals. This is of potential value in endangered species such as C. mydas and L. kempi.Key words: DNA fingerprinting, Bkm satellite, reptiles.

Female-Specific Restriction Fragments Revealed by Dna-Fingerprinting and Implications for Extra-Pair Fertilisations in the Short-Tailed Shearwater (Puffinus-Tenuirostris, Procellariiformes, Procellariidae)

1995 ◽  
Vol 43 (5) ◽  
pp. 443 ◽  
Author(s):  
JJ Austin ◽  
DT Parkin
Keyword(s):  
Dna Fingerprinting ◽  
Restriction Fragment ◽  
Population Biology ◽  
Mating Systems ◽  
Dna Fingerprints ◽  
Restriction Fragments ◽  
Genetic Method ◽  
Specific Restriction ◽  
Puffinus Tenuirostris ◽  
Female Specific

We report a female-specific restriction fragment in the DNA fingerprints of short-tailed shearwaters (Puffinus tenuirostris) that hybridises to a derivative of the human multilocus minisatellite probe 33.6. This genetic method of assigning sex has relevance to studies of population biology, reproductive success and mating systems in this species. The presence or absence of the female-specific restriction fragment has allowed us to reinterpret results from a previous DNA fingerprinting study of mating systems in the short-tailed shearwater.

Nonlethal capture of green sea turtles (Chelonia mydas) in fishing weirs as an opportunity for population studies and conservation

2021 ◽  
pp. 105437
Author(s):  
Eduardo H.S.M. Lima ◽  
Danielle Rodrigues Awabdi ◽  
Maria Thereza D. Melo ◽  
Bruno Giffoni ◽  
Leandro Bugoni
Keyword(s):  
Population Studies ◽  
Sea Turtles ◽  
Chelonia Mydas ◽  
Green Sea Turtles

Paternity testing of endangered species of birds by DNA fingerprinting and random amplified polymorphic DNA fingerprinting

1994 ◽  
pp. 220-222
Author(s):  
J. Máthé ◽  
C. Eisenmann ◽  
L. Konrad ◽  
G. Weyland ◽  
A. Seitz
Keyword(s):  
Endangered Species ◽  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Paternity Testing

scholarly journals Sample Size, Library Composition, and Genotypic Diversity among Natural Populations of Escherichia coli from Different Animals Influence Accuracy of Determining Sources of Fecal Pollution

2004 ◽  
Vol 70 (8) ◽  
pp. 4478-4485 ◽  
Author(s):  
LeeAnn K. Johnson ◽  
Mary B. Brown ◽  
Ethan A. Carruthers ◽  
John A. Ferguson ◽  
Priscilla E. Dombek ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Fingerprinting ◽  
Correlation Coefficient ◽  
Average Rate ◽  
Dna Fingerprint ◽  
Correct Classification ◽  
Dna Fingerprints ◽  
Rarefaction Analysis ◽  
E Coli ◽  
Jackknife Analysis

ABSTRACT A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was developed and evaluated as a means to differentiate human from animal sources of Escherichia coli. Box A1R primers and PCR were used to generate 2,466 rep-PCR and 1,531 HFERP DNA fingerprints from E. coli strains isolated from fecal material from known human and 12 animal sources: dogs, cats, horses, deer, geese, ducks, chickens, turkeys, cows, pigs, goats, and sheep. HFERP DNA fingerprinting reduced within-gel grouping of DNA fingerprints and improved alignment of DNA fingerprints between gels, relative to that achieved using rep-PCR DNA fingerprinting. Jackknife analysis of the complete rep-PCR DNA fingerprint library, done using Pearson's product-moment correlation coefficient, indicated that animal and human isolates were assigned to the correct source groups with an 82.2% average rate of correct classification. However, when only unique isolates were examined, isolates from a single animal having a unique DNA fingerprint, Jackknife analysis showed that isolates were assigned to the correct source groups with a 60.5% average rate of correct classification. The percentages of correctly classified isolates were about 15 and 17% greater for rep-PCR and HFERP, respectively, when analyses were done using the curve-based Pearson's product-moment correlation coefficient, rather than the band-based Jaccard algorithm. Rarefaction analysis indicated that, despite the relatively large size of the known-source database, genetic diversity in E. coli was very great and is most likely accounting for our inability to correctly classify many environmental E. coli isolates. Our data indicate that removal of duplicate genotypes within DNA fingerprint libraries, increased database size, proper methods of statistical analysis, and correct alignment of band data within and between gels improve the accuracy of microbial source tracking methods.

scholarly journals Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7268
Author(s):  
Kwanjai Pipatchartlearnwong ◽  
Piyada Juntawong ◽  
Passorn Wonnapinij ◽  
Somsak Apisitwanich ◽  
Supachai Vuttipongchaikij
Keyword(s):  
Dna Fingerprinting ◽  
Suppression Subtractive Hybridization ◽  
Transcriptome Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Subtractive Hybridization ◽  
Pcr Analysis ◽  
Dna Fingerprints ◽  
Juvenile Period ◽  
Male And Female

BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries andde novotranscriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Althoughde novotranscriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

DNA fingerprinting analysis ofPetromyces alliaceus(AspergillussectionFlavi)

2005 ◽  
Vol 51 (12) ◽  
pp. 1039-1044 ◽  
Author(s):  
Cesaria E McAlpin ◽  
Donald T Wicklow
Keyword(s):  
Dna Fingerprinting ◽  
Aspergillus Flavus ◽  
Genomic Dna ◽  
Genotypic Diversity ◽  
Dna Probe ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Close Relationship ◽  
Aspergillus Alliaceus ◽  
Aspergillus Section

The objective of this study was to evaluate the ability of the Aspergillus flavus pAF28 DNA probe to produce DNA fingerprints for distinguishing among genotypes of Petromyces alliaceus (Aspergillus section Flavi), a fungus considered responsible for the ochratoxin A contamination that is occasionally observed in California fig orchards. P. alliaceus (14 isolates), Petromyces albertensis (one isolate), and seven species of Aspergillus section Circumdati (14 isolates) were analyzed by DNA fingerprinting using a repetitive sequence DNA probe pAF28 derived from A. flavus. The presence of hybridization bands with the DNA probe and with the P. alliaceus or P. albertensis genomic DNA indicates a close relationship between A. flavus and P. alliaceus. Twelve distinct DNA fingerprint groups or genotypes were identified among the 15 isolates of Petromyces. Conspecificity of P. alliaceus and P. albertensis is suggested based on DNA fingerprints. Species belonging to Aspergillus section Circumdati hybridized only slightly at the 7.0-kb region with the repetitive DNA probe, unlike the highly polymorphic hybridization patterns obtained from P. alliaceus and A. flavus, suggesting very little homology of the probe to Aspergillus section Circum dati genomic DNA. The pAF28 DNA probe offers a tool for typing and monitoring specific P. alliaceus clonal populations and for estimating the genotypic diversity of P. alliaceus in orchards, vineyards, or crop fields.Key words: Aspergillus alliaceus, Circumdati, DNA probe, genotypic diversity, hybridization patterns, ochratoxin, Southern blot.

Development of an identification scheme for Canadian registered oat cultivars using RAPDs

1998 ◽  
Vol 78 (4) ◽  
pp. 605-610 ◽  
Author(s):  
Eduardo Guillin ◽  
Bernard R. Baum ◽  
Subbaiah Mechanda
Keyword(s):  
Key Words ◽  
Dna Fingerprinting ◽  
Cultivar Identification ◽  
Identification Key ◽  
Dna Fingerprints ◽  
Key Words Dna ◽  
Identification Scheme ◽  
Rapd Fingerprints ◽  
Oat Cultivars ◽  
Single Seeds

DNA fingerprints for all 53 oat cultivars registered in Canada were generated using random amplified polymorphic DNAs (RAPDs). Repeatability and reliability of the PCR-RAPD fingerprints were confirmed on up to 20 single seeds or seedlings, from breeders seed of five cultivars. An identification key was computer generated for the 53 cultivars. Twenty-nine potentially diagnostic bands were scored on the 53 cultivars to generate the key, but only 13 were found useful and sufficient by the computer generating key program. The identification scheme lends itself to be online. Further research is required to complete the scheme for routine cultivar identification and verification in Canada. The problems that need to be investigated are discussed. Key words: DNA fingerprinting, oat cultivars, RAPD, identification key

Genetic diversity in Puccinia striiformis Westend. f.sp. tritici revealed by pathogen genome-specific repetitive sequence

1998 ◽  
Vol 76 (4) ◽  
pp. 587-595 ◽  
Author(s):  
Wei-xing Shan ◽  
Shou-yi Chen ◽  
Zhen-sheng Kang ◽  
Li-ren Wu ◽  
Zhen-qi Li
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Fingerprinting ◽  
Puccinia Striiformis ◽  
Phenotypic Diversity ◽  
Molecular Evidence ◽  
Polymorphism Analysis ◽  
Dna Fingerprints ◽  
High Level ◽  
Virulence Variation

DNA fingerprinting was used to examine genetic variation in populations of Puccinia striiformis Westend. f.sp. tritici, an obligate fungus that causes wheat stripe rust, using as a probe a moderately repetitive DNA sequence PSR331 that shows species specificity in the genome of this pathogen. One hundred and sixty isolates sampled from six provinces throughout China were examined for genetic variation over 26 putative genetic loci defined by PSR331 and the restriction enzyme BglII. Because of the dikaryotic nature of this fungus, DNA fingerprints can not differentiate heterozygotes from homozygotes. We refer to the PSR DNA fingerprints as phenotypes rather than genotypes. Phenotypic diversity analysis revealed a high level of genetic variation. A total of 97 phenotypes was detected among 160 isolates. Phenotypic diversity varied among regions, ranging from 0.3742 in Shaanxi to 0.9380 in Gansu, as calculated with the normalized Shannon's index. Genetic subdivision analysis revealed a low level of genetic differentiation (GST = 0.0084) among regions (Gansu, Henan, Shaanxi, Sichuan, and Yunnan provinces) as well as within regions (Gansu and Sichuan provinces). This, together with the detection of the same phenotypes among regions, provided the molecular evidence for gene flow in P. striiformis f.sp. tritici. The results support conclusions from virulence surveys that Tianshui of southern Gansu is probably the most important "hotspot" area with respect to the potential to generate and maintain virulence variation. DNA polymorphism analysis also detected potential hotspot areas in addition to southern Gansu. This may result in more difficulties in management of genetic variation and thus the potential virulence variation in P. striiformis f.sp. tritici as well as providing opportunities for searching disease resistance factors.Key words: genetic diversity, Puccinia striiformis, DNA fingerprinting, virulence variation.

scholarly journals Discrimination of a selected set of turmeric, ginger, fenugreek and coriander varieties using ISSR markers

2020 ◽  
pp. 161-172
Author(s):  
A. Giridhari ◽  
I.P. Vijesh Kumar ◽  
T.E. Sheeja
Keyword(s):  
Dna Fingerprinting ◽  
Biological Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Convention On Biological Diversity ◽  
Dna Fingerprints ◽  
Dna Profile ◽  
Crop Varieties ◽  
New Varieties ◽  
Crop Variety

DNA fingerprints are unique to individuals and can be used to identify individuals as in the case of conventional fingerprints. Plant DNA fingerprinting make use of various molecular markers for identifying newly released crop varieties and are all the more important in plant variety registration under the PPV&FR Act of 2001. The trade-related intellectual property rights (TRIPS) and the convention on biological diversity (CBD) insist on the establishment of identity and ownership of genotypes for enforcement of their provisions for securing protection to plant varieties as well as for regulating access to germplasm resources. DNA fingerprints, along with morphological markers, can be efficiently utilized for plant varietal identification, detection of duplicates and adulterants. Here in this particular study, the spice samples received at the DNA fingerprinting facility (DNAFF) of ICAR-Indian Institute of Spices Research (ICAR-IISR) from various centres of All India Coordinated Project on Spices (AICRPS) were DNA fingerprinted using inter simple sequence repeat (ISSR) markers. The DNA profile of a candidate variety vis-a-vis check variety is an essential prerequisite during submission of proposal for release of crop variety to central sub-committee on crop standards notification and release of varieties. The new varieties of turmeric, ginger, coriander and fenugreek were compared with the closely resembling check varieties for establishing distinctness for varietal registration. A total of 118 ISSR primers were screened in the above-given crops, to identify the distinct markers identifying the candidate from the check varieties. Using this technique, the DNAFF at ICAR-IISR could facilitate registration of turmeric varieties, Roma, Rasmi and Suroma; ginger varieties Suruchi, Suravi and Suprabha; coriander varieties, Suguna, Susthira and Suruchi, while varieties of turmeric, Uttara Rupanjana and Uttara Ranjini; fenugreek variety Ajmer fenugreek (AFg-5); coriander varieties Ajmer coriander (ACr-2) and Chhattisgarh Shri Chandra Hasini dhaniya-2 (ICS-4) are in the process of getting registration. ISSR markers were found to be appropriate for establishing distinctness of the new varieties of spices for securing varietal registration.

scholarly journals Evaluation of the genetic diversity among maize lines (Zea mays L.) by DNA fingerprinting analysis

1996 ◽  
Vol 26 (3) ◽  
pp. 501-503
Author(s):  
Sergio Echeverrigaray ◽  
Ana Paula Longaray Delamare ◽  
Geraldo Tosello ◽  
Orit Gal ◽  
Jossi Hillel ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Zea Mays L ◽  
Genetic Distances ◽  
Dna Fingerprint ◽  
Electrophoretic Separation ◽  
Restriction Fragments ◽  
Fingerprinting Analysis ◽  
Dna Restriction Fragments ◽  
Dna Restriction ◽  
The Relationship

Informativo DNA fingerprint profiles of eight homozygotic maize lines were obtained by the electrophoretic separation of DNA restriction fragments and the ir hybridization with the minisatellite probe R18.1. The analysis of the bandsharing frequencies allowed to identify all the lines and to estimate the genetic distances between them. The relationship obtained by DNA fingerprinting analysis of the eight inbreed lines was highly consistem with the ir genetical origin.

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