Multilocus DNA fingerprints in seven species of salmonids

1995 ◽  
Vol 73 (3) ◽  
pp. 600-606 ◽  
Author(s):  
Daniel D. Heath ◽  
Robert H. Devlin ◽  
Thomas J. Hilbish ◽  
George K. Iwama
Keyword(s):  
Dna Fingerprinting ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Signal Strength ◽  
Variable Number ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Molecular Biological Technique ◽  
Evolutionary Studies ◽  
Biological Technique

DNA fingerprinting is a molecular biological technique that is widely used for identifying parentage and relatedness in plants and animals. To identify new DNA fingerprinting probes for use with salmonids, Southern blots of genomic DNA from chinook salmon (Oncorhynchus tshawytscha) were hybridized at low stringencies with 12 different oligonucleotides designed from published core sequences of variable number of tendem repeats. Seven of the 12 oligonucleotides produced highly variable fingerprint-like patterns; however, only 3 of these had clear, distinct bands. The estimated heterozygosity for one population of chinook salmon using the three oligonucleotides as probes ranged from 0.64 to 0.77. Those three oligonucleotides were further hybridized with DNA from two unrelated individuals from six other species of salmonids. A single-locus DNA fingerprint probe originally developed for chinook salmon was also hybridized with DNA from the other six species at moderate stringency. There were differences in the complexity and signal strength of the resulting banding pattern between species for a given probe. Estimates of variability (heterozygosity and band sharing) for the three oligonucleotide probes and OtSL1 were high, indicating that the probes were potentially useful genetic markers. The availability of these additional DNA fingerprint probes should assist in ecological and evolutionary studies in salmonids, as well as in efforts to estimate genetic diversity of populations.

A New Multilocus Probe for DNA Fingerprinting in Chinook Salmon (Oncorhynchus tshawytscha), and Comparisons with a Single-Locus Probe

1993 ◽  
Vol 50 (7) ◽  
pp. 1559-1567 ◽  
Author(s):  
T. A. Stevens ◽  
R. E. Withler ◽  
S. H. Goh ◽  
T. D. Beacham
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Polymorphic Locus ◽  
Pedigree Analysis ◽  
Single Locus ◽  
Dna Fingerprint ◽  
Dna Fragments ◽  
Banding Patterns ◽  
Discriminatory Ability ◽  
Juvenile Chinook Salmon

A multilocus DNA probe, B2-2, isolated from chinook salmon (Oncorhynchus tshawytscha) and a single-locus Atlantic salmon (Salmo salar) probe, 3.15.34, were examined for discriminatory ability among seven parents and 33–37 juveniles from five families of chinook salmon. DNA fingerprint patterns were observed in Hae III-digested chinook salmon DNA probed with B2-2. Between 8 and 20 fragments, from 2.20 kilobase pairs (kbp) to 19.0 kbp, were detected in each individual. The level of band sharing among unrelated parents was 0.18. Probe 3.15.34 hybridized with a total of nine DNA fragments, from 3.35 to 6.00 kbp, in the chinook salmon parents and progeny. One or two fragments were detected in each individual. Pedigree analysis confirmed that 3.15.34 detected both alleles of a single polymorphic locus whereas B2-2 detected autosomal, unlinked, predominantly heterozygous DNA fragments that were inherited in a Mendelian fashion at a minimum of 10 polymorphic loci. Among juvenile chinook salmon, levels of band sharing detected with probe B2-2 increased with increasing relatedness, and clustering based on differences in banding patterns distinguished unrelated progeny, half sibs, and full sibs even in the absence of parental genotypic data.

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.

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.

scholarly journals Application of DNA Fingerprints for Identification and Genetic Analysis of Avocado

1991 ◽  
Vol 116 (6) ◽  
pp. 1078-1081 ◽  
Author(s):  
U. Lavi ◽  
J. Hillel ◽  
A. Vainstein ◽  
E. Lahav ◽  
D. Sharon
Keyword(s):  
Genetic Analysis ◽  
Family Structure ◽  
Genomic Dna ◽  
Persea Americana ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Evolutionary Studies ◽  
Pattern Characteristic ◽  
The Individual

Application of four DNA fingerprint probes to avocado (Persea americana Mill.) resulted in identification of various cultivars, characterization of the three avocado races, and a genetic analysis of family structure. Genomic DNA from 14 cultivars was probed with four DNA fingerprint probes. Three of the probes gave well-resolved bands. The individual-specific patterns obtained for each cultivar validate the use of this technique for definitive cultivar characterization, with the probability of obtaining a similar pattern for two different cultivars being 2 × 10-9. DNA mixes representing either Mexican, Guatemalan, or West-Indian avocado races were hybridized with the DNA fingerprint probes, and a band pattern characteristic for each race was obtained. Progeny of a cross between the cultivars Ettinger and Pinkerton were analyzed. Their DNA fingerprints revealed one pair of linked bands and another band allelic to one of them. The application of these observations to identification, evolutionary studies, and breeding is discussed.

Systematic hexamitid (Protozoa: Diplomonadida) Infection in seawater pen-reared Chinook salmon Oncorhynchus tshawytscha

1992 ◽  
Vol 14 ◽  
pp. 81-89 ◽  
Author(s):  
ML Kent ◽  
J Ellis ◽  
JW Fournie ◽  
SC Dawe ◽  
JW Bagshaw ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

2021 ◽  
Author(s):  
Nicole M. Aha ◽  
Peter B. Moyle ◽  
Nann A. Fangue ◽  
Andrew L. Rypel ◽  
John R. Durand
Keyword(s):  
San Francisco ◽  
Growth Rates ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Nursery Habitat ◽  
San Francisco Estuary ◽  
Rice Fields ◽  
Fish Growth ◽  
Juvenile Chinook Salmon ◽  
Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

Analysis of straying variation in Alaskan hatchery chinook salmon (Oncorhynchus tshawytscha) following transplantation

1999 ◽  
Vol 56 (4) ◽  
pp. 578-589 ◽  
Author(s):  
Jeffrey J Hard ◽  
William R Heard
Keyword(s):  
British Columbia ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Release Site ◽  
Substantial Variation

In 1976 chinook salmon (Oncorhynchus tshawytscha) gametes from the Chickamin and Unuk rivers in southeastern Alaska were transplanted 250 km to establish hatchery runs at Little Port Walter (LPW), Baranof Island. From 1977 to 1989, 1 862 058 marked smolts from 12 broods were released from LPW. Homing and straying were estimated from adult recoveries at 25 locations in Alaska and British Columbia between 1981 and 1989. Of 22 198 LPW fish recovered over this period, 21 934 (98.8%) were collected at LPW. Of 264 fish recovered elsewhere, 38.3% were within 7 km of LPW; 64.4% were within 25 km of LPW. No LPW fish were recovered from the ancestral rivers, but nine fish were recovered from rivers supporting wild chinook salmon. Straying declined with distance from the release site but varied between hatcheries and streams. Straying declined with increasing age and run size. Straying was similar between the populations but varied among broods, and analysis of straying in experimental groups provided evidence for a heritable component. Males strayed more often than females. Population, gender, run size, and recovery age interacted to produce substantial variation in straying, indicating that run composition can produce complex straying responses.

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