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A first generation BAC-based physical map of the rainbow trout genome

Yniv Palti, Ming-Cheng Luo, Yuqin Hu, Carine Genet, Frank M You, Roger L Vallejo, Gary H Thorgaard, Paul A Wheeler, Caird E Rexroad
2009 BMC Genomics  
The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method.  ...  The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper.  ...  Fincham, Roseanna Long, Kristy Shewbridge and Brian Smith for their technical support in the microsatellites genotyping, and Zeev Frankel and Abraham Korol from Haifa University for evaluating the assembly of  ... 
doi:10.1186/1471-2164-10-462 pmid:19814815 pmcid:PMC2763887 fatcat:tfsb6tgyxve4le6bcrfcvvgtzi

DNA Fingerprinting Confirms Isogenicity of Androgenetically Derived Rainbow Trout Lines

W. P. Young, P. A. Wheeler, A. D. Fields, G. H. Thorgaard, R. C. Vrijenhoek
1996 Journal of Heredity  
The probes used and the number of bands from 5 to 25 kbp that were detected with each probe are presented in Table 1 .  ...  Figure 2 . 2 A DNA fingerprint using VNTR probe 33.6 Table 1 . 1 Homozygous and hybrid clonal rainbow trout families tested for isogenicity by DNA fingerprinting and the number of bands observed for  ... 
doi:10.1093/oxfordjournals.jhered.a022960 pmid:8742822 fatcat:lre64rc7ffe3tpuba77mphxp5q

Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication

Y. Palti, S. A. Gahr, J. D. Hansen, C. E. Rexroad
2004 Animal Genetics  
FPC analysis of HindIII and EcoRV DNA fingerprinting was used to estimate the level of redundancy in the library, to construct BAC contigs and to detect duplicated loci in the semi-duplicated rainbow trout  ...  The library was derived from the Swanson clonal line (YY male) and consists of 184 704 clones with an average insert size of 137 500 bp (PFGE) or 118 700 bp (DNA fingerprinting).  ...  We also thank Gary Thorgaard for contributing the source of the genomic DNA for the library construction and Thomas Kocher for his review of earlier version of the manuscript.  ... 
doi:10.1111/j.1365-2052.2004.01112.x pmid:15025574 fatcat:wmqutylkcfbt7hodf74seouram

Page 132 of Animal Genetics Vol. 35, Issue 2 [page]

2004 Animal Genetics  
Two hundred and 20, fourteen of the 371 clones (58%) were found to be identical by Hindill FPC analysis. The range was 2-7 clones in a group of BACs with identical DNA fingerprints.  ...  Primer sequences are listed in Table 1. The specific genes were selected because they were previously mapped and characterized in rainbow trout.  ... 

Genetic and Environmental Impacts on Litter Size and Early Infant Survival in Three Species of Callitrichids

C. E. Jaquish, J. M. Cheverud, S. D. Tardif, S. O'Brlen
1996 Journal of Heredity  
Analysis of parity effects on litter size revealed no significant effects (P > .05; Table 2).  ...  Results Phenotypic Analysis Repeatability of single litter records was low for all species (Table 1) .  ...  Inbred lines of rainbow trout should be valuable for genetic mapping and QTL analysis, and as a research model.  ... 
doi:10.1093/oxfordjournals.jhered.a022959 pmid:8742821 fatcat:5ludtnvmdfeobf2th4d52qup2u

A first generation integrated map of the rainbow trout genome

Yniv Palti, Carine Genet, Ming-Cheng Luo, Aurélie Charlet, Guangtu Gao, Yuqin Hu, Cecilia Castaño-Sánchez, Kamila Tabet-Canale, Francine Krieg, Jianbo Yao, Roger L Vallejo, Caird E Rexroad
2011 BMC Genomics  
(BES), screening of the BAC library with previously mapped markers and matching of SNPs with BES reads.  ...  In addition, 35 contigs were anchored to linkage groups of the INRA (French National Institute of Agricultural Research) genetic map through markers that were not informative for linkage analysis in the  ...  In addition, the rainbow trout BAC end sequences can be used to infer conserved synteny with other fish genomes as we have previously shown (Genet et al.: Analysis of BAC-end sequences in rainbow trout  ... 
doi:10.1186/1471-2164-12-180 pmid:21473775 pmcid:PMC3079668 fatcat:izzxi2ikfrc5pecmwvxqrh5234

Virulence and molecular variation of Flavobacterium columnare affecting rainbow trout in Idaho, USA

Jason P. Evenhuis, Haitham Mohammed, Scott E. LaPatra, Timothy J. Welch, Covadonga R. Arias
2016 Aquaculture  
Virulence phenotyping of 11 genomovar I and 1 genomovar I/II isolates, taken from 6 different farms, suggests significant variation in virulence toward rainbow trout with the most virulent strains having  ...  AFLP fingerprinting of these strains and the resulting phylogenetic tree show that all of the strains tested had a percent similarity of 75% or higher, save one, the MS-FC-4 strain had less than 60% identity  ...  of Agriculture.  ... 
doi:10.1016/j.aquaculture.2016.06.017 fatcat:zydqlmjlnjbcdkksgmn7bvsqpe

Choice of methodology for assessing genetic impacts of environmental stressors: polymorphism and reproducibility of RAPD and AFLP fingerprints

M J Bagley, S L Anderson, B May
2001 Ecotoxicology  
of rainbow trout (Oncorhynchus mykiss) to derive general rules for selective removal of problematic fingerprint bands.  ...  PCR-based multi-locus DNA fingerprints represent one of the most informative and cost-effective measures of genetic diversity and are useful population-level biomarkers of toxicologic and other anthropogenic  ...  Table 1 . 1 Average number of segregating (polymorphic) bands and reproducibility problems of RAPD and AFLP fingerprints for pedigreed populations of rainbow trout. RAPD AFLP A.  ... 
doi:10.1023/a:1016625612603 pmid:11501435 fatcat:o2hzczmb3bgytajn2xrh43unhy

Molecular Fingerprinting of Fish-Pathogenic Lactococcus garvieae Strains by Random Amplified Polymorphic DNA Analysis

C. Ravelo, B. Magarinos, S. Lopez-Romalde, A. E. Toranzo, J. L. Romalde
2003 Journal of Clinical Microbiology  
Fifty-seven strains with different hosts and geographical origins, including Japan and several countries of the Mediterranean area such as Spain, Portugal, France, Italy, England, and Turkey, were analyzed  ...  The similarity of isolates within each group, estimated on the basis of the Dice coefficient, ranged from 75 to 100%.  ...  In the present work, RAPD analysis was employed to establish DNA fingerprints for L. garvieae strains from diverse hosts and geographical areas of the world, with the aim of evaluating the applicability  ... 
doi:10.1128/jcm.41.2.751-756.2003 pmid:12574277 pmcid:PMC149703 fatcat:6mwhfx732vcnflsu5o4kpq3lb4

Molecular differentiation of Renibacterium salmoninarum isolates from worldwide locations

T H Grayson, L F Cooper, F A Atienzar, M R Knowles, M L Gilpin
1999 Applied and Environmental Microbiology  
We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples.  ...  By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.  ...  The intensities of these faint bands would render them below the limit for inclusion in any analysis of DNA fingerprints.  ... 
pmid:10049848 pmcid:PMC91129 fatcat:wjgrfbeldzcd3o3v6zfr2rz2ba

Molecular Differentiation of Renibacterium salmoninarum Isolates from Worldwide Locations

Thomas H. Grayson, Lynne F. Cooper, Franck A. Atienzar, Mark R. Knowles, Martyn L. Gilpin
1999 Applied and Environmental Microbiology  
We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples.  ...  By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.  ...  The intensities of these faint bands would render them below the limit for inclusion in any analysis of DNA fingerprints.  ... 
doi:10.1128/aem.65.3.961-968.1999 fatcat:2fij3g45ibaurbq53rvlt2hbvy

Analysis of VNTR loci in fish genomes using synthetic oligodeoxyribonucleotide probes

Mary V. John, Iqbal Parwez, Mylavarapu V.S. Sivaram, Shilpa Mehta, Nidhi Marwah, Sher Ali
1996 Gene  
Cluster analysis with respect to GGAT repeat loci revealed that Or. niloticus diverged from Or. mossambicus before the separation of On. mykiss, suggesting the relatively recent evolution of these loci  ...  Of all the oligos and enzymes (AU, MboI, HaeIII and Hinfl) used, the OAT18/HaeIII combination was found to be most informative for detecting DNA fingerprinting in rainbow trout, while the OMSl/MboI combination  ...  Hirano, Director, Ocean Research Institute, University of Tokyo for providing fish DNA, Dr. K. Majumdar for different DNA samples used in the dot blot hybridization and Dr. Seyed E.  ... 
doi:10.1016/0378-1119(96)00173-4 pmid:8682302 fatcat:pbmpcmxrhbdtldkpgk3gvnu7nq

Random Amplified Polymorphic DNA analysis provides rapid differentiation among isolates of the fish pathogen Flavobacterium psychrophilum and among Flavobacterium species

C Chakroun, MC Urdaci, D Faure, F Grimont, JF Bernardet
1997 Diseases of Aquatic Organisms  
Based on these results, the polyrnerase chain reaction (PCR) products of a selection of 60 bacterial DNAs were submitted to slow agarose gel electrophoresis for numerical analysis of the DNA fingerprintings  ...  Forty 10-mer primers were tested and 5 of them were selected for further analysis of the bacterial DNAs.  ...  In addition to those already cited in the footnotes of Tables 1 & 2, we thank M. vigneulle (Laboratoire de Pathologie des Anirnaux Aqua-  ... 
doi:10.3354/dao031187 fatcat:zijhj2vwzvgxliprr3jaibapgu

Efficient DNA Fingerprinting of Clostridium botulinum Types A, B, E, and F by Amplified Fragment Length Polymorphism Analysis

R. Keto-Timonen, M. Nevas, H. Korkeala
2005 Applied and Environmental Microbiology  
These results indicate that AFLP is a fast, highly discriminating, and reproducible DNA fingerprinting method with excellent typeability, which, in addition to its suitability for typing at strain level  ...  Amplified fragment length polymorphism (AFLP) analysis was applied to characterize 33 group I and 37 group II Clostridium botulinum strains.  ...  ACKNOWLEDGMENTS This study was supported by the Finnish Graduate School of Applied Bioscience and the Finnish Veterinary Foundation.  ... 
doi:10.1128/aem.71.3.1148-1154.2005 pmid:15746312 pmcid:PMC1065150 fatcat:76ldzis73vdcdn2y3gqv6tt7oq

Application of PCR Primer Pairs from Rainbow Trout to Detect Polymorphisms of CA Repeat DNA Loci in Five Confamilial Species

Takashi Sakamoto, Nobuaki Okamoto, Yayoi Ikeda
1996 Fisheries Science  
Five sets of primer pairs that flank rainbow trout microsatellites and that produced polymorphic PCR products, were tested with template DNA from five species.  ...  Dinucleotide repeat polymorphisms are widely used as markers for genetic analysis in mammalian genomes because of their abundance and high variability among individuals.  ...  This study was supported in part by Grants-in-Aid for Scientific Research from the Fisheries Agency, Japan and the Ministry of Education, Science, Sports and Culture, Japan (05404014, 6143).  ... 
doi:10.2331/fishsci.62.552 fatcat:m5pgoyu34jdrpgivsjpiefzntq
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