Development and evaluation of a new microsatellite multiplex system for parental allocation and management of rainbow trout (Oncorhynchus mykiss) broodstocks

Aquaculture

Volumn 266, Issue 1-4, 2007, Pages 53-62

  Johnson, Nathan A ^a,b   Rexroad III, Caird E ^a   Hallerman, Eric M ^b   Vallejo, Roger L ^a   Palti, Yniv ^a  

^a NATIONAL CENTER FOR COOL AND COLD WATER AQUACULTURE   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Multiplex; Oncorhynchus mykiss; Parentage assignment; Pedigree; Rainbow trout; Strain; Subpopulations

Indexed keywords

BROOD STOCK; FISHERY MANAGEMENT; GENETIC DIFFERENTIATION; GENETIC MARKER; GENOTYPE; PARENTAGE; SALMONID; STOCK IDENTIFICATION; SUBPOPULATION;

HEXAPLEX; ONCORHYNCHUS MYKISS;

EID: 34247215599     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2007.02.054     Document Type: Article

References (33)

1. Amos W., Barrett J.A., and Pemberton J.M. DNA fingerprinting: parentage studies in natural populations and the importance of linkage analysis. Proceedings of the Royal Society of London. Series B, Biological sciences 249 (1992) 157-162
2. Bernatchez L., and Duchesne P. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles?. Canadian Journal of Fisheries and Aquatic Sciences 57 (2000) 1-12
3. Botstein D., White R.L., Skolnick M., and Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32 (1980) 314-331
4. Chistiakov D.A., Hellemans B., and Volckaert F.A.M. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture 255 (2006) 1-29
5. Coulibaly I., Gharbi K., Danzmann R.G., Yao J., and Rexroad III C.E. Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags. Animal Genetics 36 (2005) 543-550
6. Dakin E.E., and Avise J.C. Microsatellite null alleles in parentage analysis. Heredity 93 (2004) 504-509
7. Danzmann R.G., Jackson T.R., and Ferguson M.M. Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout. Aquaculture 173 (1999) 45-58
8. Duchesne P., Godbout M.-H., and Bernatchez L. PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation. Molecular Ecology Notes 2 (2002) 191-193. http://www2.bio.ulaval.ca/louisbernatchez/downloads.htm (http://www2.bio.ulaval.ca/louisbernatchez/downloads.htm)
9. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.5c, (Distributed by Author) (1993). http://evolution.genetics.washington.edu/phylip/getme.html
10. Fishback A.G., Danzmann R.G., Sakamoto T., and Ferguson M.M. Optimization of semi-automated microsatellite multiplex polymerase chain reaction systems for rainbow trout (Oncorhynchus mykiss). Aquaculture 172 (1999) 247-254
11. Lerceteau-Kohler E., and Weiss S. Development of a multiplex PCR microsatellite assay in brown trout Salmo trutta, and its potential application for the genus. Aquaculture 258 (2006) 641-645
12. Minch E. MICROSAT, version 1.5d, (Online) (2003). http://hpgl.stanford.edu/projects/microsat/programs
13. O'Reilly P.T., Hamilton L.C., McConnell S.K., and Wright J.M. Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53 (1996) 2292-2298
14. Overturf K., Casten M.T., LaPatra S.L., Rexroad I.C., and Hardy R.W. Comparison of growth performance, immunological response and genetic diversity of five strains of rainbow trout (Oncorhynchus mykiss). Aquaculture 217 (2003) 93-106
15. Ozaki A., Sakamoto T., Khoo S., Nakamura K., Coimbra M.R.M., Akutsu T., and Okamoto N. Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Molecular Genetics and Genomics 265 (2001) 23-31
16. Page R.D.M. TREEVIEW, version 1.5, Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, Scotland (1995). http://evolution.genetics.washington.edu/phylip/getme.html
17. Palti Y., Fincham M.R., and Rexroad C.E. Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Molecular Ecology Notes 2 (2002) 449-452
18. Palti Y., Silverstein J.T., Wieman H., Phillip J.G., Barrows F.T., and Parsons J.E. Evaluation of family growth response to fishmeal and gluten-based diets in rainbow trout (Oncorhynchus mykiss). Aquaculture 255 (2006) 548-556
19. Park, S.D.E., 2001. Trypanotholerance in West African cattle and the population genetic effects of selection. PhD dissertation. University of Dublin. http://animalgenomics.ucd.ie/sdepark/ms-toolkit.
20. Porta J., Porta J.M., Martinez-Rodriguez G., and Alvarez M.C. Development of a microsatellite multiplex PCR for Senegalese sole (Solea senegalensis) and its application to broodstock management. Aquaculture 56 (2006) 159-166
21. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure from multilocus genotype data. Genetics 155 (2000) 949-959
22. Pruett C.L., Saillant E., Renshaw M.A., Patton J.C., Rexroad III C.E., and Gold J.R. Microsatellite DNA markers for population genetic studies and parentage assignment in cobia, Rachycentron canadum. Molecular Ecology Notes 5 (2005) 84-86
23. Rexroad C.E., and Palti Y. Development of ninety-seven polymorphic microsatellite markers for rainbow trout. Transactions of the American Fisheries Society 132 (2003) 1214-1221
24. Rexroad C.E., Coleman R.L., Gustafson A.L., Hershberger W.K., and Kilefer J. Development of rainbow trout microsatellite markers from repeat enriched libraries. Marine Biotechnology 4 (2002) 12-16
25. Rexroad C.E., Coleman R.L., Hershberger W.K., and Killefer J. Rapid communication: Thirty-eight polymorphic microsatellite markers for mapping in rainbow trout. Journal of Animal Science 80 (2002) 541-542
26. Rexroad C.E., Rodriguez M.F., Coulibaly I., Gharbi K., Danzmann R.G., DeKoning J., Phillips R., and Palti Y. Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 6 (2005) 54
27. Rexroad C.E., Danzmann R.G., Palti Y., and Vallejo R. The NCCCWA genetic map for rainbow trout. Plant and Animal Genome XIV, the International Conference on the Status of Plant and Animal Genome Research, San Diego, CA, USA (2006) 261
28. Rithidech K.N., Dunn J.J., and Gordon C.R. Combining multiplex and touchdown PCR to screen murine microsatellite polymorphisms. BioTechniques 23 (1997) 36-44
29. Schneider S., Roessli D., and Excoffier L. Arlequin: A Software for Population Genetics Data Analysis, Version 3.01, Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva (2006). http://lgb.unige.ch/arlequin/software
30. Silverstein J.T., Rexroad C.E., and King T.L. Genetic variation measured by microsatellites among three strains of domesticated rainbow trout (Oncorhynchus mykiss, Walbaum). Aquaculture Research 35 (2004) 40-48
31. Vandeputte M., Mauger S., and Dupont-Nivet M. An evaluation of allowing for mismatches as a way to manage genotyping errors in parentage assignment by exclusion. Molecular Ecology Notes 6 (2006) 265-267
32. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370
33. Wright S. The interpretation of population structure by F-statistics with special regard to system of mating. Evolution 19 (1965) 395-420