Relatedness determination in the absence of pedigree information in three cultured strains of rainbow trout (Oncorhynchus mykiss)

Aquaculture

Volumn 233, Issue 1-4, 2004, Pages 65-78

  McDonald, Gavin J ^a,b   Danzmann, Roy G ^a   Ferguson, Moira M ^a  

^a UNIVERSITY OF GUELPH   (Canada)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Breeding programmes; Inbreeding; Oncorhynchus mykiss; Relatedness estimation

Indexed keywords

INBREEDING; RELATEDNESS; SALMONID CULTURE; SELECTIVE BREEDING;

ANIMALIA; ONCORHYNCHUS; ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 1642318843     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2003.08.003     Document Type: Article

References (47)

1. Altmann J., Alberts S.C., Haines S.A., Dubach J., Muruthi P., Coote T., Geffen E., Cheesman D.J., Mututua R.S., Saiyalel S.N., Wayne R.K., Lacy R.C., Bruford M.W. Behaviour predicts genetic structure in a wild primate group. Pop. Biol. 93:1996;5797-5801.
2. Banks M.A., Rashbrook V.K., Calavetta M.J., Dean C.A., Hedgecock D. Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmon (Oncorhynchus tshawytscha) in California's Central Valley. Can. J. Fish. Aquat. Sci. 57:2000;915-927.
3. Bardakci F., Skibinski D.O.F. Application of the RAPD technique in tilapia fish: species and subspecies identification. Heredity. 73:1994;117-123.
4. Bernatchez L., Duchesne P. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Can. J. Fish Aquat. Sci. 57:2000;1-12.
5. Blouin M.S., Parsons M., Lacaille V., Lotz S. Use of microsatellite loci to classify individuals by relatedness. Mol. Ecol. 5:1996;393-401.
6. Caballero A., Toro M.A. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genet. Res. 75:2000;331-343.
7. Danzmann R.G. Probmax: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny. J. Heredity. 88:1997;33.
8. Danzmann R.G., Ferguson M.M., Heculuck D.M. Heterogeneity in the distribution of mitochondrial DNA haplotypes in female rainbow trout spawning in different seasons. Can. J. Fish. Aquat. Sci. 51(Suppl. 1):1994;284-289.
9. de Ruiter J.R., Geffen E. Relatedness of matrilines, dispersing males and social groups in long-tailed macaques (Macaca fascicularis). Proc. R. Soc. Lond., B. 265:1998;79-87.
10. Estoup A., Gharbi K., SanCristobal M., Chevalet C., Haffray P., Guyomard R. Parentage assignment using microsatellites in turbot (Scophthalmus maximus) and rainbow trout (Oncorhynchus mykiss) hatchery populations. Can. J. Fish Aquat. Sci. 55:1998;715-725.
11. Falconer D.S., MacKay T.F.C. Introduction to Quantitative Genetics. 4th ed. 1996;Longman Group, Essex. 464 pp.
12. Ferguson M.M., Danzmann R.G. Role of genetic markers in fisheries and aquaculture: useful tools or stamp collecting? Can. J. Fish. Aquat. Sci. 55:1998;1553-1563.
13. Ferguson M.M., Danzmann R.G., Arndt S.K.A. Mitochondrial DNA and allozyme variation in Ontario cultured rainbow trout spawning in different seasons. Aquaculture. 117:1993;237-259.
14. Fishback A.G., Danzmann R.G., Sakamoto T., Ferguson M.M. Optimization of semi-automated microsatellite multiplex polymerase chain reaction systems for rainbow trout (Oncorhynchus mykiss). Aquaculture. 172:1999;247-254.
15. Fishback A.G., Danzmann R.G., Ferguson M.M. Microsatellite allelic heterogeneity among hatchery rainbow trout maturing in different seasons. J. Fish Biol. 57:2000;1367-1380.
16. Goodnight K.F., Queller D.C. Computer software for performing likelihood tests of pedigree relationship using genetic markers. Mol. Ecol. 8:1999;1231-1234.
17. Hansson B., Bensch S., Hasselquist D., Lillandt B.G., Wennerberg L., Von Schantz T. Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting. Mol. Ecol. 9:2000;1259-1538.
18. Harris A.S., Bieger S., Doyle R.W., Wright J.M. DNA fingerprinting of tilapia, Oreochromis niloticus, and its application to aquaculture genetics. Aquaculture. 92:1991;157-163.
19. Herbinger C.M., Doyle R.W., Pitman E.R., Paquet D., Mesa K.A., Morris D.B., Wright J.M., Cook D. DNA fingerprint based analysis of paternal and maternal effects on offspring growth and survival in communally reared rainbow trout. Aquaculture. 137:1995;245-256.
20. Kays R.W., Gittleman J.L., Wayne R.K. Microsatellite analysis of kinkajou social organization. Mol. Ecol. 9:2000;743-751.
21. Leary R.F., Allendorf F.W., Knudsen K.L. Genetic differences among rainbow trout spawned on different days within a single season. Prog. Fish-Cult. 51:1989;10-19.
22. Lynch M., Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 152:1999;1753-1766.
23. McConnell S.K.J., O'Reilly P., Hamilton L., Wright J.M., Bentzen P. Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Can. J. Fish. Aquat. Sci. 52:1995;1863-1872.
24. McDonald, G.J., 2001. Relatedness determination and the detection of spawning time QTL in rainbow trout (Oncorhynchus mykiss). MSc thesis, Department of Zoology, University of Guelph, Guelph, ON, Canada.
25. McKay L.R., McMillan I. Growth, maturation and spawning times in crosses of three strains of rainbow trout. Bull.-Aquac. Assoc. Can. 97:1997;15-17.
26. Morris D.B., Richard K.R., Wright J.M. Microsatellites from rainbow trout (Oncorhynchus mykiss) and their use for genetic study of salmonids. Can J. Fish. Aquat. Sci. 53:1996;120-126.
27. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 89:1978;583-590.
28. Norris A.T., Bradley D.G., Cunningham E.P. Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations. Aquaculture. 180:1999;247-264.
29. Norris A.T., Bradley D.G., Cunningham E.P. Parentage and relatedness determination in farmed Atlantic salmon (Salmo salar) using microsatellite markers. Aquaculture. 182:2000;73-83.
30. O'Connell M., Danzmann R.G., Cornuet J.M., Wright J.M., Ferguson M.M. Differentiation of rainbow trout populations in Lake Ontario and the evaluation of the stepwise mutation and infinite allele mutation models using microsatellite variability. Can. J. Fish. Aquat. Sci. 54:1997;1391-1399.
31. O'Reilly P.T., Hamilton L.C., McConnell S.K., Wright J.M. Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Can. J. Fish Aquat. Sci. 53:1996;2292-2298.
32. O'Reilly P.T., Herbinger C., Wright J.M. Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Anim. Genet. 29:1998;363-370.
33. Painter I. Sibship reconstruction without parental information. J. Agric. Biol. Environ. Stat. 2:1997;212-229.
34. Pante M.J.R., Gjerde B., McMillan I. Effect of inbreeding on body weight at harvest in rainbow trout, Oncorhynchus mykiss. Aquaculture. 192:2001;201-211.
35. Pante M.J.R., Gjerde B., McMillan I. Inbreeding levels in selected populations of rainbow trout, Oncorhynchus mykiss. Aquaculture. 192:2001;213-224.
36. Queller D.C., Goodnight K.F. Estimating relatedness using genetic markers. Evolution. 43:1989;258-275.
37. Quinton, C.D., 2001. Growth rate and spawning time in diallele crosses of three strains of rainbow trout (Oncorhynchus mykiss). MSc thesis, Department of Animal and Poultry Science, University of Guelph, Guelph, ON.
38. Raymond M., Rousset F. GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity. 86:1995;248-249.
39. Sakamoto, T., 1996. Study for the introduction of positional cloning method using DNA markers in fisheries science. PhD thesis, Tokyo University of Fisheries, Tokyo, Japan.
40. Sakamoto T., Okamoto N., Ikeda Y. Dinucleotide repeat polymorphism of rainbow trout, FGT5. J. Anim. Sci. 72:1994;2768.
41. Sanchez J.A., Clabby C., Ramos D., Blanco G., Flavin F., Vasquez E., Powell R. Protein and microsatellite single locus variability in Salmo salar L. (Atlantic salmon). Heredity. 77:1996;423-432.
42. Scribner K.T., Gust J.R., Fields R.L. Isolation and characterization of novel microsatellite loci: cross-species amplification and population genetics applications. Can. J. Fish. Aquat. Sci. 53:1996;841-883.
43. Smith B.R., Herbinger C.M., Merry H.R. Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics. 158:2001;1329-1338.
44. Su G.S., Liljedahl L.E., Gall G.A.E. Effects of inbreeding on growth and reproductive traits in rainbow trout (Oncorhynchus mykiss). Aquaculture. 142:1996;139-148.
45. Su G.S., Liljedahl L.E., Gall G.A.E. Estimates of phenotypic and genetic parameters for within-season date and age at spawning of female rainbow trout. Aquaculture. 171:1999;209-220.
46. Thomas S.C., Hill W.G. Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics. 155:2000;1961-1972.
47. Van de Casteele T., Galbusera P., Matthysen E. A comparison of microsatellite-based pairwise relatedness estimators. Mol. Ecol. 10:2001;1539-1549.