Identification of quantitative genetic components of fitness variation in farmed, hybrid and native salmon in the wild

Heredity

Volumn 115, Issue 1, 2015, Pages 47-55

  Besnier, F ^a   Glover, K A ^a   Lien, S ^b   Kent, M ^b   Hansen, M M ^a,c   Shen, X ^d,e   Skaala, O ^a  

^a INSTITUTE OF MARINE RESEARCH   (Norway)

^b NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^c AARHUS UNIVERSITY   (Denmark)

^d KAROLINSKA INSTITUTE   (Sweden)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; DOMESTICATION; FERAL ORGANISM; GENETIC VARIATION; PHENOTYPIC PLASTICITY; POPULATION GENETICS; RIVER WATER; SALMONID CULTURE;

NORWAY;

ANIMALIA; SALMO SALAR;

ALLELE; ANIMAL; AQUACULTURE; BIOLOGICAL MODEL; CROSS BREEDING; GENETICS; GENOTYPE; NORWAY; PHENOTYPE; POPULATION GENETICS; PROCEDURES; QUANTITATIVE TRAIT LOCUS; REPRODUCTIVE FITNESS; RIVER; SALMO SALAR; WILD ANIMAL;

ALLELES; ANIMALS; ANIMALS, WILD; AQUACULTURE; CROSSES, GENETIC; GENETIC FITNESS; GENETICS, POPULATION; GENOTYPE; MODELS, GENETIC; NORWAY; PHENOTYPE; QUANTITATIVE TRAIT LOCI; RIVERS; SALMO SALAR;

EID: 84930866123     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2015.15     Document Type: Article

References (51)

1. Allendorf FW, Leary RF, Spruell P, Wenburg JK (2001). The problems with hybrids: setting conservation guidelines. Trends Ecol Evol 16: 613-622.
2. Baranski M, Moen T, Vage DI (2010). Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar). Genet Sel Evol 42: 17.
3. Belyaev DK, Ruvinsky AO, Trut LN (1981). Inherited activation-inactivation of the star gene in foxes: its bearing on the problem of domestication. JHered72: 267-274.
4. Bourret V, Kent MP, Primmer CR, Vasemagi A, Karlsson S, Hindar K et al. (2013). SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar). Mol Ecol 22: 532-551.
5. Carlson SM, Seamons TR (2008). A review of quantitative genetic components of fitness in salmonids: implications for adaptation to future change. Evol Appl 1: 222-238.
6. Churchill GA, Doerge RW (1994). Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
7. Clifford SL, McGinnity P, Ferguson A (1998). Genetic changes in an Atlantic salmon population resulting from escaped juvenile farm salmon. J Fish Biol 52: 118-127.
8. Darwin C (1868). The Variation of Animals and Plants under Domestication. John Murray: London.
9. Debes PV, Normandeau E, Fraser DJ, Bernatchez L, Hutchings JA (2012). Differences in transcription levels among wild, domesticated, and hybrid Atlantic salmon (Salmo salar) from two environments. Mol Ecol 21: 2574-2587.
10. Einum S, Fleming IA (1997). Genetic divergence and interactions in the wild among native, farmed and hybrid Atlantic salmon. J Fish Biol 50: 634-651.
11. Fischer J, Lindenmayer DB (2000). An assessment of the published results of animal relocations. Biol Conserv 96: 1-11.
12. Fleming IA, Einum S (1997). Experimental tests of genetic divergence of farmed from wild Atlantic salmon due to domestication. ICES J Mar Sci J Cons 54: 1051-1063.
13. Garcia de Leaniz C, Fleming IA, Einum S, Verspoor E, Jordan WC, Consuegra S et al. (2007). A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation. Biol Rev Camb Philos Soc 82: 173-211.
14. George AW, Visscher PM, Haley CS (2000). Mapping quantitative trait loci in complex pedigrees: a two-step variance component approach. Genetics 156: 2081-2092.
15. Gjedrem T, Gjøen HM, Gjerde B (1991). Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 98: 41-50.
16. Glover K, Pertoldi C, Besnier F, Wennevik V, Kent M, Skaala O (2013). Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs. BMC Genet 14: 74.
17. Houston RD, Bishop SC, Hamilton A, Guy DR, Tinch AE, Taggart JB et al. (2009). Detection of QTL affecting harvest traits in a commercial Atlantic salmon population. Anim Genet 40: 753-755.
18. Johnson DL, Thompson R (1995). Restricted maximum likelihood estimation of variance components for univariate animal models using sparse matrix techniques and average information. JDairySci78: 449-456.
19. Jonsson B, Jonsson N (2006). Cultured Atlantic salmon in nature: a review of their ecology and interaction with wild fish. ICES J Mar Sci J Cons 63: 1162-1181.
20. Karlsson S, Moen T, Lien S, Glover KA, Hindar K (2011). Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip. Mol Ecol Resour 11 (Suppl 1): 247-253.
21. Koljonen M-L, Tähtinen J, Säisä M, Koskiniemi J (2002). Maintenance of genetic diversity of Atlantic salmon (Salmo salar) by captive breeding programmes and the geographic distribution of microsatellite variation. Aquaculture 212: 69-92.
22. Lewin HA (2009). Genetics. It's a bull's market. Science 324: 478-479.
23. Lien S, Gidskehaug L, Moen T, Hayes B, Berg P, Davidson W et al. (2011). A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics 12: 615.
24. Malek TB, Boughman JW, Dworkin I, Peichel CL (2012). Admixture mapping of male nuptial colour and body shape in a recently formed hybrid population of threespine stickleback. Mol Ecol 21: 5265-5279.
25. Martinez V, Dettleff P, Lopez P, Fernandez G, Jedlicki A, Yañez JM et al. (2013). Assessing footprints of selection in commercial Atlantic salmon populations using microsatellite data. Anim Genet 44: 223-226.
26. McGinnity P, Prodöhl P, Ferguson A, Hynes R, Maoiléidigh Nó, Baker N et al. (2003). Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon. Proc R Soc Lond B Biol Sci 270: 2443-2450.
27. McGinnity P, Stone C, Taggart JB, Cooke D, Cotter D, Hynes R et al. (1997). Genetic impact of escaped farmed Atlantic salmon (Salmo salar L.) on native populations: use of DNA profiling to assess freshwater performance of wild, farmed, and hybrid progeny in a natural river environment. ICES J Mar Sci J Cons 54: 998-1008.
28. Millis D (1991). Ecology and Management of Atlantic Salmon. illustrated Springer Science & Business Media. 1991.
29. O'Reilly PT, Hamilton LC, McConnell SK, Wright JM (1996). Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucleotide and tetranucleotide microsatellites. Can J Fish Aquat Sci 53: 2292-2298.
30. Pong-Wong R, George AW, Woolliams JA, Haley CS (2001). A simple and rapid method for calculating identity-by-descent matrices using multiple markers. Genet Sel Evol 33: 453-471.
31. Price EO (1999). Behavioral development in animals undergoing domestication. Appl Anim Behav Sci 65: 245-271.
32. Price EO, King JA (1968). Domestication and adaptation. In: Hafez ESE (Ed) Adaptation of Domestic Animals. Lea and Febiger: Philadelphia. pp 34-45.
33. Pulcini D, Wheeler PA, Cataudella S, Russo T, Thorgaard GH (2013). Domestication shapes morphology in rainbow trout Oncorhynchus mykiss. J Fish Biol 82: 390-407.
34. Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM (2005). QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Hered Edinb 94: 166-172.
35. Rhymer J, Simberloff D (1996). Extinction by hybridization and introgression. Annu Rev Ecol Syst 27: 83-109.
36. Roberts LJ, Taylor J, Gough PJ, Forman DW, Garcia de Leaniz C (2014). Silver spoons in the rough: can environmental enrichment improve survival of hatchery Atlantic salmon Salmo salar in the wild? J Fish Biol 85: 1972-1991.
37. Ronnegard L, Besnier F, Carlborg O (2008). An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs. Genetics 178: 2315-2326.
38. Rönnegård L, Carlborg O (2007). Separation of base allele and sampling term effects gives new insights in variance component QTL analysis. BMC Genet 8: 1.
39. Ronnegard L, Shen X, Alam M (2010). hglm: A package for fitting hierarchical generalized linear models. RJ2: 20-28.
40. Skaala Ø, Glover KA, Barlaup BT, Sv\aasand T, Besnier F, Hansen MM et al. (2012). Performance of farmed, hybrid, and wild Atlantic salmon (Salmo salar) families in a natural river environment. Can J Fish Aquat Sci 69: 1994-2006.
41. Skaala Ø, Høyheim B, Glover K, Dahle G (2004). Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and identification of individuals. Aquaculture 240: 131-143.
42. Slate J, Santure AW, Feulner PGD, Brown EA, Ball AD, Johnston SE et al. (2010). Genome mapping in intensively studied wild vertebrate populations. Trends Genet 26: 275-284.
43. Slate J, Visscher PM, MacGregor S, Stevens D, Tate ML, Pemberton JM (2002). A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). Genetics 162: 1863-1873.
44. Slettan A, Olsaker I, Lie O (1995). Atlantic salmon, Salmo-salar, microsatellites at the SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Anim Genet 26: 281-282.
45. Solberg MF, Skaala Ø, Nilsen F, Glover KA (2013). Does domestication cause changes in growth reaction norms? a study of farmed, wild and hybrid atlantic salmon families exposed to environmental stress. PLoS ONE 8: e54469.
46. Taggart JB (2007). FAP: an exclusion-based parental assignment program with enhanced predictive functions. Mol Ecol Notes 7: 412-415.
47. Team RC (2013). R: A Language and Environment for Statistical Computing. Vienna, Austria.
48. Thurber CS, Jia MH, Jia Y, Caicedo AL (2013). Similar traits, different genes? Examining convergent evolution in related weedy rice populations. Mol Ecol 22: 685-698.
49. Vehvilainen H, Kause A, Kuukka-Anttila H, Koskinen H, Paananen T (2012). Untangling the positive genetic correlation between rainbow trout growth and survival. Evol Appl 5: 732-745.
50. Verspoor E, Beardmore JA, Consuegra S, García de Leániz C, Hindar K, Jordan WC et al. (2005). Population structure in the Atlantic salmon: insights from 40 years of research into genetic protein variation. J Fish Biol 67: 3-54.
51. Webb AA, Cullen CL (2010). Coat color and coat color pattern-related neurologic and neuro-ophthalmic diseases. Can Vet J 51: 653-657.