Genetic mapping of quantitative trait loci (QTL) for body-weight in Atlantic salmon (Salmo salar) using a 6.5K SNP array

Aquaculture

Volumn 358-359, Issue , 2012, Pages 61-70

  Gutierrez, Alejandro P ^a   Lubieniecki, Krzysztof P ^a   Davidson, Evelyn A ^a   Lien, Sigbjørn ^b   Kent, Matthew P ^b   Fukui, Steve ^c   Withler, Ruth E ^d   Swift, Bruce ^e   Davidson, William S ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^c Mainstream Canada   (Canada)

^d PACIFIC BIOLOGICAL STATION   (Canada)

^e TRI GEN Fish Improvement Ltd   (Canada)

Author keywords

Atlantic salmon; Body weight; Breeding program; Quantitative trait loci

Indexed keywords

ALLELE; AQUACULTURE PRODUCTION; BROOD STOCK; CHROMOSOME; DATA SET; GENOME; GROWTH RATE; POLYMORPHISM; QUANTITATIVE ANALYSIS; SALMONID CULTURE; SOFTWARE;

CANADA;

SALMO SALAR;

EID: 84863832635     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2012.06.017     Document Type: Article

References (61)

1. Allendorf F.W., Thorgaard G.H. Tetraploidy and evolution of salmonid fishes. Evolutionary Genetics of Fishes 1984, 1-53. Plenum Press, New York. B.J. Turner (Ed.).
2. Baranski M., Moen T., Vage D. Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar). Genetics Selection Evolution 2010, 42:17.
3. Beavis W.D. The power and deceit of QTL experiments: lessons from comparative QTL studies. Proceedings of the Forty-Ninth Annual Corn & Sorghum Industry Research Conference 1994, 250-266. American Seed Trade Association, Washington, DC.
4. Boulding E.G., Culling M., Glebe B., Berg P.R., Lien S., Moen T. Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses. Heredity 2008, 101:381-391.
5. Churchill G.A., Doerge R.W. Empirical threshold values for quantitative trait mapping. Genetics 1994, 138:963-971.
6. Danzmann R.G., Cairney M., Davidson W.S., Ferguson M.M., Gharbi K., Guyomard R., Holm L.-E., Leder E., Okamoto N., Ozaki A., Rexroad C.E., Sakamoto T., Taggart J.B., Woram R.A., Traut W. A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome 2005, 48:1037-1051.
7. Danzmann R.G., Davidson E.A., Ferguson M.M., Gharbi K., Koop B.F., Hoyheim B., Lien S., Lubieniecki K.P., Moghadam H.K., Park J., Phillips R.B., Davidson W.S. Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (rainbow trout and Atlantic salmon). BMC Genomics 2008, 9:557.
8. Davidson W.S., Koop B.F., Jones S.J.M., Iturra P., Vidal R., Maass A., Jonassen I., Lien S.W., Omholt S. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biology 2010, 11:403.
9. Ford M.J. Applications of selective neutrality tests to molecular ecology. Molecular Ecology 2002, 11:1245-1262.
10. Gabreski N., Brooks S., Miller D., Anczak D. Mapping of lavender foal syndrome using the EquineSNP50 Chip. Journal of Equine Veterinary Science 2009, 29:321-322.
11. Garcia de Leaniz C., Fleming I.A., Einum S., Verspoor E., Jordan W.C., Consuegra S., Aubin-Horth N., Lajus D., Letcher B.H., Youngson A.F., Webb J.H., Vøllestad L.A., Villanueva B., Ferguson A., Quinn T.P. A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation. Biological Reviews 2007, 82:173-211.
12. Gjedrem T., Gjøen H.M., Gjerde B. Genetic origin of Norwegian farmed Atlantic salmon. Aquaculture 1991, 98:41-50.
13. Gjerde B., Simianer H., Refstie T. Estimates of genetic and phenotypic parameters for body weight, growth rate and sexual maturity in Atlantic salmon. Livestock Production Science 1994, 38:133-143.
14. Goddard M.E., Hayes B.J. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Reviews Genetics 2009, 10:381-391.
15. Green B.S. Maternal effects in fish populations. Advances in Marine Biology 2008, 1-105. Academic Press. W.S. David (Ed.).
16. Gunnes K., Gjedrem T. Selection experiments with salmon : IV. Growth of Atlantic salmon during two years in the sea. Aquaculture 1978, 15:19-33.
17. Haidle L., Janssen J.E., Gharbi K., Moghadam H.K., Ferguson M.M., Danzmann R.G. Determination of quantitative trait loci (QTL) for early maturation in rainbow trout (Oncorhynchus mykiss). Marine Biotechnology 2008, 10:579-592.
18. Haseman J.K., Elston R.C. The investigation of linkage between a quantitative trait and a marker locus. Behavior Genetics 1972, 2:3-19.
19. Hayes B.J., Gjuvsland A., Omholt S. Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males. Heredity 2006, 97:19-26.
20. Hayes B., Laerdahl J.K., Lien S., Moen T., Berg P., Hindar K., Davidson W.S., Koop B.F., Adzhubei A., Høyheim B. An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 2007, 265:82-90.
21. Hohenlohe P.A., Amish S.J., Catchen J.M., Allendorf F.W., Luikart G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources 2011, 11:117-122.
22. Houston R.D., Bishop S.C., Hamilton A., Guy D.R., Tinch A.E., Taggart J.B., Derayat A., McAndrew B.J., Haley C.S. Detection of QTL affecting harvest traits in a commercial Atlantic salmon population. Animal Genetics 2009, 40:753-755.
23. Hubert S., Higgins B., Borza T., Bowman S. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 2010, 11:191.
24. Jónasson J., Gjedrem T. Genetic correlation for body weight of Atlantic salmon grilse between fish in sea ranching and land-based farming. Aquaculture 1997, 157:205-214.
25. Kent M.P., Hayes B., Xiang Q., Berg P.R., Gibbs R.A., Lien S. Development of 16.5K SNP-Chip for Atlantic salmon. Plant & Animal Genomes XVII Conference, San Diego, CA 2009.
26. Kijas J.W., Townley D., Dalrymple B.P., Heaton M.P., Maddox J.F., McGrath A., Wilson P., Ingersoll R.G., McCulloch R., McWilliam S., Tang D., McEwan J., Cockett N., Oddy V.H., Nicholas F.W., Raadsma H. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE 2009, 4:e4668.
27. Knott S.A., Haley C.S. Simple multiple-marker sib-pair analysis for mapping quantitative trait loci. Heredity 1998, 81:48-54.
28. Knott S.A., Elsen J.M., Haley C.S. Methods for multiple-marker mapping of quantitative trait loci in half-sib populations. Theoretical and Applied Genetics 1996, 93:71-80.
29. Küttner E., Moghadam H.K., Skúlason S., Danzmann R.G., Ferguson M.M. Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus). Molecular Genetics and Genomics 2011, 1-13.
30. Lien S., Gidskehaug L., Moen T., Hayes B., Berg P., Davidson W., Omholt S., Kent M. 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 2011, 12:615.
31. Lynch M., Walsh B. Genetics and Analysis of Quantitative Traits 1998, Sinauer, Sunderland, MA.
32. Mackay T.F.C., Stone E.A., Ayroles J.F. The genetics of quantitative traits: challenges and prospects. Nature Reviews Genetics 2009, 10:565-577.
33. Martyniuk C.J., Perry G.M.L., Mogahadam H.K., Ferguson M.M., Danzmann R.G. The genetic architecture of correlations among growth-related traits and male age at maturation in rainbow trout. Journal of Fish Biology 2003, 63:746-764.
34. Matukumalli L.K., Lawley C.T., Schnabel R.D., Taylor J.F., Allan M.F., Heaton M.P., O'Connell J., Moore S.S., Smith T.P.L., Sonstegard T.S., Van Tassell C.P. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 2009, 4:e5350.
35. McClelland E.K., Naish K.A. A genetic linkage map for coho salmon (Oncorhynchus kisutch). Animal Genetics 2008, 39:169-179.
36. McClelland E.K., Naish K.A. Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch. Heredity 2010, 105:562-573.
37. Miller M.R., Brunelli J.P., Wheeler P.A., Liu S., Rexroad C.E., Palti Y., Doe C.Q., Thorgaard G.H. A conserved haplotype controls parallel adaptation in geographically distant salmonid populations. Molecular Ecology 2012, 21:237-249.
38. Moen T., Hoyheim B., Munck H., Gomez-Raya L. A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Animal Genetics 2004, 35:81-92.
39. Moen T., Hayes B., Baranski M., Berg P.R., Kjoglum S., Koop B.F., Davidson W.S., Omholt S.W., Lien S. A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 2008, 9:223.
40. Moghadam H.K., Ferguson M.M., Rexroad C.E., Coulibaly I., Danzmann R.G. Genomic organization of the IGF1, IGF2, MYF5, MYF6 and GRF/PACAP genes across Salmoninae genera. Animal Genetics 2007, 38:527-532.
41. Moghadam H.K., Poissant J., Fotherby H., Haidle L., Ferguson M.M., Danzmann R.G. Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Molecular Genetics and Genomics 2007, 277:647-661.
42. Muir W.M., Wong G.K.-S., Zhang Y., Wang J., Groenen M.A.M., Crooijmans R.P.M.A., Megens H.-J., Zhang H., Okimoto R., Vereijken A., Jungerius A., Albers G.A.A., Lawley C.T., Delany M.E., MacEachern S., Cheng H.H. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of the National Academy of Sciences USA 2008, 105:17312-17317.
43. O'Malley K.G., Sakamoto T., Danzmann R.G., Ferguson M.M. Quantitative trait loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. Journal of Heredity 2003, 94:273-284.
44. O'Malley K.G., McClelland E.K., Naish K.A. Clock genes localize to quantitative trait loci for stage-specific growth in juvenile coho salmon, Oncorhynchus kisutch. Journal of Heredity 2010, 101:628-632.
45. Phillips R.B., Keatley K.A., Morasch M.R., Ventura A.B., Lubieniecki K.P., Koop B.F., Danzmann R.G., Davidson W.S. Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss). BMC Genetics 2009, 10:46.
46. Quinton C.D., McMillan I., Glebe B.D. Development of an Atlantic salmon (Salmo salar) genetic improvement program: genetic parameters of harvest body weight and carcass quality traits estimated with animal models. Aquaculture 2005, 247:211-217.
47. Ramos A.M., Crooijmans R.P.M.A., Affara N.A., Amaral A.J., Archibald A.L., Beever J.E., Bendixen C., Churcher C., Clark R., Dehais P., Hansen M.S., Hedegaard J., Hu Z.-L., Kerstens H.H., Law A.S., Megens H.-J., Milan D., Nonneman D.J., Rohrer G.A., Rothschild M.F., Smith T.P.L., Schnabel R.D., Van Tassell C.P., Taylor J.F., Wiedmann R.T., Schook L.B., Groenen M.A.M. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE 2009, 4:e6524.
48. Reid D.P., Szanto A., Glebe B., Danzmann R.G., Ferguson M.M. QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity 2005, 94:166-172.
49. Sanchez C., Smith T., Wiedmann R., Vallejo R., Salem M., Yao J., Rexroad C. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 2009, 10:559.
50. Seaton G., Hernandez J., Grunchec J.A., White I., Allen J., De Koning D., Wei W., Berry D., Haley C., Knott S. GridQTL: a grid portal for QTL mapping of compute intensive datasets, 8th World Congress on Genetics Applied to Livestock Production 2006, Belo Horizonte, MG, Brasil.
51. Skaala Ø., Høyheim B., Glover K., Dahle G. Microsatellite analysis in domesticated and wild Atlantic salmon (Salmo salar L.): allelic diversity and identification of individuals. Aquaculture 2004, 240:131-143.
52. Sonesson A. Within-family marker-assisted selection for aquaculture species. Genetics Selection Evolution 2007, 39:1-17.
53. Sonesson A.K. Possibilities for marker-assisted selection in aquaculture breeding schemes. Marker-assisted selection: current status and future perspectives in crops, livestock, forestry and fish 2007, 309-328. FAO, Rome. E. Guimarães, J. Ruane, B. Scherf, A. Sonnino, J. Dargie (Eds.).
54. Sumpter J.P. Control of growth of rainbow trout (Oncorhynchus mykiss). Aquaculture 1992, 100:299-320.
55. Wang S., Peatman E., Abernathy J., Waldbieser G., Lindquist E., Richardson P., Lucas S., Wang M., Li P., Thimmapuram J., Liu L., Vullaganti D., Kucuktas H., Murdock C., Small B., Wilson M., Liu H., Jiang Y., Lee Y., Chen F., Lu J., Wang W., Xu P., Somridhivej B., Baoprasertkul P., Quilang J., Sha Z., Bao B., Wang Y., Wang Q. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 2010, 11:R8.
56. Withler R.E., Supernault K.J., Miller K.M. Genetic variation within and among domesticated Atlantic salmon broodstocks in British Columbia, Canada. Animal Genetics 2005, 36:43-50.
57. Withler R.E., Supernault J., Swift B., Peterson R., Fukui S. Microsatellite DNA assignment of progeny to parents enables communal freshwater rearing in an Atlantic salmon selective breeding program. Aquaculture 2007, 272:S318.
58. Woram R.A., McGowan C., Stout J.A., Gharbi K., Ferguson M.M., Hoyheim B., Davidson E.A., Davidson W.S., Rexroad C., Danzmann R.G. A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents. Genome 2004, 47:304-315.
59. Wringe B.F., Devlin R.H., Ferguson M.M., Moghadam H.K., Sakhrani D., Danzmann R.G. Growth-related quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss). BMC Genetics 2010, 11:63.
60. Xu S. Theoretical basis of the Beavis effect. Genetics 2003, 165:2259-2268.
61. Yan J., Yang X., Shah T., Sánchez-Villeda H., Li J., Warburton M., Zhou Y., Crouch J., Xu Y. High-throughput SNP genotyping with the GoldenGate assay in maize. Molecular Breeding 2010, 25:441-451.