Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): Population-level associations between markers and trait

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Moen, Thomas ^a,b,c   Baranski, Matthew ^b,c   Sonesson, Anna K ^b   Kjøglum, Sissel ^a  

^a Aqua Gen AS   (Norway)

^b NOFIMA   (Norway)

^c NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ATLANTIC SALMON; DNA POLYMORPHISM; DOMINANT INHERITANCE; GENE FREQUENCY; GENETIC LINKAGE; GENETIC MARKER; GENETIC RESISTANCE; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; MICROSATELLITE MARKER; MORTALITY; NONHUMAN; PANCREAS NECROSIS; PARENT; PHENOTYPE; PROGENY; QUANTITATIVE TRAIT LOCUS MAPPING; SURVIVAL; ANIMAL; ANIMAL DISEASE; CHROMOSOME MAP; DISEASE TRANSMISSION; FISH DISEASE; GENETICS; GENOME; NECROSIS; PANCREAS DISEASE; QUANTITATIVE TRAIT LOCUS; VALIDATION STUDY;

ANIMALIA; SALMO SALAR;

MICROSATELLITE DNA;

ANIMALS; CHROMOSOME MAPPING; FISH DISEASES; GENETIC MARKERS; GENOME; MICROSATELLITE REPEATS; NECROSIS; PANCREATIC DISEASES; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SALMO SALAR;

EID: 69049105456     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-368     Document Type: Article

References (48)

1. Wedemeyer G Physiology of fish in intensive culture systems London: Chapman & Hall 1996
2. Duarte CM Marbá N Holmer M Rapid Domestication of Marine Species Science 2007, 316:383-383 10.1126/science.1138042 17446381
3. Ariel E Olesen NJ Finfish in aquaculture and their diseases - a retrospective view in the European Community Bulletin of the European Association of Fish Pathologists 2002, 22:72-85
4. Murray AG Busby CD DW B Infectious pancreatic necrosis on Scottish salmon farms 1996-2001 Emerging Infectious Diseases 2003, 9:2-31
5. Brun E Epidemiology IPN in salmonids: A review Oslo: The Fisheriers and Aquaculture Industries Research Fund (FHF) Skjelstad B 2003
6. Mikalsen AB Torgersen J Alestrom P Hellemann AL Koppang EO Rimstad E Protection of Atlantic salmon Salmo salar against infectious pancreatic necrosis after DNA vaccination Diseases of aquatic organisms 2004, 60:11-20 10.3354/dao060011 15352520
7. Gjedrem T Gjøen HM Gjerde B Genetic origin of Norwegian farmed Atlantic salmon Aquaculture 1991, 98:41-50 10.1016/0044-8486(91)90369-I
8. AquaBreeding survey on the Breeding Practices in the European aquaculture industry http://aquabreeding.eu/Portals/2/ AquaBreeding%20Survey%20-%20Updated%20version%202009.pdf
9. Ozaki A Khoo SK Yoshiura Y Ototake M Sakamoto T Dijkstra JM Okamoto N Identification of Additional Quantitative Trait Loci (QTL) Responsible for Susceptibility to Infectious Pancreatic Necrosis Virus in Rainbow Trout Gyobyo kenkyu 2007, 42:131-140 10.3147/jsfp.42.131
10. Ozaki A Sakamoto T Khoo SK Nakamura K Coimbra MRM Akutsu T Okamoto N Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss) Mol Genet Genomics 2001, 265:23-31 10.1007/ s004380000392 11370869
11. Palti Y Nichols KN Waller KI Parsons JE Thorgaard GH Association between DNA polymorphisms tightly linked to MHC class II genes and IHN virus resistance in backcrosses of rainbow and cutthroat trout Aquaculture 2001, 194:283-289 10.1016/S0044-8486(00)00526-3
12. Palti Y Parsons JE Thorgaard GH Identification of candidate DNA markers associated with IHN virus resistance in backcrosses of rainbow (Oncorhynchus mykiss) and cutthroat trout (O clarki) Aquaculture 1999, 173:81-94 10.1016/S0044-8486(98)00471-2
13. Langefors Å Lohm J Grahn M Andersen Ø von Schantz T Association between major histocompatibility complex class IIB alleles and resistance to Aeromonas salmonicida in Atlantic salmon Proc R Soc Lond B 2001, 268:479-485 10.1098/rspb.2000.1378
14. Miller KM Winton JR Schulze AD Purcell MK Ming TJ Major histocompatibility complex loci are associated with susceptibility of Atlantic salmon to infectious hematopoietic necrosis virus Environmental Biology of Fishes 2004, 69:307-316 10.1023/B:EBFI.0000022874.48341.0f
15. Khoo SK Ozaki A Nakamura F Arakawa T Ishimoto S Identification of a novel chromosomal region associated with IHNV resistance in rainbow trout Fish Pathology 2004, 39:95-102
16. Moen T Fjalestad KT Munck H Gomez-Raya L A Multistage Testing Strategy for Detection of Quantitative Trait Loci Affecting Disease Resistance in Atlantic Salmon Genetics 2004, 167:851-858 1470919 15238533 10.1534/ genetics.103.013227
17. Moen T Sonesson AK Hayes B Lien S Munck H Meuwissen THE Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): Comparing survival analysis with analysis on affected/resistant data BMC Genetics 2007, 8:53 2000910 17697344 10.1186/1471-2156-8-53
18. Nichols KM Bartholomew J Thorgaard GH Mapping multiple genetic loci associated with Ceratomyxia shasta resistance in Ochorynchus mykiss Dis Aquat Org 2003, 56:145-154 10.3354/dao056145 14598990
19. Zimmerman AM Evenhuis JP Thorgaard GH Ristow SS A single major chromosomal region controls natural killer cell-like activity in rainbow trout Immunogenetics 2004, 55:825-835 10.1007/s00251-004-0645-6 14968267
20. Barroso R Wheeler PA Lapatra S Drew RE Thorgaard GH QTL for IHNV resistance and growth identified in a rainbow (Oncorhynchus mykiss) X Yellowstone cutthroat (Oncorhynchus clarki bouvieri) trout cross Aquaculture 2008, 277:156-163 10.1016/j.aquaculture.2008.03.001
21. Gilbey J Verspoor E Mo TA Sterud E Olstad K Hytterød S Jones C Noble L Identification of genetic markers associated with Gyrodactylus salaris resistance in Atlantic salmon Salmo salar Dis Aquat Organ 2006, 71:119-129 10.3354/dao071119 16956059
22. Rodriguez MF Lapatra S Williams S Famula T May B Genetic markers associated with resistance to infectious hematopoietic necrosis in rainbow and steelhead trout (Oncorhynchus mykiss) backcrosses Aquaculture 2005, 241:93-115 10.1016/j.aquaculture.2004.08.003
23. Grimholt U Larsen S Nordmo R Midtlyng P Kjøglum S Storset A Sæbø S Stet RJM MHC polymorphism and disease resistance in Atlantic salmon (Salmo salar); facing pathogens with single expressed major histocompatibility class I and class II loci Immunogenetics 2003, 55:210-219 10.1007/s00251-003-0567-8 12811427
24. Kjøglum S Larsen S Bakke HG Grimholt U How specific MHC class I and class II combinations affect disease resistance against infectious salmon anaemia in Atlantic salmon (Salmo salar) Fish & Shellfish Immunology 2006, 21:431-441 10.1016/j.fsi.2006.02.001 16616518
25. Houston RD Haley CS Hamilton A Guy DR Tinch AE Taggard JB McAndrew BJ Bishop SC Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar) Genetics 2008, 178:1109-1115 2248365 18245341 10.1534/genetics.107.082974
26. Beavis WD The power and deceit of QTL experiments: Lessons from comparative QTL studies 49th Annual Corn and Sorghum Industry Research Conference ASTA, Washington DC 1994:250-266
27. Georges M Nielsen D Mackinnon M Mishra A Okimoto R Pasquino AT Sargeant LS Sorensen A Steele MR Zhao X et al Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing Genetics 1995, 139:907-920 1206390 7713441
28. Xu S Theoretical basis of the Beavis effect Genetics 2003, 165:2259-2268 1462909 14704201
29. Bootland LM Dobos P Stevenson RMW Fry age and size effects on immersion immunization of brook trout, Salvelinus fontinalis Mitchell, against infectious pancreatic necrosis virus Journal of Fish Diseases 1990, 13:113-125 10.1111/j.1365-2761.1990.tb00764.x
30. Tatner MF Natural changes in the immune system of fish The Fish Immune System: Organism, Pathogen, and Environment San Diego, CA: Academic Press, Inc Iwama G, Nakanishi T 1996:255-287
31. Moen T Hayes B Baranski M Berg PR Kjøglum S Koop BF Davidson WS Omholt SW Lien S A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers BMC Genomics 2008, 9:223 2405805 18482444 10.1186/1471-2164-9-223
32. Zapata A Diez B Cejalvo T Gutierrez-de Frýas C Corte A Ontogeny of the immune system of fish Fish & Shellfish Immunology 2006, 12:126-136 10.1016/j.fsi.2004.09.005
33. Taksdal T Thorud K Evaluation of a rapid coagglutination (COA) test for the detection of infectious pancreatic necrosis virus (IPNV) in tissue samples of Atlantic salmon, Salmo salar L Journal of Fish Diseases 1999, 22:117-124 10.1046/j.1365-2761.1999.00154.x
34. Ramstad A Romstad AB Knappskog DH Midtlyng PJ Field validation of experimental challenge models for IPN vaccines Journal of Fish Diseases 2007, 30:723-731 10.1111/j.1365-2761.2007.00858.x 18034679
35. Darvasi A Soller M Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus Theoretical and Applied Genetics 1992, 85:353-359 10.1007/BF00222881
36. ASalBase http://www.asalbase.org
37. Danzmann RG Davidson EA Ferguson MM Gharbi K Hoyheim B Koop BF Lien S Lubieniecki KP Moghadam HK Park J et al 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 2632648 19032764 10.1186/1471-2164-9-557
38. Knott SA Elsen JM Haley CS Methods for multiple-marker mapping of quantitative trait loci in half-sib populations Theoretical and applied genetics 1996, 93:71-80 10.1007/BF00225729
39. Seaton G Haley CS Knott SA Kearsey M Visscher PM QTL Express: Mapping quantitative trait loci in simple and complex pedigrees Bioinformatics 2002, 18:339-340 10.1093/bioinformatics/18.2.339 11847090
40. Visscher PM Haley CS Knott SA Mapping QTLs for binary traits in backcross and F2 populations Genetical Research 1996, 68:55-63
41. Kadarmideen HM Dekkers JCM Generalized marker regression and interval QTL mapping methods for binary traits in half-sib family designs J Anim Breed Genet 2001, 118:297-309 10.1046/j.1439-0388.2001.00301.x
42. Zhang C de Koning D-J Hernández-Sánchez J Haley CS Williams JL Wiener P Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy Genetics 2004, 167:1863-1872 1470995 15342524 10.1534/genetics.104.026401
43. Churchill GA Doerge RW Empirical threshold values for quantitative mapping Genetics 1994, 138:963-971 1206241 7851788
44. Visscher PM Thompson R Haley RS Confidence intervals in QTL mapping by bootstrapping Genetics 1996, 143:1013-1020 1207319 8725246
45. Cramer H Mathematical Models of Statistics Princeton, New Jersey, USA: Princeton University Press 1946
46. Abecasis GR Cookson WO GOLD-graphical overview of linkage disequilibrium Bioinformatics 2000, 16:182-183 10.1093/bioinformatics/16.2.182 10842743
47. Hill WG Estimation of effective population size from data on linkage disequilibrium Genetical Research 1981, 38:209-216
48. Sved JA Linkage disequilibrium and homozygosity of chromosome segments in finite populations Theoretical Population Biology 1971, 2:124-141 10.1016/0040-5809(71)90011-6