A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

Allendorf FW, Thorgaard GH: Tetraploidy and the evolution of salmonid fishes. Evolutionary Genetics of Fishes. Edited by: Turner BJ. 1984, New York: Plenum Press, 1-53.

Phillips RB, Rab P: Chromosome evolution in the Salmonidae (Pisces): an update. Biol Rev. 2001, 76: 1-25. 10.1017/S1464793100005613.

Allendorf FW, Danzmann RG: Secondary tetrasomic segregation of MDH-B and preferential pairing of homeologues in rainbow trout. Genetics. 1997, 145: 1083-1092.

Ohno S: Evolution by Gene Duplication. 1970, New York: Springer

Wolfe KH: Yesterday's polyploids and the mystery of diploidization. Nat Rev Genet. 2001, 2: 333-341.

Danzmann RG, Davidson EA, Ferguson MM, Gharbi K, Koop BF, Hoyheim B, Lien S, Lubieniecki KP, Moghadam HK, Park J, Phillips RB, Davidson WS: Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics. 2008, 9: 557-10.1186/1471-2164-9-557.

Gilbey J, Verspoor E, McLay A, Houlihan D: A microsatellite linkage map for Atlantic salmon (Salmo salar). Animal Genet. 2004, 35: 98-105. 10.1111/j.1365-2052.2004.01091.x.

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 Genet. 2004, 35: 81-92. 10.1111/j.1365-2052.2004.01097.x.

Gharbi K, Gautier A, Danzmann RG, Gharbi S, Sakamoto T, Høyheim B, Taggart JB, Cairney M, Powell R, Krieg F, Okamoto N, Ferguson MM, Holm LE, Guyomard R: A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish. Genetics. 2006, 172: 2405-2419.

Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm LE, Guyomard R, Hoyheim B: A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics. 2000, 155: 1331-1345.

Danzmann RG, Cairney M, Davidson WS, Ferguson MM, Gharbi K, Guyomard R, Holm LE, Leder E, Okamoto N, Ozaki A, Rexroad CE, Sakamoto T, Taggart JB, Woram RA: 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: 1037-51. 10.1139/g05-067.

Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F, Quillet E: A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics. 2006, 7: 302-10.1186/1471-2164-7-302.

Rexroad CE, Palti Y, Gahr SA, Vallejo RL: A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet. 2008, 9: 74-

Lindner KR, Seeb JE, Habicht C, Knudsen KL, Kretschmer E, Reedy DJ, Spruell P, Allendorf FW: Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis. Genome. 2000, 43: 538-549. 10.1139/g00-016.

McClelland EK, Naish KA: A genetic linkage map for coho salmon (Oncorhynchus kisutch). Anim Genet. 2008, 39: 169-179. 10.1111/j.1365-2052.2008.01699.x.

Sánchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE: Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics. 2009, 10: 559-10.1186/1471-2164-10-559.

Gidskehaug L, Kent M, Hayes BJ, Lien S: Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics. 2011, 27: 303-310. 10.1093/bioinformatics/btq673.

Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K, Davidson WS, Koop BF, 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. 10.1016/j.aquaculture.2007.01.037.

Hayes BJ, Nilsen K, Berg PR, Grindflek E, Lien S: SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. Bioinformatics. 2007, 23: 1692-1693. 10.1093/bioinformatics/btm154.

Phillips RB, Keatley KA, Morasch MR, Ventura AB, Lubieniecki KP, Koop BF, Danzmann RG, Davidson WS: 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 Genet. 2009, 10: 46-

Moen T, Hayes B, Baranski M, Berg PR, Kjoglum 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: 223-10.1186/1471-2164-9-223.

Lorenz S, Brenna-Hansen S, Moen T, Roseth A, Davidson WS, Omholt SW, Lien S: BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon. Anim Genet. 2010, 41: 48-54. 10.1111/j.1365-2052.2009.01963.x.

Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, Brookes AJ: Complex SNP-related sequence variation in segmental genome duplications. Nat Genet. 2004, 36: 861-866. 10.1038/ng1401.

Mank JE, Avise JC: Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes. Genetica. 2006, 127: 321-327. 10.1007/s10709-005-5248-0.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.

Dernburg AF, Sedat JW, Hawley RS: Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell. 1996, 86: 135-46. 10.1016/S0092-8674(00)80084-7.

Nielsen HM, Sonesson AK, Meuwissen TH: Optimum contribution selection using traditional best linear unbiased prediction and genomic breeding values in aquaculture breeding schemes. J Anim Sci. 2011, 89: 630-638. 10.2527/jas.2009-2731.

Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM: 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. 10.1038/sj.hdy.6800590.

Houston RD, Haley CS, Hamilton A, Guy DR, Tinch AE, Taggart 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. 10.1534/genetics.107.082974.

Moen T, Baranski M, Sonesson AK, Kjøglum S: 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. 2009, 10: 368-10.1186/1471-2164-10-368.

Baranski M, Moen T, Våge DI: Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar). Genet Sel Evol. 2010, 4: 17-

Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW: Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2010, 11: 403-

Green P, Falls K, Crooks S: Documentation for CRI-MAP version 2.4. Washington University School of Medicine. 1990, St. Louis, Mo., USA