SNP Analysis with Duplicated Fish Genomes: Differentiation of SNPs, Paralogous Sequence Variants, and Multisite Variants

Next Generation Sequencing and Whole Genome Selection in Aquaculture

Volumn , Issue , 2010, Pages 133-150

  Sánchez, Cecilia Castaño ^a   Palti, Yniv ^a   Rexroad, Caird ^a  

^a APPALACHIAN FRUIT RESEARCH STATION   (United States)

Author keywords

Applications of SNP markers; Atlantic and Pacific salmons important aquaculture commodities and the common carp; Genome duplication in fish 2R genome duplication hypothesis, two rounds of genome duplication in ancestral vertebrates; Genome wide dense maps, estimating animals' breeding values evaluating and summing effects of genes or chromosomal segments simultaneously; Ray finned fish, and additional (3R) round of ancestral genome duplication in evolutionary history compared with mammals and birds; Salmonid genome duplication event and tetraploidization within same ancestral species (autotetraploidy), 25 100 MYA; SNP analysis with duplicated fish genomes differentiation of SNPs, paralogous sequence variants and multisite variants; SNP markers in agriculture advances in DNA sequencing technologies, propelling discovery of SNP markers; SNP markers in aquaculture species; SNPs, within or near a coding sequence altering biological function of a protein

Indexed keywords

EID: 84886212667     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470958964.ch9     Document Type: Chapter

References (109)

1. Akhunov E, Nicolet C, and Dvorak J. 2009. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet, 119: 119-507.
2. Allendorf FW and Thorgaard GH. 1984. Tetraploidy and the evolution of salmonid fishes. In: Evolutionary Genetics of Fishes, edited by BJ Turner. Plenum Press, New York.
3. Amaral AJ, Megens HJ, Kerstens HH, Heuven HC, Dibbits B, Crooijmans RP, Den Dunnen JT, and Groenen MA. 2009. Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics, 10: 374.
4. Amores A, Force A, Yan Y-L, Joly L, Amemiya C, Fritz A, Ho RK, Langeland J, Prince V, Wang Y-L, Westerfield M, Ekker M, and Postlethwait J. 1998. Zebrafish hox clusters and vertebrate genome evolution. Science, 282: 282-1711.
5. Amores A, Suzuki T, Yan Y-L, Pomeroy J, Singer A, Amemiya C, and Postlethwait JH. 2004. Developmental roles of pufferfish hox clusters and genome evolution in ray-fin fish. Genome Res, 14: 14-1.
6. Araneda C, Lam N, Diaz NF, Cortez S, Perez C, Neira R, and Iturra P. 2009. Identification, development and characterization of three molecular markers associated to spawning date in Coho salmon ( Oncorhynchu kisutch ). Aquaculture, 296: 296-21.
7. Barbazuk WB, Emrich SJ, Chen HD, Li L, and Schnable PS. 2007. SNP discovery via 454 transcriptome sequencing. Plant J, 51: 51-910.
8. Barroso RM, Wheeler PA, Lapatra SE, Drew RE, and Thorgaard GH. 2008. QTL for IHNV resistance and growth identified in a rainbow trout ( Oncorhynchus mykiss ) × Yellowstone cutthorat ( Oncorhynchus clarki bouvieri ) trout cross. Aquaculture, 277: 277-156.
9. Becker D, Tetens J, Brunner A, Burstel D, Ganter M, Kijas J, and Drogemuller C. 2010. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS ONE, 5: e8689.
10. Bester AE, Roodt-Wilding R, and Whitaker HA. 2008. Discovery and evaluation of single nucleotide polymorphisms (SNPs) for Haliotis midae: A targeted EST approach. Anim Genet, 39: 39-321.
11. Boulding EG, Culling M, Glebe B, Berg PR, Lien S, and Moen T. 2008. Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans -Atlantic backcrosses. Heredity, 101: 101-381.
12. Castaño Sánchez C, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, and Rexroad CE, 3rd. 2009. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics, 10: 559.
13. Christoffels A, Koh EGL, Chia J-M, Brenner S, Aparicio S, and Venkatesh B. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol, 21: 21-1146.
14. Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn BP, Plastow GS, Van Der Steen HA, and Mileham AJ. 2009. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp ( Litopenaeus vannamei ). Anim Genet, 41: 41-39.
15. Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, Deyoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, and Waugh R. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics, 10: 582.
16. Cnaani A, Hallerman EM, Ron M, Weller JI, Indelman M, Kashi Y, Gall GAE, and Hulata G. 2003. Detection of a chromosomal region with two quantitative trait loci, affecting cold tolerance and fish size, in an F2 tilapia hybrid. Aquaculture, 223: 223-117.
17. Cnaani A, Zilberman N, Tinman S, Hulata G, and Ron M. 2004. Genome-scan analysis for quantitative trait loci in an F 2 tilapia hybrid. Mol Genet Genomics, 272: 272-162.
18. Daetwyler HD, Schenkel FS, Sargolzaei M, and Robinson JA. 2008. A genome scan to detect quantitative trait loci for economically important traits in Holstein cattle using two methods and a dense single nucleotide polymorphism map. J Dairy Sci, 91: 91-3225.
19. Danzmann RG, Jackson TR, and Ferguson MM. 1999. Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout. Aquaculture, 173: 173-45.
20. David L, Blum S, Feldman MW, Lavi U, and Hillel J. 2003. Recent duplication of the common carp ( Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. Mol Biol Evol, 20: 20-1425.
21. Decker JE, Pires JC, Conant GC, Mckay SD, Heaton MP, Chen K, Cooper A, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim J-J, Kim KS, Sonstegard TS, Van Tassell CP, Neibergs HL, Mcewan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, Mcclure MC, Rolf MM, Kim J, Schnabel RD, and Taylor JF. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci U S A, 106: 106-18644.
22. Editorial NB. 2009. The genome-assisted barnyard. Nat Biotechnol, 27: 27-487.
23. Gabreski N, Brooks S, Miller D, and Anczak D. 2009. Mapping of lavender foal syndrome using the EquineSNP50 chip. J Equine Vet Sci, 29: 29-321.
24. Gharbi K, Glover KA, Stone LC, Macdonald ES, Matthews L, Grimholt U, and Stear MJ. 2009. Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon. BMC Genet, 10: 20.
25. Goddard ME and Hayes BJ. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet, 10: 10-381.
26. Gorbach DM, Hu ZL, Du ZQ, and Rothschild MF. 2009. SNP discovery in Litopenaeus vannamei with a new computational pipeline. Anim Genet, 40: 40-106.
27. Groenen MA, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RP, Besnier F, Lathrop M, Muir WM, Wong GK, Gut I, and Andersson L. 2009. A high- density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res, 19: 19-510.
28. Haidle L, Janssen JE, Gharbi K, Moghadam HK, Ferguson MM, and Danzmann RG. 2008. Determination of quantitative trait loci (QTL) for early maturation in rainbow trout ( Oncorhynchus mykiss ). Mar Biotechnol (NY), 10: 10-579.
29. Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K, Davidson WS, Koop BF, Adzhubei A, and Hoyhem B. 2007a. An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon ( Salmo salar ) expressed sequences. Aquaculture, 265: 82-90.
30. Hayes BJ, Nilsen K, Berg PR, Grindflek E, and Lien S. 2007b. SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. Bioinformatics, 23: 1692-1693.
31. Hayes BJ, Bowman PJ, Chamberlain AJ, Savin K, Van Tassell CP, Sonstegard TS, and Goddard ME. 2009. A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS ONE, 4: e6676.
32. He C, Chen L, Simmons M, Li P, Kim S, and Liu ZJ. 2003. Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis. Anim Genet, 34: 34-445.
33. Houston RD, Gheyas A, Hamilton A, Guy DR, Tinch AE, Taggart JB, Mcandrew BJ, Haley CS, and Bishop SC. 2008a. Detection and confirmation of a major QTL affecting resistance to infectious pancreatic necrosis (IPN) in Atlantic salmon ( Salmo salar ). Dev Biol (Basel), 132: 199-204.
34. Houston RD, Haley CS, Hamilton A, Guy DR, Tinch AE, Taggart JB, Mcandrew BJ, and Bishop SC. 2008b. Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon ( Salmo salar ). Genetics, 178: 1109-1115.
35. Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, and Cregan PB. 2010. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics, 11: 38.
36. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biemont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, Mckernan KJ, Mcewan P, Bosak S, Kellis M, Volff JN, Guigo R, Zody MC, Mesirov J, Lindblad-Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quetier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, and Roest Crollius H. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature, 431: 431-946.
37. Kent MP, Moen T, Hayes B, Gibbs RA, Weinstock GM, Omholt S, and Lien S. 2008. SNP discovery and linkage mapping in Atlantic salmon. Plant and Animal Genomes XVI Conference, San Diego, CA.
38. Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, Chin AWT, Den Dunnen JT, and Groenen MA. 2009. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: Applied to turkey. BMC Genomics, 10: 479.
39. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, Mcgrath A, Wilson P, Ingersoll RG, Mcculloch R, Mcwilliam S, Tang D, Mcewan J, Cockett N, Oddy VH, Nicholas FW, and Raadsma H. 2009. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE, 4: e4668.
40. Kim ES, Berger PJ, and Kirkpatrick BW. 2009. Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium. Anim Genet, 40 (3): 300-307.
41. Koop B, Von Schalburg K, Leong J, Walker N, Lieph R, Cooper G, Robb A, Beetz-Sargent M, Holt R, Moore R, Brahmbhatt S, Rosner J, Rexroad C, Mcgowan C, and Davidson W. 2008. A salmonid EST genomic study: Genes, duplications, phylogeny and microarrays. BMC Genomics, 9: 545.
42. Kucuktas H, Wang S, Li P, He C, Xu P, Sha Z, Liu H, Jiang Y, Baoprasertkul P, Somridhivej B, Wang Y, Abernathy J, Guo X, Liu L, Muir W, and Liu Z. 2009. Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics, 181: 181-1649.
43. Larhammar D and Risinger C. 1994. Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio. Mol Phylogenet Evol, 3: 3-59.
44. Lee BY, Penman DJ, and Kocher TD. 2003. Identification of a sex-determining region in Nile tilapia ( Oreochromis niloticus ) using bulked segregant analysis. Anim Genet, 34: 34-379.
45. Lee BY, Hulata G, and Kocher TD. 2004. Two unlinked loci controlling the sex of blue tilapia ( Oreochromis aureus ). Heredity, 92: 92-543.
46. Li Y, Dierens M, Byrne K, Miggiano E, Lehnert S, Preston N, and Lyons R. 2006. QTL detection of production traits for the Kuruma prawn Penaeus japonicus (Bate) using AFLP markers. Aquaculture, 258: 258-198.
47. Lindsay SJ, Khajavi M, Lupski JR, and Hurles ME. 2006. A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am J Hum Genet, 79: 79-890.
48. Liu ZJ, ed. 2007. Aquaculture Genome Technologies. Blackwell Publishing, Ames, IA.
49. Liu ZJ and Cordes JF. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238: 238-1.
50. Lorenz S, Brenna-Hansen S, Moen T, Roseth A, Davidson WS, Omholt SW, and Lien S. 2009. BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon. Anim Genet, 41: 41-48.
51. Lyons RE, Dierens LM, Tan SH, Preston NP, and Li Y. 2007. Characterization of AFLP markers associated with growth in the Kuruma prawn, Marsupenaeus japonicus, and identification of a candidate gene. Mar Biotechnol (NY), 9: 9-712.
52. Massault C, Bovenhius H, Haley C, and De Koning DJ. 2008. QTL mapping designs for aquaculture. Aquaculture, 285: 285-23.
53. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TP, Sonstegard TS, and Van Tassell CP. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE, 4: e5350.
54. Mckay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, Gill CA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF, and Moore SS. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genet, 9: 37.
55. Meuwissen TH, Hayes BJ, and Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157: 157-1819.
56. Moen T, Agresti JJ, Cnaani A, Moses H, Famula TR, Hulata G, Gall GAE, and May B. 2004. A genome scan of a four way tilapia cross supports the existence of a quantitative trait loci for cold tolerance on linkage group 23. Aquac Res, 35: 35-893.
57. Moen T, Sonesson AK, Hayes B, Lien S, Munck H, and Meuwissen TH. 2007. 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 Genet, 8: 53.
58. Moen T, Hayes B, Baranski M, Berg PR, Kjoglum S, Koop BF, Davidson WS, Omholt SW, and Lien S. 2008a. A linkage map of the Atlantic salmon ( Salmo salar ) based on EST-derived SNP markers. BMC Genomics, 9: 223.
59. Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad KT, Fevolden SE, Berg PR, and Lien S. 2008b. Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection. BMC Genet, 9: 18.
60. Moen T, Baranski M, Sonesson AK, and Kjoglum S. 2009. 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, 10: 368.
61. Moghadam HK, Ferguson MM, and Danzmann RG. 2005a. Evidence for Hox gene duplication in rainbow trout ( Oncorhynchus mykiss ): A tetraploid model species. J Mol Evol, 61: 804-818.
62. Moghadam HK, Ferguson MM, and Danzmann RG. 2005b. Evolution of Hox clusters in Salmonidae: A comparative analysis between Atlantic salmon ( Salmo salar ) and rainbow trout ( Oncorhynchus mykiss ). J Mol Evol, 61: 636-649.
63. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, Crooijmans RP, Megens HJ, Zhang H, Okimoto R, Vereijken A, Jungerius A, Albers GA, Lawley CT, Delany ME, Maceachern S, and Cheng H. 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci U S A, 105: 105-17312.
64. Murdoch BM, Clawson ML, Laegreid WW, Stothard P, Settles M, Mckay S, Prasad A, Wang Z, Moore SS, and Williams JL. 2010. A 2cM resolution genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genet, 11: 20.
65. Nakamura Y, Ozaki A, Akutsu T, Iwai K, Sakamoto T, Yoshizaki G, and Okamoto N. 2001. Genetic mapping of the dominant albino locus in rainbow trout ( Oncorhynchus mykiss ). Mol Genet Genomics, 265: 265-687.
66. Nichols KM, Bartholomew J, and Thorgaard GH. 2003. Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. Dis Aquat Organ, 56: 56-145.
67. Nichols KM, Broman KW, Sundin K, Young JM, Wheeler PA, and Thorgaard GH. 2007. Quantitative trait loci x maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics, 175: 175-335.
68. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Jr., Grattapaglia D, Sederoff RR, and Kirst M. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 9: 312.
69. Ohno S. 1999. Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999. Semin Cell Dev Biol, 10: 10-517.
70. Ohno S, Muramoto J, Christian L, and Atkin NB. 1967. Diploid-tetraploid relationship among Old World members of the fish family Cyprinidae. Chromosoma, 23: 23-1.
71. Ott J. 1991. Analysis of Human Genetic Linkage. The John Hopkins University Press, Baltimore, MD.
72. Ozaki A, Sakamoto T, Khoo SK, Nakamura Y, Coimbra MR, Akutsu T, and Okamoto N. 2001. Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pencreatic necorsis virus (IPNV) in rainbow trout ( Oncorhynchus mykiss ). Mol Genet Genomics, 265: 265-23.
73. Palti Y, Shirak A, Cnaani A, Hulata G, Avtalion RR, and Ron M. 2002. Detection of genes with deleterious alleles in an inbred line of tilapia ( Oreochromis aureus ). Aquaculture, 206: 206-151.
74. Palti Y, Silverstein JT, Wieman H, Phillips JG, Barrows FT, and Parsons JE. 2006. Evaluation of family growth response to fishmeal and gluten-based diets in rainbow trout ( Oncorhynchus mykiss ). Aquaculture, 255: 255-548.
75. Pant SD, Schenkel FS, Verschoor CP, You Q, Kelton DF, Moore SS, and Karrow NA. 2010. A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in Holstein cattle. Genomics, 95: 95-176.
76. Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, and Feuillet C. 2010. Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J, 8: 8-196.
77. Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, and Bousquet J. 2008. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: Application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics, 9: 21.
78. Perry GM, Danzmann RG, Ferguson MM, and Gibson JP. 2001. Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout ( Oncorhynchus mykiss ). Heredity, 86: 86-333.
79. Phillips RB, Zimmerman A, Noakes MA, Palti Y, Morasch MR, Eiben L, Ristow SS, Thorgaard GH, and Hansen JD. 2003. Physical and genetic mapping of the rainbow trout major histocompatibility regions: Evidence for duplication of the class I region. Immunogenetics, 55: 55-561.
80. Pierce LR, Palti Y, Silverstein JT, Barrows FT, Hallerman EM, and Parsons JE. 2008. Family growth response to fishmeal and plant-based diets shows genotype × diet interaction in rainbow trout ( Oncorhynchus mykiss ). Aquaculture, 278: 278-37.
81. Ramos AM, Crooijmans RP, Affara NA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Churcher C, Clark R, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TP, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RT, Schook LB, and Groenen MA. 2009. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE, 4: e6524.
82. Rodriguez MF, Lapatra S, Williams S, Famula T, and May B. 2004. Genetic markers associated with resistance to infectious necrosis in rainbow trout and steelhead trout ( Oncorhynchus mykiss ) backcrosses. Aquaculture, 241: 241-93.
83. Rothschild MF and Ruvinsky A. 2007. Marker-assisted selection for aquaculture species. In: Aquaculture Genome Technologies, edited by Z. Liu. Blackwell Publishing Professional, Ames, IA, pp. 199-214.
84. Ruane J and Sonnino A. 2007. Chapter 1. Marker-assisted selection as a tool for genetic improvement of crops, livestock, forestry and fish in developing countries: An overview of the issues. In: Marker Assisted Selection: Curent Status and Future Perspectives in Crops, Livestock, Forestry and Fish, edited by J Ruane, BD Schert, A Sonnino, and JR Dorgie. Food and Agriculture of United Nations, Rome.
85. Ryynanen HJ and Primmer CR. 2006. Single nucleotide polymorphism (SNP) discovery in duplicated genomes: Intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon ( Salmo salar ) and other salmonid fishes. BMC Genomics, 7: 192.
86. Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, and Ihssen PE. 1999. Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout ( Oncorhynchus mykiss ). Aquaculture, 173: 173-33.
87. Sargolzaei M, Schenkel FS, Jansen GB, and Schaeffer LR. 2008. Extent of linkage disequilibrium in Holstein cattle in North America. J Dairy Sci, 91: 91-2106.
88. Sarropoulou E, Nousdili D, Magoulas A, and Kotoulas G. 2008. Linking the genomes of nonmodel teleosts through comparative genomics. Mar Biotechnol (NY), 10: 10-227.
89. Satkoski JA, Malhi R, Kanthaswamy S, Tito R, Malladi V, and Smith D. 2008. Pyrosequencing as a method for SNP identification in the rhesus macaque ( Macaca mulatta ). BMC Genomics, 9: 256.
90. Sherman EL, Nkrumah JD, and Moore SS. 2010. Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J Anim Sci, 88: 88-16.
91. Shirak A, Palti Y, Cnaani A, Korol A, Hulata G, Ron M, and Avtalion RR. 2002. Association between loci with deleterious alleles and distorted sex ratios in an inbred line of tilapia ( Oreochromis aureus ). J Hered, 93: 93-270.
92. Smith CT, Elfstrom CM, Seeb LW, and Seeb JE. 2005. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol, 14: 14-4193.
93. Snelling WM, Allan MF, Keele JW, Kuehn LA, Mcdaneld T, Smith TP, Sonstegard TS, Thallman RM, and Bennett GL. 2010. Genome-wide association study of growth in crossbred beef cattle. J Anim Sci, 88: 88-837.
94. Sonesson AK. 2007. Within-family marker-assisted selection for aquaculture species. Genet Sel Evol, 39: 39-301.
95. Sundin K, Brown KH, Drew RE, Nichols KM, Wheeler PA, and Thorgaard GH. 2005. Genetic analysis of a development rate QTL in backcrosses of clonal rainbow trout, Onchorhynchus mykiss. Aquaculture, 247: 247-75.
96. Tanguy A, Bierne N, Saavedra C, Pina B, Bachere E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapegue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, and Canario A. 2008. Increasing genomic information in bivalves through new EST collections in four species: development of new genetic markers for environmental studies and genome evolution. Gene, 408: 408-27.
97. Thanh NM, Barnes AC, Mather PB, Li Y, and Lyons RE. 2010. Single nucleotide polymorphisms in the actin and crustacean hyperglycemic hormone genes and their correlation with individual growth performance in giant freshwater prawn Macrobrachium rosenbergii. Aquaculture, 301: 301-7.
98. Uyeno T and Smith GR. 1972. Tetraploid origin of the karyotype of catostomid fishes. Science, 175: 175-644.
99. Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, and Sonstegard TS. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods, 5: 5-247.
100. Vanraden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, and Schenkel FS. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J Dairy Sci, 92: 92-16.
101. Verbyla KL, Bowman PJ, Hayes B, and Goddard ME. 2009. Sensitivity of genomic selection to using different prior distributions. 13th European Workshop on QTL Mapping and Marker Assisted Selection. Wageningen, The Netherlands.
102. Wang S, Sha Z, Sonstegard TS, Liu H, Xu P, Somridhivej B, Peatman E, Kucuktas H, and Liu Z. 2008. Quality assessment parameters for EST-derived SNPs from catfish. BMC Genomics, 9: 450.
103. 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 BC, 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, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, and Liu Z. 2010. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol, 11: R8.
104. Wiedmann RT, Smith TP, and Nonneman DJ. 2008. SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genet, 9: 81.
105. Wiggans GR, Sonstegard TS, Vanraden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, and Van Tassell CP. 2009. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. J Dairy Sci, 92: 92-3431.
106. Wolfe KH. 2001. Yesterday ' s polyploids and the mystery of diploidization. Nat Rev Genet, 2: 2-333.
107. Yan J, Yang X, Shah T, Sanchez-Villeda H, Li J, Warburton M, Zhou Y, Crouch JH, and Xu Y. 2010. High-throughput SNP genotyoing with the GoldenGate assay in maize. Mol Breed, 25: 25-441.
108. Yu Z and Guo X. 2006. Identification and mapping of disease-resistance QTLs in the Easter oyster, Crassostrea virginica Gmelin. Aquaculture, 254: 254-160.
109. Zeng D, Chen X, Li Y, Peng M, Ma N, Jiang W, Yang C, and Li M. 2008. Analysis of HSP70 in Litopenaeus vannamei and detection of SNPs. J Crustacean Biol, 28: 28-727.