Association between polymorphism in myostatin gene (MSTN) with quantitative traits in domesticated rainbow trout (Oncorhynchus mykiss) using PCR-SSCP method

Allendorf, F.W. and Thorgaard, G.H., 1984. Tetraploidy and the evolution of salmonid fishes. In: Evolutionary Genetics of Fishes (ed. Turner BJ), pp. 1–46. Plenum Press, New York. Amish, S.J., Hohenlohe, P.A., Painter, S., Leary, R.F., Muhlfeld, C. and Allendorf, F.W., 2012. Rad sequencing yields a high success rate for west slope cutthroat and rainbow trout species-diagnostics passays. Molecular Ecology Resources, 12: 653–660. Botstein, D., White, R.L., Skolnick, M. and Davis, R.W., 1980. Construction of a genetic linkage map inman using restriction fragment length polymorphisms. American Journal of Human Genetic, 32: 314–331. Capon, F, Allen, M.H., Ameen, M., Burden, A.D., Tillman, D., Barkerand, J.N. and Trembath, R.C., 2004. A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. Human Molecular Genetic, 13: 2361–2368. Chen, M. and Manley, J.L., 2009. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Review in Molecular Cell Biology, 10: 741–754. Christensen, K.A., Brunelli, J.P., Lambert, M.J., Dekoning, J., Phillips, R.B. and Thorgaard, G.H., 2013. Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication. BMC Bioinformatics 14(325): 23-34. Doerge, R.W., 2002. Mapping and analysis of quantitative trait loci in experimental populations. . Nature Review in Genetics, 3: 43. Ewing, B. and Green, P., 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research, 8:186–194. Genet, C., Dehais, P. and Palti, Y., 2011. Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes. BMC Genomics, 12(314): 48-62. Gjedrem, T., 2012. Genetic improvement for the development of efficient global aquaculture: A personal opinion review. Aquaculture, pp. 344–349. Gjedrem, T., Robinson, N. and Rye, M., 2012. The importance of selective breeding in aquaculture to meet future demands for animal protein: A review. Aquaculture, pp. 350-353, 117-129. Glover, K.A., Otterå, H., Olsen, R.E., Slinde, E., Taranger G.L. and Skaala, Ø., 2009. A comparison of farmed, wild and hybrid Atlantic salmon (Salmo salar L.) reared under farming conditions. Aquaculture, 286: 203-210. Guyomard, R., Boussaha, M., Krieg, F., Hervet, C. and Quillet, E., 2012. A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts. BMC Genetics, 13:15, 1-12. Hale, M.C., Thrower, F.P., Berntson, E.A., Miller, M.R. and Nichols, K.M., 2014. Mapping and expression of candidate genes for development rate in rainbow Trout (Oncorhynchus mykiss). Journal of Heredity, pp.1-15. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symposium Series, 41: 95-98. Hemmer-Hansen, J., Nielsen, E.E., Meldrup, D. and Mittelholzer, C., 2011. Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua. Molecular Ecology Resources, 11: 71–80. Holzer, C. and Precht, M., 1992. Multiple comparison procedures for normally distributed ANOVA models in SAS, SPSS, BMDP, and MINITAB. Computer Statistic Data Analysis, 13: 351–358. Hu, X., Li, C. and Shi, L., 2013. A novel 79-bp insertion/deletion polymorphism in 3′-flanking region of IGF-I gene is associated with growth-related traits in common carp (Cyprinus carpio L.). Aquaculture Research, 44: 1632–1638. Joulia, D., Bernardi, H., Garandel, V., Rabenoelina, F., Vernus, B. and Cabello, G., 2003. Mechanisms involved in the inhibition of myoblast proliferation and differentiation by myostatin. Experimental Cell Research, 286(2): 263–275. Kimchi-Sarfaty, C., Oh, J.M, Kim, I.W., Sauna, Z.E., Calcagno, A.M., Ambudkar, S.V. and Gottesman, M.M., 2007. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science, 315: 525- 528. Ko, C.F., Chiou, T.T., Chen, T., Wu, J.L., Chen, J.C. and Lu, J.K., 2007. Molecular cloning of myostatin gene and characterization of tissue-specific and developmental stage-specific expression of the gene in orange-spotted grouper, Epinephelus coioides. Marine Biotechnology, 9: 20–32. Kocour, M. and Kohlmann. K., 2011. Growth hormone gene polymorphisms in tench, Tinca tinca L. Aquaculture, 310: 298–304. Kretz, K.A. and O’Brien, J. S., 1993. Direct sequencing of polymerase chain reaction products from low melting temperature agarose. Methods in Enzymology, 218: 72–79. Lee, S.J., 2004. Regulation of muscle mass by myostatin. Annual Review of Cell Development Biology, 20: 61-86. Librado, P. and Rozas, J., 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. Liu, L., Yu, X. and Tong, J., 2012. Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis). Molecular Biology Reproduction 39: 9211–9221. Lynch, M., and Walsh, B., 1997. Genetics and Analysis of Quantitative Traits, p. 980. Sinauer, Sunderland, Massachusetts. Meng, X., Wang, H., Qiu, X., Liu, H. and Wang, X., 2015. SNPs of myostatin (MSTN) gene and their association with growth traits in three bay scallop (Argopecten irradians) populations. Aquaculture Research, 10: 1-6. Nackley, A.G., Shabalina, S.A., Tchivileva, I.E., Satterfield, K., Korchynskyi, O., Makarov, S.S., Maixner, W. and Diatchenko, L., 2006. Human catechol O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science, 314: 1930–1933. Nei, M., 1973. Analysis of gene diversity in subdivided populations. Proceeding National of Academic Science. U. S. A. 70, 3321–3323. Ostbye, T.K., Galloway, T.F., Nielsen, C., Gabestad, I., Bardal, T. and Andersen, O., 2001. The two myostatin genes of Atlantic salmon (Salmo salar) are expressed in a variety of tissues. European Journal of Biochemistry, 268: 5249–5257. Palti, Y., Gahr, S.A., Hansen, J.D. and Rexroad, C.E., 2004. Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication. Animal Genetics, 35: 130–133. Palti, Y., Genet, C. and Gao, G., 2012. A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes. Marine Biotechnology, 14: 343–357. Palti, Y.G., Gao, M.R., Miller, R.L., Vallejo, P.A., Wheeler, E., Quillet, J., Yao, G.H. Thorgaard, M., Salem, and Rexroad, C.E., 2014. A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. Molecular Ecology Resources, 14: 588–596. Peñaloza, C., Hamilton, A., Guy, D.R., Bishop, S.C. and Houston, R.D., 2013. A SNP in the 50 flanking region of the myostatin-1b gene is associated with harvest traits in Atlantic salmon (Salmo salar). BMC Genetics, 14, 112: 1-11. Pourkazemi, M., Nazari, S., Khoshkholgh, M.R. and Azizzadeh, L., 2012. Genetic Relationships among Populations of the Persian sturgeon, Acipenser percicus, in the south Caspian Sea detected by mitochondrial DNA–Restriction Fragment Length Polymorphisms.. Caspian Journal of Environmental Sciences, 10(2): 215-226. Qu, L.J., Li, X.Y., Wu, G.Q. and Yang, N., 2005. Efficient and sensitive method of DNA silver staining in polyacrylamide gel. Electrophoresis, 26(1): 99–101. Rescan, P.Y., Jutel, I. and Ralliere, C., 2001. Two myostatin genes are differentially expressed in myotomal muscles of the trout (Oncorhynchus mykiss). Journal of Experimental Biology, 204: 3523–3529. Rice, W.R, 1989. Analyzing tables of statistical tests. Evolution, 43:223-225. Roberts, S.B. and Goetz, F.W., 2003. Myostatin protein and RNA transcript levels in adult and developing brook trout. Molecular and Cellular Endocrinology, 210: 9–20. Rodgers, B.D. and Garikipati, D.K., 2008. Clinical, agricultural, and evolutionary biology of myostatin: a comparative review. Endocrinology Review, 29(5): 513–534. Sambrook, J. and Russell, D., 2001. Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory. Pp. 23-44. Sánchez, C.C., Weber, G.M., Gao, G., Cleveland, B.M., Yao, J. and Rexroad, C.E., 2011. Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors. BMC Genomics 12(626): 23-34. Sawayama, E. and Takagi, M., 2015. Parental contribution and growth hormone gene polymorphism associated with growth phenotypes of red sea bream Pagrus major in mass production: A case study Aquaculture Reports, 2: 144–151. Stephens, M., Smith, N. and Donnelly, P., 2001. A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetic, 69:978–989. Sun, X., Shin, G. and Hedgecock, D., 2015. Inheritance of high-resolution melting profiles in assays targeting single nucleotide polymorphisms in protein-coding sequences of the Pacific oyster Crassostrea gigas: Implications for parentage assignment of experimental and commercial broodstocks. Aquaculture, pp.127-139. Sun, Y., Yu, X. and Tong, J., 2012. Polymorphisms in Myostatin Gene and Associations with Growth Traits in the Common Carp (Cyprinus carpio L.). International Journal of Molecular Science, 13: 14956-14961. Tao, W.J. and Boulding, E.G., 2003. Associations between single nucleotide polymorphisms in candidate genes and growth rate in Arctic charr (Salvelinus alpinus L.), Heredity, 91: 60–69. Thomas, M., Langley, B., Berry, C., Sharma, M., Kirk, S., Bass, J. and Kambadur, R., 2000. Myostatin, a negative regulator of muscle growth, functions by inhibiting myoblast proliferation. Journal of Biology and Chemistry, 275: 40235-40243. Thomas, S.C., Coltman, D.W. and Pemberton, J.M., 2002. The use of marker-based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale. Journal of Evolutionary Biology, 15: 92–99. Tian, C., Yang, M.L., Lv, Y., Yuan, X., Liang, W., Guo, Y., Song, and Zhao C., 2014. Single Nucleotide Polymorphisms in growth hormone gene and their association with growth traits in Siniperca chuatsi (Basilewsky). International Journal of Molecular Sciences, 15: 7029-7036. Vandeputte, M. and Haffray, P., 2014. Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals. Frontiers in Genetics, 5(432): 1-8. Vera, M., Alvarez-Dios, J., Fernandez, C., Bouza, C. and Vilas, R., 2013. Development and validation of Single Nucleotide Polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) using high throughput genotyping. International Journal of Molecular Science, 14: 5694–5711. Vong, Q.P., Chan, K.M., Leung, K. and Cheng, C.H.K., 2003. Common carp insulin-like growth factor-I gene: complete nucleotide sequence and functional characterization of the 5′-flanking region. Gene, 322: 145–156. Wallis, A.E. and Devlin, R.H., 1993. Duplicate insulin-like growth factor-I genes in salmon display alternative splicing pathways. Molecular Endocrinology, 7: 409–422. Wang, S., Sha, Z., Sonstegard, T.S., Liu, H. and Xu, P., 2008. Quality assessment parameters for EST-derived SNPs from catfish. BMC Genomics, 9(450): 11-23. Yang, J., Liu, Z., Shi, H.N., Zhang, J.P., Wang, J.F., Huang, J.Q. and Kang, Y.J., 2016. Association between MHC II beta chain gene polymorphisms and resistance to infectious haematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss, Walbaum, 1792). Aquaculture Research, 47: 570–578. Yeh, F.C., Yang, R. and Boyle, T., 1999. POPGENE Version 3.1, Microsoft Window-based Freeware for Population Genetic Analysis. University of Alberta, Edmonton, AB, Canada. Yu, J.H., Li, H.X., Tang, Y.K., Li, J.L. and Dong, Z.J., 2010. Isolation and expression of Myostatin (MSTN) genes, and their polymorphism correlations with body form and average daily gain in Cyprinus carpio var. Journal of Agriculture and Biotechnology, 18: 1062–1072. Zhang, H.W., Yin, S.W., Zhang, L.J., Hou, X.Y. and Wang, Y.Y., 2015. Development and validation of single nucleotide polymorphism markers in Odontobutis potamophila from transcriptomic sequencing. Genetic Molecular Resources 14(1): 2080–2085.