مطالعه پویش کل ژنومی صفات ترکیبات لاشه در جمعیت F2 حاصل از تلاقی مرغ بومی آذربایجان غربی وسویه گوشتی آرین

نوع مقاله: مقاله پژوهشی

نویسندگان

1 دانش آموخته دکتری، گروه علوم دامی، دانشکده کشاورزی، دانشگاه تربیت مدرس، تهران، ایران

2 دانشیار گروه علوم دامی، دانشکده کشاورزی، دانشگاه تربیت مدرس، تهران.

3 استادیار، گروه علوم دامی، دانشکده کشاورزی، دانشگاه تربیت مدرس، تهران، ایران

چکیده

ترکیبات لاشه جزء صفات مهم اقتصادی در جوجه های گوشتی محسوب می شود. به منظور شناسایی جایگاهها و ژنهای مرتبط با صفات ترکیبات لاشه، مطالعه پویش کل ژنوم(GWAS) با استفاده از یک تراشه SNP ژنوم مرغ (SNP Beadchip (Illumnia 60k Chicken در یک جمعیت F2 حاصل از تلاقی دوطرفه مرغ بومی آذربایجان غربی و خط B سویه گوشتی آرین انجام شد. برای هر پرنده، صفات وزن لاشه، وزن سینه و وزن ران و درصدهای مربوطه مورد اندازه گیری قرار گرفت. با استفاده از دو مدل GLM و CMLM ارتباط هر یک SNP ها با این صفات مورد بررسی قرار گرفت. در مجموع تعداد 22 نشانگر SNP برای صفات ترکیبات لاشه شناسایی شد. این نشانگرهای SNP شناسایی‌شده در داخل، ناحیه بالادست و یا در ناحیه پایین‌دست ژن‌های کاندیدا قرار‌داشتند. ژن‌های کاندیدای شناسایی‌شده عملکرد مولکولی مرتبط با هر یک از صفات مورد مطالعه را داشتند و لذا می‌توان از این ژن‌های کاندیدا در برنامه‌های اصلاحی طیور مورد استفاده قرار‌داد.

کلیدواژه‌ها

موضوعات


Abasht, B. and Lamont, S. J. (2007). Genome-Wide Association Study of Fatness in Chickens. Animal Industry Report: AS 653, ASL R2218.Available at: http://lib.dr.iastate.edu/ans_air/vol653/iss1/44.   

Adler, H.J., Winnicki, R.S., Gong, T.W.L. and Lomax, M.I. (1999). A gene upregulated in the acoustically damaged chick basilar papilla encodes a novel WD40 repeat protein. Genomics, 56:59-69.

Atzmon, G., Ronin, Y.I., Korol, A., Yonash, N., Cheng, H. Hillel, J. (2006). QTLs associated with growth traits and abdominal fat weight and their interactions with gender and hatch in commercial meat-type chickens. Animal genetics, 37(4): 352-8.

Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. (2007). TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, 23(19):2633-2635.

Broer, A., Tietze, N., Kowalczuk, S., Chubb, S., Munzinger, M., Bak, L.K. and Broer, S. (2006). The orphan transporter v7-3 (slc6a15) is a Na+-dependent neutral amino acid transporter. Biochemistry Journal, 393:421-430.

 

Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V.B., Brenner, S.E., Batalov, S., Forrest, A.R., Zavolan, M., Davis, M.J. and Hayashizaki Y. (2005). The transcriptional landscape of the mammalian genome. Science, 309:1559-1563.

Church, D.M., Goodstadt, L., Hillier, L.W., Zody, M.C., Goldstein, S., She, X., Bult, C.J., Agarwala, R., Cherry, J.L., DiCuccio, M., Hlavina, W., Kapustin, Y., Meric, P., Maglott, D.,Birtle, Z., Marques, A.C., Graves, T., Zhou, S. and  Ponting, C.P. (2009). Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biology, 7:E1000112.

 

De Koning, D J., Haley, C .S., Windsor, D., Hocking, P.M., Griffin, H., Morris, A., Vincent, J. and Burt, D.W. (2004). Segregation of QTL for production traits in commercial meat-type chickens. Genetical Research, 83(3): 211-20.

Demeure, O., Duclos, M. J., Bacciu, N., Mignon, G. L., Filangi, O., Pitel, F., Boland, A., Lagarrigue, S.,Cogburn, L. A., Simon, J., Roy, P. L. and Bihan-Duval, E.L. (2013). Genome wide interval mapping using SNPs identifies new QTL for growth, body composition and several physiological variables in an F2 intercross between fat and lean chicken lines. Genetic Selection Evolution, 45: 36.

Di Pietro, C., Ragusa, M., Duro, L., Guglielmino, M.R., Barbagallo, D., Carnemolla, A., Lagana, A., Buffa, P., Angelica, R., Rinaldi, A., Calafato, M.S., Milicia, I., Caserta, C., Giugno, R., Pulvirenti, A., Giunta, V., Rapisarda, A. and  Purrello, M. (2007). Genomics, evolution, and expression of TBPL2, a member of the TBP family. DNA Cell Biology, 26:369-385.

Fornari, M.B., Zanella, R., Ibelli, A.M., Fernandes, L.T., Cantão, M.E., Thomaz-Soccol, V., Ledur, M.C., Peixoto, J.O. (2014). Unraveling the associations of osteoprotegerin gene with production traits in a paternal broiler line. Springer Plus, 3: 682.

Gao, Y., Du, Z.Q., Wei, W.H.,Yu, X.J., Deng, X.M., Feng, C.G., Fei, J., Feng, J.D., Li, N. and Hu, X.X. (2009). Mapping quantitative trait loci regulating chicken body composition traits. Animal genetics, 40(6):952-4.

Hang, X.H., Wei, X.H., Sang, T., Zhao, Q.A., Feng, Q., Zhao, Y., Li, C., Zhu, C., Lu, T. and Zhang, Z. (2010). Genome-wide association studies of 14 agronomic traits in rice Iandraces. Natutal genetics, 42:961-976.

Hillier, L.W., Miller W., Birney, E., Warren, W., Hardison, R.C., Ponting, C.P., Bork, P., Burt, D.W., Groenen, M.A.M., Delany, M.E., Dodgson, J.B., Chinwalla, A.T., Cliften, P.F., Clifton, S.W., Delehaunty, K.D., Fronick, C., Fulton, R.S., Graves, T.A. and Wilson, R.K. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. International Chicken Genome Sequencing Consortium. Nature, 432:695-716.

Hu, Z.L., Park, C.A. and Reecy, J.M. (2016). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44 (D1): D827-D833.

Huttlin, E.L., Jedrychowski, M.P., Elias, J.E., Goswami, T., Rad, R., Beausoleil, S.A., Villen, J., Haas, W., Sowa, M.E. and Gygi, S.P. (2010). A tissue-specific atlas of mouse protein phosphorylation and expression. Cell, 143:1174-1189.

Ikeobi, C.O.N., Woolliams, J. A., Morrice, D. R., Law, A., windsor, D., Burt, D. W.  and Hocking, P. M.  (2004). Quantitative trait loci for meat yield and muscle distribution in a broiler layer cross. Livestock Production Science, 87: 143-151.

            Javanrouh, A., Banabazi., M.H.,  Esmaeilkhanian, S., Amirinia, C., Seyedabadi, H.R. and Emrani, H. (2006). Optimization on salting out method for DNA extraction from animal and poultry blood cells. The 57th Annual Meeting of the European Association for Animal Production. Antalya, Turkey.

Kile, B.T., Metcalf, D., Mifsud, S., DiRago, L., Nicola, N.A., Hilton, D.J. and Alexander, W.S. (2001). Functional analysis of Asb-1 using genetic modification in mice. Molecular Cell Biology, 21:6189-6197.

Liu, R., Sun, Y., Zhao, G., Wang, F., Wu, D., Zheng, M., Chen, J., Zheng, L., Hu, Y. and Wen, J. (2013). Genome-Wide Association Study Identifies Loci and Candidate Genes for Body Composition and Meat Quality Traits in Beijing-You Chickens. PLoS ONE, 8(4): e61172.

Liu, R., Sun, Y., Zhao, G., Wang, H., Zheng, M., Li, P. Liu, L. and Wen, J. (2015). Identification of loci and genes for growth related traits from a genome-wide association study in a slow × fast-growing broiler chicken cross. Genes & Genomics, 37:  829-836.

Madeja, Z., Adamowicz, T., Chamurzynska, A., Jan Kowski, T., Melonek, J.M., Switonski, M.  and Strable, T. (2004). Short Communication: Effect of Leptin gene polymorphisms on breeding value for milk production traits. Journal of Dairy Science. 87: 3925-3927.

Mahmood, R., Kiefer, P., Guthrie, S., Dickson, C. and Mason, I. (1995). Multiple roles for FGF-3 during cranial neural development in the chicken. Development, 121:1399-1410.

McElroy, J.P., Kim, J.J., Harry, D.E., Brown, S.R., Dekkers, J.C. and Lamont, S.J. (2006). Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens. Poultry Science, 85(4):593-605.

Nassar, M.K., Goraga, Z.S. and Brockmann, G.A. (2012). Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition. Animal genetics, 43(6):739-45.

NCBI Resource Coordinators (2013). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research, 41 (Database issue): D8–D20. Available at http://www.ncbi.nlm.nih.gov/UniGene/.

Nones, K., Ledur, M.C., Ruy, D.C., Baron, E.E.,  Melo, C.M.R.,  Moura, A.S.A.M.T.,  Zanella, E.L.,  Burt, D.W.  and Coutinho, L.L.  (2005). Mapping QTLs on chicken chromosome 1 for performance and carcass traits in a broiler x layer cross. Animal Genetics, 37: 95-100.

Obholz, K.L., Akopyan, A., Waymire, K.G. and MacGregor G.R. (2006). FNDC3A is required for adhesion between spermatids and Sertoli cells. Development Biology, 298:498-513.

Pundir, S., Magrane, M., Martin, M.J. and O’Donovan, C. (2015). UniProt Consortium: Searching and Navigating UniProt Databases. Current. Proteomics Bioinformatics, 50:1.27.1-1.27.10.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J. and Sham, P.C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses.The American Journal of Human Genetics,  81(3):559-75.

Setsuie, R., Suzuki, M., Tsuchiya, Y. and Wada, K. (2010). Skeletal muscles of Uchl3 knockout mice show polyubiquitinated protein accumulation and stress responses. Neurochemistry International Journal, 56:911-918.

Sharman, P.W.A., Morrice, D.R., Law, A.S., Burt, D.W. and Hocking, P.M. (2007). Quantitative trait loci for bone traits segregating independently of those for growth in an F2 broiler x layer cross. Cytogenetic and Genome Research, 117: 296-304.

Sun, Y., Zhao, G., Liu, R., Zheng, M., Hu, Y., Wu, D. and Wen, J. (2013). The identification of 14 new genes for meat quality traits in chicken using a  genome wide association study. BMC Genomics, 14: 458.

The UniProt Consortium. (2015). UniProt: a hub for protein information. Nucleic Acids Research, 43: D204-D212.

Turner, S. (2014). R Package: qqman ver. 0.1.2. Q-Q and manhattan plots for GWAS data.

Van Raden, P.M. (2008). Efficient Methods to Compute Genomic Predictions. Journal of Dairy Science, 91: 4414–4423.

Wang, W.,  Zhang, T.,  Wang, J.,  Zhang, G., Wang,Y., Zhang, Y., Zhang, J., Li, G., Xue, Q., Han, K., Zhao, X. and Zheng, H. (2015). Genome-wide association study of 8 carcass traits in Jinghai Yellow chickens using specific-locus amplified fragment sequencing technology. Poultry Science, 60:1–7.

Zhang, Z., Ersoz, E., Lai, C.Q., Todhunter, R.J., Tiwari, H.K., Gore, M.A., Bradbury, P.J., Yu, J., Arnett, D.K., Ordovas,  J.M. and Buckler, E.S. (2010). Mixed linear model approach adapted for genome-wide association studies. Nature Genetics, 42(4):355-60.

Zhao, J.H. (2007). gap: A genetic analysis package. Journal of statistical software, 23(8):1-18.

Zhou, H., Deeb, N., Evock-Clover, CM. Ashwell, CM. and Lamont, S.J. (2006). Genome-wide Linkage Analysis to Identify Chromosomal Regions Affecting Phenotypic Traits in the Chicken II. Body Composition. Poultry Science, 85(10):1712