Study of SNPs associated with carcass fat in Afshari,Moghani and Qezel sheep breeds

Document Type : Research Paper

Authors

1 animal science/ agricultur / Zanjan University / iran

2 Animal science/agriculture/zanjan university/iran

3 Animal science/ agriculture /zanjan university/ iran

Abstract

Identification of genomic regions controlling economic traits is one of the most challenging uses of dense markers in animal genetics. Fat storage is economically important for breeding sheep. Therefore, identification of lipid-associated gene positions was the main goals of this study.In this study, 49034 Single Nucleotide Polymorphisms (SNPs) were used to identify the genomic regions affecting fat deposition of 106 sheep individuals include Afshari (n=37), Moghani (n=34) and Qezel (n=35) breeds were used. All samples were genotyped by Illumina OvineSNP50K bead chip. By running the quality control on the raw genotype, from tolal 49,034 SNP markers only 46,676 SNPs remained then genomic relationship principal component analysis (PCA) was used in order to assign correct individual to each breed. Theta and Fst analysis were applied to survey the population differentiation in three breeds, so five regions in 99.99 percentile FST score of the genome distribution were selected for further analysis. These regions are stated on chromosomes number 3, 13 (two areas), 15 and 22 were associated with LDL and HDL receptors Lipolise regulation in fat cells and fatty acid metolism. To verify those regions, Extended Haplotype Homozygosity (EHH) test based on linkage disequilibrium was perform. The results of this study shows that SNP bead chip are useful for population differentiation and GWAS so this can help us to achive an genetic improvement by genomic selection.

Keywords

References

خالداری، م. (1388). چالش­ها و راهبردهای کیفیت لاشه گوسفند در ایران. اولین سمینار کیفیت لاشه گوسفند در ایران، پردیس کشاورزی و منابع طبیعی کرج-دانشگاه تهران. 25 خردادماه. صفحات 79-68 .
مرادی، م. ح. (1391).کاوش ژنومیک نشانه­های انتخاب در سطح ژنوم برخی از نژادهای گوسفند و شناسایی مناطق ژنومی کاندیدای مرتبط با ذخیره چربی. پایان نامه دکترا، دانشکده کشاورزی دانشگاه تهران.
Akey, J.M. (2009). Constructing genomic maps of positive selection in humans: Where do we go from here?. Genome research, 19(5): 711-722.
Akey, J.M., Zhang, G., Zhang, K., Jin, L. and Shriver, M.D. (2002). Interrogating a high density SNP map for signatures of natural selection. Genome Research 12:1805-14.
Kashan, N.E.J., ManafiAzar, G., Afzalzade, A. and Salehi, A. (2005). Growth performance and carcass quality of fattening lambs from fat-tailed and tailed sheep breeds. Small Ruminant Research, 60: 267-271.
Kijas, J.W., Townleyt, D., Dalrymple, B. P., Heaton, M.P., Maddox, J. F., McGrath, A., Wilson, P., Ingersoll, R.G., McCulloch, R., McWilliam, S., Tang, D., McEwan, J. and et al.( 2009): A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE.: 4:e4668.
Li, D. F., Liu, W.B., Liu, J.F., Yi, G.Q., Lian, L., Qu, L.J. and Yang, N. (2012). Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens. Poultry science, 91(8): 1804-1812.
Ma, Y., Wei, J., Zhang, Q., Chen, L., Wang, J., Liu, J. and Ding, X. (2015). A genome scan for selection signatures in pigs. PloS one, 10(3): e0116850.
Makina, S.O., Muchadeyi, F.C., Marle-Köster, E., Taylor, J. F., Makgahlela, M. L. and Maiwashe, A. (2015). Genome-wide scan for selection signatures in six cattle breeds in South Africa. Genetics Selection Evolution, 47(1): 92.
Mickelson, J. (2014). Genomic Signatures of Selection in the Modern Horse. In: 10th World Congress on Genetics Applied to Livestock Production.
Moioli, B., Pilla, F. and Ciani, E. (2015). Signatures of selection identify loci associated with fat tail in sheep. Journal of animal science, 93(10): 4660-4669.
Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds, K. G. and McEwan, J. C. (2012). Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC genetics, 13(1): 10.
Nejati-Javaremi, A., Izadi, F. and Rahmati, G. h. M. M. (2007). Selection in fat-tailed sheep based on two traits of fat-tail and body weight versus single-trait total body weight. Int J Agri Biol, 9(4): 645-648.
Qanbari, S., Pimentel, E.C.G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R. and Simianer, H. (2010). A genome‐wide scan for signatures of recent selection in Holstein cattle. Animal genetics, 41(4): 377-389.
Sabeti, P.C., Reich, D.E., Higgins, J. M., Levine, H. Z., Richter, D.J., Schaffner, S.F. and Ackerman, H.C. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419(6909): 832-837.
Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller. J., Varilly, P., Shamovsky, O. and Lander, E.S. (2006). Positive natural selection in the human lineage. Science, 312(5780): 1614-1620
Safdarian, M., Zamiri, M.J., Hashemi, M. and Noorolahi, H. (2008). Relationships of fat-tail dimensions with fat-tail weight and carcass characteristics at different slaughter weights of Torki-Ghashghaii sheep. Meat science, 80(3): 686-689.
Stainton, J.J., Haley, C.S., Charlesworth, B., Kranis, A., Watson, K. and Wiener, P. (2015). Detecting signatures of selection in nine distinct lines of broiler chickens. Animal genetics, 46(1): 37-49.
Stephens, M., Smith, N. J. and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. The American Journal of Human Genetics, 68(4): 978-989.
The Ovine Genome Browser [http://www.livestockgenomics.csiro.au/sheep/oar1.0.php].
The UCSC Genome Browser [http://genome.ucsc.edu/].
Weir, B. S., and Cockerham, C. C. (1984). Estimating F‐statistics for the analysis of population structure. evolution, 38(6), 1358-1370.
Wellcome Trust Case Control Consortium. (2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447(7145), 661.
Wood, J. D., Enser, M., Fisher, A.V., Nute, G.R., Sheard, P.R., Richardson, R. I. and Whittington, F.M. (2008). Fat deposition, fatty acid composition and meat quality: A review. Meat science, 78(4): 343-358.
Yuan, Z., Liu, E., Liu, Z., Kijas, J. W., Zhu, C., Hu, S. and Wei, C. (2016). Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Animal Genetics.
Zandi, M. B., Javaremi, A. N. and Pakdel, A. (2014). Assessment of Body Measurement Characteristics of Iranian Turkmen and Caspian horses. Bull. Env. Pharmacol. Life Sci, 3(4): 207-214.
Animal Sciences Journal
Volume 32, Issue 123
September 2019
Pages 247-258

Files

Share

How to cite

Statistics