Esin ÇALIK, Volkan BALTACI, Prof. Dr. Kezban CANDOĞAN

3714

Next Generation Sequencing (NGS) Based Variation Analysis: A New Practical Biomarker for Beef Tenderness Assessment

Evaluation of some meat quality attributes using genetic analysis is steadily increasing. PCR based targeted variation analysis is one of the most commonly preferred techniques for this purpose. Recently, Next Generation Sequencing (NGS) method has drawn considerable attention because of its’ high analysis capacity. The purpose of the current study was to determine variations in CAST gene from Brangus and Simmental cattle by performing whole gene sequencing using NGS, and to investigate the potential of NGS method in evaluating meat tenderness based on the high genomic data it provides. Whole gene sequence analysis was performed on Calpastatin (CAST) gene of samples acquired from 52 Brangus and 52 Simmental beef cattle breeds using NGS method, and the variations detected were evaluated in terms of their potential in measuring meat tenderness and quality. NGS outputs were analyzed in Ensemble “cow” database platform and 13 variations were detected. One of these variations (EXON 8 c.439C>G/ p.L147V ) was evaluated as undeclared before. In 20 Brangus cattle and in 9 Simmental cattle, no variations were detected whereas 6 variations (V1, V2, V5, V8, V10 and V13) were found significantly different (p<0.05) based on their distribution in breeds. 
Keywords:

Beef tenderness, Polymorphisms, Calpastatin (CAST) gene,

PDF

___

  • Aaslyng, M. D., and Meinert, L. (2017). Meat flavour in pork and beef – From animal to meal. Meat Science,132,112–117. https://doi.org/10.1016/j.meatsci.2017.04.012
  • Barendse, W. G. (2002). DNA markers for meat tenderness. International patent application. No. Vol. 1. PCT/AU02/00122. World Intellectual Property Organization Inernational Publication, No. WO 02/064820. https://patents.google.com/patent/WO2002064820A1/tr
  • Bhat, Z. F., Morton, J. D., Mason, S. L., and Bekhit, A. E. A. (2018). Role of calpain system in meat tenderness: A review. Food Science and Human Wellness, 7, 196-204. https://doi.org/10.1016/j.fshw.2018.08.002
  • Cavin, C., Cotteneta, G., Cooperb, K. M., and Zbinden, P. (2018). Meat Vulnerabilities to Economic Food Adulteration Require New Analytical Solutions. CHIMIA International Journal for Chemistry, 697–703. https://doi.org/10.2533/chimia.2018.697
  • Curi, R. A., Chardulo, L. A., Mason, M. C., Arrigoni, M. D., Silveira, A. C., and de Oliveira, H. N. (2009). Effect of single nucleotide polymorphisms of CAPN1 and CAST genes on meat traits in Nellore beef cattle (Bos indicus) and in their crosses with Bos taurus. Animal Genetics, 40, 456–462. https://doi.org/10.1111/j.1365-2052.2009.01859.x
  • De Koning, T. J., Jongbloed, J. D., Sikkema-Raddatzand, B., and Sinke, R. J. (2014). Targeted next-generation sequencing panels for monogenetic disorders in clinical diagnostics: The opportunities and challenges. Expert Review of Molecular Diagnostic, 15(1), 61-70. https://doi.org/10.1586/14737159.2015.976555
  • Djadid, N. D., Nikmard, M., Zakeri, S., and Gholizadeh, S. (2011). Characterization of calpastatin gene in Iranian Afshari sheep. Iranian Journal of Biotechnology, 9(2), 145-149. https://www.researchgate.net/publication/286044765
  • Enriquez-Valencia, C. E., Pereira, G. L., Malheiros, J. M., de Vasconcelos Silva, J. A. I., Albuquerque, L. G., de Oliveira, H. N., Chardulo, L. A. L., and Curi, R. A. (2017). Effect of the g. 98535683A > G SNP in the CAST gene on meat traits of Nellore beef cattle (Bos indicus) and their crosses with Bos Taurus. Meat Science, 123, 64–66. http://dx.doi.org/10.1016/j.meatsci.2016.09.003
  • Ensembl Cow Database, 2019. https://www.ensembl.org/Bos_taurus/Gene/Summary?db=core; g=ENSBTAG 0000000 0874; r=7:96033978-96167151
  • Gao, Y., Zhang, R., Hu, X., and Li, N. (2007). Application of genomic technologies to the improvement of meat quality of farm animals. Meat Science, 77, 36–45. https://doi.org/10.1016/j.meatsci.2007.03.026
  • Goodwin, S., McPherson, J.D., and Mc Combie, W.R. (2016). Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics, 17, 333–351. https://doi.org/10.1038/nrg.2016.49
  • Herrera-Mendez, C. H., Becila, S., Boudjellal, A., and Ouali, A. (2006). Meat ageing: Reconsideration of the current concept. Trends Food Sci Technol, 17(8), 394-405. https://doi.org/10.1016/j.tifs.2006.01.011
  • Klont, R. E., Brocks, L., and Eikelenboom, G. (1998). Muscle fibre type and meat quality. Meat Science, 49, 219–229. uscle fibre type and meat quality. Meat Science, 49, 219–229. https://doi.org/10.1016/S0309-1740(98)90050-X
  • Leal-Gutiérrez, J. D., and Mateescu, R. G. (2019). Genetic basis of improving the palatability of beef cattle: current insights. Food Biotechnology, 33(3), 193-216. https://doi.org/10.1080/08905436.2019.1616299
  • Linderman, M. D., Brandt, T., Edelmann Jabado, O., Kasai, Y., Kornreich, R., Mahajan, M., Shah, H., Kasarskis, A. and Schadt, E. E. (2014). Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Medical Genomics, 7, 20. https://doi.org/10.1186/1755-8794-7-20
  • Lu, D., Sargolzaei, M., Kelly, M., Voort, G. V., Wang, Z., Mandell, I., Moore, S., Plastow, G., and Miller, S. P. (2013). Genome-wide association analyses for carcass quality in cross bred beef cattle. BMC Genetics, 14(80), 1471-2156. http://www.biomedcentral.com/1471-2156/14/80
  • Mateescu, R. G., Garrick, D. J., and Reecy, J. M. (2017). Network Analysis Reveals Putative Genes Affecting Meat Quality in Angus Cattle. Frontier in Genetics, 8, 171. https://doi.org/10.3389/fgene.2017.00171
  • Page, B. T., Casas, E., Quaas, R. L., Thallman, R. M., Wheeler, T. L., Shackelford, S. D., Koohmaraie, M., White, S. N., Bennett, G. L., and Keele, J. W. (2004). Association of markers in the bovine CAPN1 gene with meat tenderness in large cross bred populations that sample influential industry sires. Journal of Animal Science, 82, 3474–3481. https://doi.org/10.2527/2004.82123474x
  • Parra-Bracamonte, M., Martinez-Gonzales, J.C., Sifuentes-Rincon, A., and Ortega-Rivas, E. (2015). Meat tenderness genetic polymorphisms occurrence and distribution in five Zebu breeds in Mexico. Electronic Journal of Biotechnology,18(5). https://doi.org/10.1016/j.ejbt.2015.07.002
  • Raynaud, P., Gillard, M., Parr, T., Bardsley, R., Amarger, V., and Levéziel, H. (2005). Correlation between bovine calpastatin mRNA transcripts and protein isoforms. Archives of Biochemistry and Biophysics, 440, 46-53. https://doi.org/10.1016/j.abb.2005.05.028
  • Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Elaine Lyon Spector, E., Voelkerding, K., and Rehm, H. L. (2015). Standards and Guidelines for the Interpretation of SequenceVariants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–424. https://doi.org/10.1016/j.jmoldx.2016.10.002
  • Sanger, F., Nicklen, S., and Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, USA, 74, 5463–5467. https://doi.org/10.1073/pnas.74.12.5463
  • Van Eenennaam, A. L., Li, J., Thallman, R. M., Quaas, R. L., Dikeman, M. E., Gill, C. A., Franke, D. E., and Thomas, M. G. (2007). Validation of commercial DNA tests for quantitative beef quality traits. Journal of Animal Science, 85, 891–900. https://doi.org/10.2527/jas.2006-512
  • Wheeler, T., Shackelford, S., and Koohmaraie, M. (2000). Variation in proteolysis, sarcomere length, collagen content, and tenderness among major pork muscles. Journal of Animal Science, 78, 958–965. https://doi.org/10.2527/2000.784958x
  • Yousefi, S., and Azari, M. A. (2012). Study of Calpastatin gene polymorphism in Holstein cattle and buffalo. Animal Sciences and Biotechnologies, 45 (1), 285-288. https://www.researchgate.net/publication/267247830
  • Zhou, Y. G., Xiong, Y., WuYang, C., Jiang, X. S., Ran, J. S., Jin, J., Wang, Y., Lan, D., Ren, P., Hu, Y. D., and Liu, Y. P. (2017). Experimental verification of CAPN1 and CAST gene polymorphisms in different generations of Da-Heng broilers. Hindawi BioMed Research International. https://doi.org/10.1155/2017/7968450
International Journal of Agriculture Environment and Food Sciences-Cover
  • Yayın Aralığı: Yılda 4 Sayı
  • Başlangıç: 2017
  • Yayıncı: Gültekin ÖZDEMİR
Arşiv
Sayıdaki Diğer Makaleler

Esin ÇALIK, Volkan BALTACI, Prof. Dr. Kezban CANDOĞAN

Abdullah ULAŞ, Alim AYDIN, Firdes ULAS, Halit YETİŞİR

Ayse INCE, Mehmet KARACA

Reşat ESGİCİ

Serhat USANMAZ

Mahmud SANİ, İbraheem ALHASSAN, Dantata, J. ISHAKU, Auwalu GARBA G., Musa ADAMU A.

Mehmet UGURLU

Aykut BURĞUT

Derya TAPLAMACIOĞLU, İsmail KARACA

Şehriban Gül ÖZÇELİK, Erkan KARACABEY