Polymorphism and Association of 5’UTR CAPN1 Gene with Growth Traits in Bali Cattle by PCR-RFLP

D. E. W. T. Sihite, R. Priyanto, Jakaria Jakaria


The aim of this study was to identify the variation of 5’UTR CAPN1 gene and its association to growth traits in Bali cattle. DNA samples were obtained from 80 heads of Bali cattle originated from BPTU-HPT Denpasar. The average of Bali cattle age was 784 days (631 days-1098 days). Bali cattle were divided into 3 age groups namely, the first group (1.5 years to 2 years), the second group (2 years to 2.5 years), and the third group (2.5 years to 3 years). The observed growth traits were birth weight (kg), live weights (kg), average daily gain (kg), body length (cm), chest depth (cm), withers height (cm), hip height (cm), and heart girth (cm). Polymorphism identification of 5’UTR CAPN1 gene was conducted by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) with BglII as the restriction enzyme. Growth traits data association were analyzed using the General Linear Model (GLM) analysis. The 5’UTR CAPN1 gene|BglII was polymorphic in Bali cattle (GG, GT, and TT). Genotype frequencies for Bali cattle were 0.30 (GG), 0.66 (GT), and 0.04 (TT). The allele frequencies of G and T allele were 0.63 and 0.37, respectively. The G allele was the most frequent allele and GT genotype was the most frequent genotype among the cattle. The CAPN1|BglII had a significant effect (p<0.05) on growth traits in Bali cattle. Animal carrier of GG genotype had higher live weight and average daily gain than those with GT genotype, while the lowest values were associated with TT genotype.


Araujo, P. R., Y. Kihoon, K. Daijin, D. S. Andrew, M. Qiao, U. Suresh, C. B., Suzanne, & O.F.P. Luiz. 2012. Before it gets started : regulating translation at 5’UTR [review]. Comp. Funct. Genom. 2012:1-8. https://doi.org/10.1155/2012/475731

Ardicli, S., H. Samli, D. Dincel, B. Soyudal, & F. Balci. 2017. Individual and combined effects of CAPN1, CAST, LEP and GHR gene polymorphisms on carcass characteristics and meat quality in Holstein bulls. Arch. Anim. Breed. 60:303-313. https://doi.org/10.5194/aab-60-303-2017

Bhattacharya, T. K., R. N. Chatterjee, R. P. Sharma, M. Niranjan, & U. Rajkumar. 2011. Associations between novel polymorphisms at the 5-UTR region of the prolactin gene and egg production and quality in chickens. Theriogenology. 75:655-661. https://doi.org/10.1016/j.theriogenology.2010.10.005

Bosques, J., M. Pagán-Morales, A. Casas, A. Rivera, & , D. Cianzio. 2015. Effect of polymorphisms in the µ-calpain and calpastatin genes on economically important traitsof beef cattle in Puerto Rico. The Journal of Agriculture of the University of Puerto Rico. 99: 87-104.

Brenig, B., Y. Duan, Y. Xing, N. Ding, L. Huang, & E. Schütz. 2015. Porcine SOX9 gene expression is influenced by an 18bp indel in the 5’-untranslated region. PLOS ONE. 10: 1-17. https://doi.org/10.1371/journal.pone.0139583

Dear, T. N., N. T. Meier, M. Hunn, & T. Boehm. 2000. Gene structure, chromosomal localization, and expression pattern of CAPN12, a new member of the Calpain large subunit gene family. Genomics. 68:152-160. https://doi.org/10.1006/geno.2000.6289

Fang, M., H. Du, Y. Hu, X. Zhou, H. Ouyang, W. Zhang, X. Jia, J. Li, Y. Wang, Q. Nie, & X. Zhang. 2011. Identification and characterization of the pig abin-1gene and investigation of its association with reproduction traits. J. Genet. 90: e10–e20. https://doi.org/10.1007/s12041-011-0025-6

Fedota, O. M., S. Y. Ruban, N. G. Lysenko, A. I. Kolisnyk, & I. V. Goraichuk. 2016. SNPS of Calpain/Calpastatin system genes in commercial population of Aberdeen Angus in Kharkiv region, eastern Ukraine. Journal for Veterinary Medicine, Biotechnology and Biosafety. 2:20-28.

Glading, A., P. Chang, D. A. Lauffenburger, & A. Wells. 2000. Epidermal growth factor receptor activation of calpain is required for fibroblast motility and occurs via an ERK/MAP kinase signaling pathway. J. Biol. Chem. 275: 2390–2398. https://doi.org/10.1074/jbc.275.4.2390

Gunawan, A. & Jakaria. 2011. Genetic and non-genetics effect on birth, weaning, and yearling weight of Bali cattle. Med Pet. 34: 93-98. https://doi.org/10.5398/medpet.2011.34.2.93

Gunawan, A., C. Sumantri, & R. Juniarti. 2017. Gen dan Keragaman Genetik Ternak. IPB Press, Indonesia.

Hartl, D. L. & A. G. Clark. 1997. Principle of Population Genetic. Sinauer Associates, MA, United Kingdom.

Hou, G., H. Meng, G. Xue, L. Junya, G. Huijiang, R. Hongyan, & X. Shangzhong. 2011. Association of Calpain 1 (CAPN1) and HRSP12 allelic variants in beef cattle with carcass traits. Afr. J. Biotechnol. 10: 13714-13718. https://doi.org/10.5897/AJB11.338

Khasanah, H., A. Gunawan, R. Priyanto, M. F. Ulum, & Jakaria. 2016. Polymorphism of myostatin (MSTN) promoter gene and its association with growth and muscling traits in Bali cattle. Med Pet. 39: 95-103. https://doi.org/10.5398/medpet.2016.39.2.95

Korwin-Kossakowska, A., J. Wyszynska-Koko, G. Sender, A. Gajewska, M. Pierzchala, M. Kamyczek, & K. Kochman. 2009. Effect of the polymorphism in 5-UTR region of pig prolactin gene on prolactin gene expression and reproduction performance in the female pig. Neuro Endocrinol Lett. 30:221-226.

Mahrous, K. F., M. S. Hassanane, H. I. Shafey, M. A. Mordy, & H. E. Rushdi. 2016. Association between single nucleotide polymorphism in ovine Calpain gene and growth performance in three Egyptian sheep breeds. J. Genet. Eng. Biotechnol. 14:233-240. https://doi.org/10.1016/j.jgeb.2016.09.003

Manzoor, S., A. Nadeem, M. Javed, & M. E. Babar. 2013. Identification of single nucleotide polymorphism in 5’-UTR of CYP11B1 gene in Pakistani Sahiwal cattle. International Journal of Biotechnology and Bioengineering 7: 995-997.

McKenzy, G. W., R. Arora & J. G. Hickford. 2012. Genetic variation in the 5’UTR of the KRT2.13 gene of sheep. Anim. Sci. J. 83:194-198. https://doi.org/10.1111/j.1740-0929.2011.00933.x

Mignone, F., C. Gissi, S. Liuni, & G. Pasole. 2002. Untranslated regions of mRNAs. Rev. Genom. Biol. 3:0004.1-0.004.10. https://doi.org/10.1186/gb-2002-3-3-reviews0004

Miquel, M.C., E. Villarreal, C. Mezzadra, L. Melucci, L. Soria, P. Corva, & A. Schor. 2009. The association of CAPN1 316 marker genotypes with growth and meat quality traits of steers finished on pasture. Genet. Mol. Biol. 32:491-496. https://doi.org/10.1590/S1415-47572009000300011

Nei, M. & S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford Univ Press, United States of America.

Öner, Y., A. Keskin, H. Üstüner, D. Soysal, & V. Karakaş. 2017. Genetic diversity of the 3ꞌ and 5ꞌ untranslated regions of the HSP70.1 gene between native Turkish and Holstein Friesian cattle breeds. South Afric.Anim Sci. 47: 424-439. https://doi.org/10.4314/sajas.v47i4.2

Pinto, L. F. B., J. B. S. Ferraz, F. V.Meirelles, J. P. Eler, F. M. Rezende, M. E. Carvalho, H. B.Almeida, & R. C. G. Silva. 2010. Association of SNPs on CAPN1 and CAST genes with tenderness in Nellore cattle. Genet. Mol. Res. 9: 1431-1442. https://doi.org/10.4238/vol9-3gmr881

Pintos, D. & P. M. Corva. 2010. Association between molecular markers for beef tenderness and growth traits in Argentinian Angus cattle. Anim. Genet. 42:329-332. https://doi.org/10.1111/j.1365-2052.2010.02160.x

Prasojo, G., I. Arifiantini, & K. Mohamad. 2010. Korelasi antara lama kebuntingan, bobot lahir dan jenis kelamin pedet hasil inseminasi buatan pada sapi bali. J. Vet. 11: 41-45.

Sahu, A.R., V. Jeichitra, R. Rajendran, & A. Raja. 2016. Genetic polymorphism in 5’UTR of myostatin (MSTN) gene in Nilagiri sheep. Journal of Livestock Biodiversity 6:7-10. https://doi.org/10.5958/2277-940X.2016.00013.9

Shen, H., S. H.Zhao, J. H.Cao, X. Y. Li, & B. Fan. 2011. Porcine MuRF2 and MuRF 3: molecular cloning, expression and association analysis with muscle production traits. Mol. Biol. Rep. 38:5115-5123. https://doi.org/10.1007/s11033-010-0659-0

Sjakste, T., N. Paramonova, Z. Grislis, I. Trapina, & D. Kairisa. 2011. Analysis of the single-nucleotide polymorphism in the 5’UTR and part of intron I of the sheep mstn gene. DNA Cell Biol. 30: 433-444. https://doi.org/10.1089/dna.2010.1153

Sugimoto, M., T. Watanabe, & Y. Sugimoto. 2012. The molecular effects of a polymorphism in the 5’UTR of solute carrier family 44, member 5 that is associated with birth weight in Holsteins. PloS ONE. 7: 1-10. https://doi.org/10.1371/journal.pone.0041267

Tait, R. G., S. D. Shackelford, T. L. Wheeler, D. A. King, E. Casas, R. M. Thallman, T. P. L. Smith, & G. L. Bennett. 2014. µ-calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies. J. Anim. Sci. 92:456-466. https://doi.org/10.2527/jas.2013-7075


D. E. W. T. Sihite
R. Priyanto
Jakaria Jakaria
jakaria_karman@yahoo.co.id (Primary Contact)
Author Biography

D. E. W. T. Sihite, Magister Program in Animal Science, Faculty of Animal Science, IPB University (Bogor Agricultural University)

Department of Animal Production and Technology, Faculty of Animal Science, IPB University
SihiteD. E. W. T., PriyantoR., & JakariaJ. (2019). Polymorphism and Association of 5’UTR CAPN1 Gene with Growth Traits in Bali Cattle by PCR-RFLP. Tropical Animal Science Journal, 42(3), 175-179. https://doi.org/10.5398/tasj.2019.42.3.175

Article Details