Association of SNP g.232 G>T Calpain Gene with Growth and Live Meat Quality Prediction using Ultrasound Images in Bali Cattle

Dairoh Dairoh, Jakaria Jakaria, Mokhamad Fakhrul Ulum, Andi Baso Lompengeng Ishak, Cece Sumantri


Bali cattle (Bos javanicus) are native Indonesian cattle domesticated from banteng (Bibos banteng). Genes that have an important role in meat quality are calcium-activated neutral protease genes, known as calpains (CAPN). The objective of this study was to evaluate the polymophisms of calpain gene SNP g.232 G>T by PCR-RFLP technique and its influence on growth trait and meat quality detected by ultrasound imaging in the form of longissimus dorsi thickness (LDT), back fat thickness (BFT), marbling score (MS), and intramuscular fat percentage (PIMF) in Bali cattle. The polymorphisms of CAPN1 gene were analyzed by PCR-RFLP using BglII restriction enzyme in Bali cattle (n=52 cattle). The ultrasound images of longissimus dorsi muscle were carried out transversally and longitudinal between 12th -13th thoracic vertebrae then analyzed by Image-J NIH software. The result showed that the SNP g.232 G>T of CAPN1 gene was polymorphic in Bali cattle. SNP g.232 G>T of CAPN1 gene in Bali cattle has higher diversity which was showed of 0.48 heterozygosity value and was in Hardy-Weinberg equilibrium. The polymorphisms of SNP g.232 G>T was associated significantly (P<0.05) with bodyweight at 730 days, marbling score (MS), and intramuscular fat percentage (PIMF) in Bali cattle. It suggests that the CAPN1 gene in Bali cattle is a candidate for Marker Assisted Selection (MAS), which influences body weight at 730 days, marbling score, and percentage of intramuscular fat.


Bali cattle, Calpain gene, Growth, Meat quality, Ultrasound


Allendorf FW, Luikart GH, Aitken SN. 2013. Conservation and the Genetics of Population. 2nd ed. West Sussex (UK): Wiley-Blackwell.

Araujo PR, Yoon K, Ko D, Smith AD, Qiao M, Suresh U, Burns SC, Penalva LOF. 2012. Before it gets started: regulating translation at the 5′ UTR. Comp Funct Genomics. 2012:1–8. DOI: 10.1155/2012/475731.

Avilés C, Juárez M, Peña F, Domenech V, Clemente I, Molina A. 2013. Association of single nucleotide polymorphisms in&nbsp;CAPN1 and CAST genes with beef tenderness from&nbsp;Spanish commercial feedlots. Czech J Anim Sci. 58:479–487. DOI: 10.17221/6997-CJAS.

Bonin MN, Ferraz JBS, Pedrosa VB, Silva SL, Gomes RC, Cucco DC, Santana MHA, Campos JHA, Barbosa VN, Castro FSF, et al. 2015. Visual body-scores selection and its influence on body size and ultrasound carcass traits in Nellore cattle1. J Anim Sci. 93:5597–5606. DOI: 10.2527/jas.2015-9280.

Cheong H, Yoon D-H, Park B, Kim L, Bae J, Namgoong S, Lee H, Han C, Kim J, Cheong I-C, Shin H. 2008. A single nucleotide polymorphism in CAPN1 associated with marbling score in Korean cattle. BMC Genet. 9:33. DOI: 10.1186/1471-2156-9-33.

Chung H, Shin S, Chung E. 2014. Effects of genetic variants for the bovine calpain gene on meat tenderness. Mol Biol Rep. 41:2963–2970. DOI: 10.1007/s11033-014-3152-3.

Coria MS, Carranza PG, Palma GA. 2018. Calpain system in meat tenderization: A molecular approach. Rev MVZ Córdoba. 23:6523–6536. DOI: 10.21897/rmvz.1247.

Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JE. 2017. Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Res. 45:6981–6992. DOI: 10.1093/nar/gkx430.

[DGLS] Directorate General of Livestock Service. 2003. National Report on Animal Genetics Resources in Indonesia. Jakarta (Indones): Directorate General of Livestock Services.

Duff C, Van Der Werf J, Parnell P, Clark S. 2018. Prediction of carcass intramuscular fat and marbling scoroe using live ultrasound in Australian Angus. In: 64th Int Congr Meat Sci Technol. Sidney (AUS): Australian Meat Processor Corporation; p. 1–2.

EnsemblGenomes. 2021. 5 prime UTR variant of bovine CAPN gene (ensemble SNP reference). [accessed 2021 Mar 4]. :


Gu W, Xu Y, Xie X, Wang T, Ko J-H, Zhou T. 2014. The role of RNA structure at 5′ untranslated region in microRNA-mediated gene regulation. RNA. 20:1369–1375. DOI: 10.1261/rna.044792.114.

Hafid H, Hasnudi, Bain HA, Nasiu F, Inderawati, Patriani P, Ananda SH. 2019. Effect of fasting time before slaughtering on body weight loss and carcass percentage of Bali cattle. In: IOP Conf Ser Earth Environ Sci. 260: p. 012051. DOI: 10.1088/1755-1315/260/1/012051.

Hardjosubroto W. 1994. Aplikasi Pemuliabiakan Ternak di Lapangan. Jakarta (Indones): Gramedia Widiasarana Indonesia.

Işık R. 2019. The identification of novel single nucleotide polymorphisms in Calpain1 (CAPN1) gene of Japanese Quail (Coturnix coturnix Japonica). J Anim Prod. 60:25–29. DOI: 10.29185/hayuretim.529317.

Jakaria J, Khasanah H, Priyanto R, Baihaqi M, Ulum MF. 2017. Prediction of meat quality in Bali cattle using ultrasound imaging. J Indones Trop Anim Agric. 42:59. DOI: 10.14710/jitaa.42.2.59-65.

Jakaria, Ulum M, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas J Biol Divers. 21:2971–2976. DOI: 10.13057/biodiv/d210713.

Juszczuk-Kubiak E, Flisikowski K, Wicińska K. 2010. A new SNP in the 3′UTR region of the bovine calpain small subunit (CAPNS1) gene. Mol Biol Rep. 37:473–476. DOI: 10.1007/s11033-009-9654-8.

Khan TA, Nanjundan GK, Basvarajaih DM, Azharuddin M. 2018. Statistical model derivation and extension of Hardy – Weinberg Equilibrium. Int J Curr Microbiol Appl Sci. 7:2402–2409. DOI: 10.20546/ijcmas.2018.710.279.

Koohmaraie M, Kent MP, Shackelford SD, Veiseth E, Wheeler TL. 2002. Meat tenderness and muscle growth: Is there any relationship?. Meat Sci. 62: 345-352.

Lee B, Choi YM. 2019. Correlation of marbling characteristics with meat quality and histochemical characteristics in longissimus thoracis muscle from Hanwoo steers. Food Sci Anim Resour. 39:151–161. DOI: 10.5851/kosfa.2019.e12.

Lee JS, Kim JM, Hong JS, Lim KS, Hong KC, Lee YS. 2012. Effects of polymorphisms in the 30 untranslated region of the porcine PPARGC1A gene on muscle fiber characteristics and meat quality traits. Mol. Biol. Rep. 39:3943–3950. DOI: 10.1007/s11033-011-1173-8.

Lian T, Wang L, Liu Y. 2013. A new insight into the role of calpains in post-mortem meat tenderization in domestic animals: A review. Asian-Australasian J Anim Sci. 26:443–454. ADOi: 10.5713/ajas.2012.12365.

Lim K-S, Kim J-M, Lee E-A, Choe J-H, Hong K-C. 2014. A candidate single nucleotide polymorphism in the 3′ untranslated region of stearoyl-CoA desaturase gene for fatness quality and the gene expression in Berkshire Pigs. Asian-Australasian J Anim Sci. 28:151–157. DOI: 10.5713/ajas.14.0529.

Lozano MSR, Alfaro-Zavala S, Sifuentes-Rincón AM, Parra-Bracamonte GM, Varela DB, Medina RDM, Pérez Linares CP, Rincón FR, Escalante AS, Urrutia GT, Saavedra FF. 2016. Meat tenderness genetic and genomic variation sources in commercial beef cattle. J Food Qual. 39:150–156. DOI: 10.1111/jfq.12185.

Malheiros JM, Balsassini WA, Dias VAD, Silva JAI V., Curi RA, Chardulo LAL. 2015. Chemical and sensory meat characteristics of Nellore cattle (Bos indicus) finished with different levels of backfat thickness in the longissimus thoracis muscle. Bol Indústria Anim. 72:341–348. DOI: 10.17523/bia.v72n4p341.

Martojo H. 2012. Indigenous Bali cattle is most suitable for sustainable small farming in Indonesia. Reprod Domest Anim. 47:10–14. DOI: 10.1111/j.1439-0531.2011.01958.x.

Mayr C. 2017. Regulation by 3′-Untranslated Regions. Annu Rev Genet. 51:171–194. DOI: 10.1146/annurev-genet-120116-024704.

Moon SS, Hwang IH, Jin SK, Lee J, Joo ST, Park GB. 2003. Carcass traits determining quality and yield grade of Hanwoo steers. AJAS. 16:1049. DOI: 10.5713/ajas.2003.1049.

[NCBI] National Center For Biotechnology Information. 2021. Bos Taurus micromolar activated neutral protease 1 (CAPN1) gene, complete cds. [accessed 2021 Mar 4].

Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. 1st ed. New Jersey (USA): Oxford University Press.

Newlacil I, Demkowicz M, Paczyńska K, Kuropka P, Szulc T. 2013. Factors affecting ultrasound intramuscular fat content in musculus longissimus dorsi of beef bulls estimated with bia pro plus software. Ann Anim Sci. 13:633–644. DOI: 10.2478/aoas-2013-0023.

Nogalski Z, Pogorzelska-Przybyłek P, Sobczuk-Szul M, Nogalska A, Modzelewska-Kapituła M, Purwin C. 2018. Carcass characteristics and meat quality of bulls and steers slaughtered at two different ages. Ital J Anim Sci. 17:279–288. DOI: 10.1080/1828051X.2017.1383861.

[OECD-FAO] Organization for Economic Co-Operation and Development and Agriculture Organization on The United Natios. 2020. FAO Agriculture Product [Internet]. [accessed 2021 Jan 27].

Pintos D, Corva PM. 2011. Association between molecular markers for beef tenderness and growth traits in Argentinian Angus cattle. Anim Genet. 42:329–332. DOI: 10.1111/j.1365-2052.2010.02160.x.

Pogorzelska-Przybylek P, Nogalski Z, Bialobrzewski I, Wielgosz-Groth Z, Sobczuk-Szul M. 2015. Prediction of the fattening performance of young slaughter cattle based on selected live animal measurement. Acta Sci Pol Zootech. 14:67–84.

Robinson DL, McDonald CA, Hammond K, Turner JW. 1992. Live animal measurement of carcass traits by ultrasound: assessment and accuracy of sonographers. J Anim Sci. 70:1667–1676. DOI: 10.2527/1992.7061667x.

Salamena JF, Papilaja J. 2010. Characterization and genetic relationships analysis of buffalo population in MOA island of South-East West Maluku regency of Maluku Province. J Indones Trop Anim Agric. 35:75–82. DOI: 10.14710/jitaa.35.2.75-82.

Schuster SL, Hsieh AC. 2019. The untranslated regions of mRNAs in cancer. Trends in Cancer. 5:245–262. DOI: 10.1016/j.trecan.2019.02.011.

Sharma R, Kumar B, Arora R, Ahlawat S, Mishra AK, Tantia MS. 2016. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India. Meta Gene. 8:14–20. DOI: 10.1016/j.mgene.2016.01.002.

Sheriff O, Alemayehu K. 2018. Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs: A review.González-Redondo P, editor. Cogent Food Agric. 4:1459062. DOI: 10.1080/23311932.2018.1459062.

Sihite DEWT, Priyanto R, Jakaria J. 2019. Polymorphism and Association of 5’UTR CAPN1 Gene with Growth Traits in Bali Cattle by PCR-RFLP. Trop Anim Sci J. 42:175–179. DOI: 10.5398/tasj.2019.42.3.175.

Silva SR, Cadavez VP. 2012. Real-time ultrasound (RTU) imaging methods for quality control of meats. In: Comput Vis Technol Food Beverage Ind. Elsevier; p. 277–329. DOI: 10.1533/9780857095770.3.277.

Steri M, Idda ML, Whalen MB, Orrù V. 2018. Genetic variants in mRNA untranslated regions. Wiley Interdiscip Rev RNA. 9:e1474. DOI: 10.1002/wrna.1474.

Suryanto E, Bulkaini B, Ashari A, Karda I. W. 2014. Carcass quality, marbling and cholesterol content of male bali cattle fed fermented cocoa shell. J Indones Trop Anim Agric. 39:249–255. DOI: 10.14710/jitaa.39.4.249-255.

Ulum M, Suprapto E, Jakaria. 2014. Ultrasunograpgy image or longissimus dorci muscle of Bali cattle. In: KIVNAS PDHI XIII. Padang (Indones): Perhimpunan Dokter Hewan Indonesia; p. 368–369.

Wang F, Zhang Y, Li J, Guo X, Cui B, Peng Z. 2016. Contribution of cross-links and proteoglycans in intramuscular connective tissue to shear force in bovine muscle with different marbling levels and maturities. LWT - Food Sci Technol. 66:413–419. DOI: 10.1016/j.lwt.2015.10.059.

Wawo AA. 2018. Effect of Bulls on Birth Rate and Birth Weight by Using Semi-Intensive Bali Cattle Maintenance. Chalaza J Anim Husb. 3:24–28. DOI: 10.31327/chalaza.v3i1.539.

Xin J, Zhang L, Li Z, Liu X, Jin H, Yan C. 2010. Association of polymorphisms in the calpain I gene with meat quality traits in Yanbian Yellow Cattle of China. Asian-Australasian J Anim Sci. 24:9–16. DOI: 10.5713/ajas.2011.90407.

Zhang L, Ma X, Xuan J, Wang H, Yuan Z, Wu M, Liu R, Zhu C, Wei C, Zhao F, Du L. 2016. Identification of MEF2B and TRHDE gene polymorphisms related to growth traits in a new Ujumqin sheep population.Zhang Q, editor. PLoS One. 11:e0159504. DOI: 10.1371/journal.pone.0159504.

Zhang R, Li X. 2011. Association between IGF-IR, m-calpain and UCP-3 gene polymorphisms and growth traits in Nanyang cattle. Mol Biol Rep. 38:2179–2184. DOI: 10.1007/s11033-010-0346-1.


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