Restriction Mapping of MC4R Gene on Bali Cattle (Bos sondaicus) as Genetic Marker for Breeding Program in Compared to Bos taurus and Bos indicus

Yoga Cipta Perdana(1), Tety Hartatik(2*)

(1) Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna No.3, Yogyakarta, Indonesia
(2) Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna No.3, Yogyakarta, Indonesia
(*) Corresponding Author


MC4R is a gene that has potential effects on growth traits such as body weight and feed intake. The usage of single nucleotide polymorphism (SNPs) in melanocortin-4 receptor (MC4R) as selection markers could help achieve effectiveness in the breeding program. This study aimed to analyze the restriction mapping based on SNPs in the MC4R gene for Bali cattle (Bos sondaicus) compared to various breeds of cattle. Partial MC4R gene was amplified using a primer (F: 5’-ACC AAT GTC AGT GAG TCC CC- 3’ and R: 5’-CTT CAT GTT GGC GCC CTG-3’) with a polymerase chain reaction (PCR) method. Genotype and allele frequencies were calculated using Chi-Square test and analyzed with Hardy–Weinberg law. Restriction enzyme was analyzed using Nebcutter V.2 to see the association between SNPs and the recognition site of restriction enzyme. The result showed four SNPs g.554 T>C, g.634 G>T, g.673 C>T, and g.742 G>A were found in the exon region. SNP g.742 G>A was found as a heterozygote genotype and the rest are SNP g.554 T>C, g.634 G>T, and g.673 C>T were found as homozygote genotypes. All SNPs were synonymous which did not change the amino acid translated. Three restriction enzymes were identified as MmeI, TspRI, and BsrI which attach to SNPs g.554 T>C, g.634 G>T, and g. 742 G>A respectively.  SNPs found notably g. 742 G>A can be used as genetic markers associated with growth traits for further research on Bali cattle.



Bali cattle; MC4R; Restriction enzyme; SNP

Full Text:



Albakri, M.W. & Hartatik, T., 2021. Restriction mapping of melanocortin 4 receptor in Bos taurus and Bos indicus based on GenBank data. Research Journal of Biotechnology, 16(1), pp.107–112. Retrived from

Chuang, L.Y. et al., 2008. Restriction Enzyme Mining for SNPs in Genomes. Anticancer Research, 28, pp.2001–2008. Retrieved from

Fathoni, A. et al., 2020. Association between the Melanocortin‐4 Receptor (MC4R) Gene Polymorphisms and Growth Trait in Sumba Ongole Cattle. Iranian Journal of Applied Animal Science, 10(4), pp.603–609. doi: 20.1001.1.2251628.2020.

Hunt, R. et al., 2009. Silent (Synonymous) SNPs: Should We Care About Them?. Methods Mol Biol, 578, pp.23–39. doi: 10.1007/978-1-60327-411-1_2

Koren, A. et al., 2012. Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation. The American Journal of Human Genetics, 91, pp.1033–1040. doi: 10.1016/j.ajhg.2012.10.018

Kurniawati, N. et al., 2021. Identification of MC4R gene markers in Bligon goats with single and twin birth type. The 2nd International Conference on Agriculture and Bio-industry, 667, pp.1–6. doi: 10.1088/1755-1315/667/1/012074

Latifah, L. et al., 2020. Polymorphism of MC4R gene associated with feed intake, nutrient digestibility, ADG and FCR at post-weaning in Bligon goats. Journal of the Indonesian Tropical Animal Agriculture, 45(3), pp.173–180. doi: 10.14710/jitaa.45.3.173-180

Liu, H. et al., 2009. Mutations of MC4R gene and its association with economic traits in Qinchuan cattle. Mol Biol Rep, 37, pp.535–540. doi: 10.1007/s11033-009-9706-0

Maharani, D. et al., 2018. Identification of MC4R gene and its association with body weight and body size in Kebumen Ongole Grade cattle. Journal of the Indonesian Tropical Animal Agriculture, 43(2), pp.87–93. doi: 10.14710/jitaa.43.2.87-93

Prihandini, P.W. et al., 2019. Melanocortin-4 Receptor (MC4R) gene polymorphism and its effect on growth traits in Madura cattle. Journal of the Indonesian Tropical Animal Agriculture, 44(1), pp.38–46. doi: 10.14710/jitaa.44.1.38-46

Switonski, M. et al., 2013., Family of melanocortin receptor (MCR) genes in mammals—mutations, polymorphisms and phenotypic effects. J. Appl Genetics, 54, pp.461–472. doi: 10.1007/s13353-013-0163-z

Yang, Y., 2011. Structure, function and regulation of the melanocortin receptors. European Journal of Pharmacology, 660(1), pp.125–130. doi: 10.1016/j.ejphar.2010.12.020


Article Metrics

Abstract views : 459 | views : 354


  • There are currently no refbacks.

Copyright (c) 2022 Journal of Tropical Biodiversity and Biotechnology

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Editoral address:

Faculty of Biology, UGM

Jl. Teknika Selatan, Sekip Utara, Yogyakarta, 55281, Indonesia

ISSN: 2540-9581 (online)