Allelic and Genotypic Distribution in Single Nucleotide Polymorphism (SNP) G.676A > G of Melanocortin-1 Receptor (MC1R) Gene in Indonesian Goat Breeds

Subject Areas : Camel

د. ماهارانی ¹ , اس. الیسر ² , آ.جی.اس. بودیساتریا ³ , آ. باتوبارا ⁴ , د.ن.اچ. هاریونو ⁵ , آ.پی.ز.ن.ل. ساری ⁶

1 - Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna 3, Bulaksumur, Yogyakarta 55281, Indonesia
2 - Indonesian Goat Research Institute Sei Putih, Galang 20585, North Sumatera, Indonesia
3 - Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna 3, Bulaksumur, Yogyakarta 55281, Indonesia
4 - Indonesian Goat Research Institute Sei Putih, Galang 20585, North Sumatera, Indonesia
5 - Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna 3, Bulaksumur, Yogyakarta 55281, Indonesia
6 - Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Jl. Fauna 3, Bulaksumur, Yogyakarta 55281, Indonesia

Received: 2018-12-18 Accepted : 2019-02-16 Published : 2019-12-01

Keywords: local goat, allele distribution, <i>MC1R</i> gene,

Abstract :

The melanocortin-1 receptor (MC1R) gene has been investigated by many studies regarding the pigmentation variation in various species. In order to determine its allelic and genotypic distribution, we sequenced the goat MC1R gene from 78 individuals in ten populations (Gembrong, Senduro, Ettawa Grade, Boerawa, Boerka, Kosta, Samosir, Muara, Boer and Kacang). Direct sequencing method was performed to detect the single nucleotide polymorphisms (SNPs). Three SNPs (g.676A>G, g.748G>T and g.801C>G) were identified in the gene target. The SNP g.676 A > G was used to genotype the investigated animals by using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method with EarI restriction enzyme. In all studied populations, the A allele had the highest frequency (83%) and the G allele had the lowest frequency (17%). The frequency of homozygous AA genotype was the highest (90%) in Kacang goats, while that of heterozygous AG genotype was fixed in Senduro and Boer goats. Analysis of observed heterozygosity, expected heterozygosity, Nei’s (1973) expected heterozygosity, and Shannon index were found to be 0.3425, 0.2858, 0.2838 and 0.4578, respectively.The distribution of MC1R gene in overall breeds confirmed with Hardy-Weinberg equilibrium (P>0.05).

References:

Ditjenpkh. (2017). Livestock and Animal Health Statistics. Directorate General of Livestock and Animal Health Service, Jakarta, Indonesia.

Chen S., Huang Y., Zhu Q., Fontanesi L., Yao Y. and Liu Y. (2009). Sequence characterization of the MC1R gene in yak (Poephagus grunniens) breeds with different coat colors. J. Biomed. Biotechnol. 2009, 1-6.

Fontanesi L., Barreti F., Riggio V., Dall’Olio S., Gonzales E.G., Finocchiaro R., Davoli R., Russo V. and Partolano B. (2009). Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: Association with red and black colour phenotypes but with unpected evidences. BMC Genet. 10, 1-12.

Jackson I.J. (1997). Homologous pigmentation mutations in human, mouse and other model organisms. Hum. Mol. Genet. 6, 1613-1624.

Kijas J.M., Wales R., Tornsten A., Chardon P., Moller M. and Andersson L. (1998). Melanocortin 1 receptor (MC1R) mutations and coat color in pigs. Genetics. 150, 1177-1185.

Li B., He X., Zhao Y., Bai D., Shiraigo W., Zhao Q. and Manglai D. (2017). Regulatory pathway analysis of coat color genes in Mongolian horses. Hereditas. 155, 13-23.

Maharani D., Budisatria I.G.S. and Panjono P. (2016). Identification of single nucleotide polymorphisms and allele distribution of MC1R gene in different head and neck color of Ettawa grade goat. Asian J. Anim. Sci. 10, 219-233.

Nei M. (1973). Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA. 70, 3321-3323.

Rieder S., Taourit S., Mariat D., Langlois B. and Guérin G. (2001). Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus). Mamm. Genome. 12, 450-455.

Rouzaud F., Martin J., Gallet P.F., Delourme D., Goulemotleger V., Amigues Y., Menissier F., Levezie H., Julien R. and Oulmouden A. (2000). A first genotyping assay of French cattle breeds based on a new allele of the extension gene encoding the melanocortin-1 receptor (MC1R). Genet. Sel. Evol. 32, 511-520.

Valverde P., Healy E., Jackson I.J., Rees J.L. and Thody A.J. (1995). Variants of the melanocyte stimulating hormone receptor gene are associated with red hair and fair skin in humans. Nat. Genet. 11, 328-330.

Vage D.I., Klungland H., Lu D. and Cone R.D. (1999). Molecular and pharmacological characterization of dominant black coat color in sheep. Mamm. Genome. 10, 39-43.

Wu Z.L., Li X.L., Liu Y.Q., Gong Y.F., Liu Z.Z., Wang X.J., Xin T.R. and Ji Q. (2006). The red head and neck of Boer goats may be controlled by recessive allele of the MC1R gene. Anim. Res. 55, 313-323.

Yeh F.C., Rong-Cai Y. and Tim B. (1999). POPGENE VERSION Microsoft Window-based Freeware for Population Genetic Analysis. University of Alberta and Tim Boyle, Centre for International Forestry Research, Bogo.