Genetic Polymorphism of g.3768T>C loci of NRAMP1 gene in Kampung and KUB Chickens
DOI:
10.29303/jbt.v24i2.6682Published:
2024-05-14Downloads
Abstract
Natural Resistance-Associated Macrophage Protein 1 (NRAMP1) is a gene that regulates the body's resistance to illness. The genetic diversity of Kampung and KUB chicken population in Lombok island West Nusa Tenggara province was investigated based on g.3768T>C loci of NRAMP1 gene. Experimental animal consisted of 105 KUB and 67 Kampung chickens. The NRAMP1 gene polymorphisms in both population were identified using PCR-RFLP method. Genetic parameters of g.3768T>C loci were calculated using PopGene32. In this study, the locus g.3768T>C of the NRAMP1gene found three genotypes (TT, CT, CC) with the frequency of the C allele was higher than the T allele, respectively 0.709 and 0.210 in Kampung chicken, and 0.738 and 0.262 in KUB chicken. The mean value of observed heterozygosity (Ho) and expected heterozygosity (He) of g.3768T>C loci in both populations revealed low to medium genetic diversity, with the values 0.222 and 0.400, respectively. The mean value of observed heterozygosity is lower than expected, indicating that the population is heading towards a heterozygosity deficit and proving that the two populations are not in Hardy-Weinberg equilibrium. The mean PIC value of the NRAMP1 gene (g.3768T>C) in both chicken population was 0.319 and classified as fairly informative (0.50 > PIC > 0.25). Meanwhile, the value of the genetic differentiation index (Fst) for Kampung and KUB chicken population were 0.385 and 0.433, indicating that there is differentiation between two chicken population at the observed loci.
Keywords:
Fst and chickens, heterozygosity, NRAMP1 gene, polymorphism.References
Al-Koofee, D. A., & Mubarak, S. M. (2019). Genetic polymorphisms. The Recent Topics in Genetic Polymorphisms, 1-10.
Ardiyana, M., Gunawan, A., Murtini, S., Sartika, T., & Sumantri, C. (2020). Polymorphisms and associations of the Nramp-1 and inos genes on Newcastle disease and Salmonella enteritidis resistances in sensi-1 Agrinak Chickens. Tropical Animal Science Journal, 43(2), 95-102. https://www.doi.org/10.5398/tasj.2020.43.2.95
Barrandeguy, M. E., & García, M. V. (2021). The sensitiveness of expected heterozygosity and allelic richness estimates for analyzing population genetic diversity. Genetic variation.
Carcò, G., Grajewski, B., Cassandro, M., Lisowski, M., & Szwaczkowski, T. (2018). Genetic variability of some Italian and Polish duck breeds. Italian Journal of Animal Science, 17(4), 899-906. https://doi. org/10.1080/1828051X.2018.1436006
Desmond AU, Olajide AK and Olufunmilayo OB. (2019). Sequence Variability in the NRAMP1 Gene among Indigenous and Exotic Chicken Types. Makara J Sci., 23(2): 103-108.
Calenge, F., Kaiser, P., Vignal, A., & Beaumont, C. (2010). Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review. Genetics Selection Evolution, 42, 1-11.
Hadrawi, J., Gunawan, A., Ulupi, N., Darwati, S., & Sumantri, C. (2016). Association analysis of NRAMP1 gene related to resistance against Salmonella pullorum infection in Kampung Chicken.
Hasnelly, Z., Rinaldi dan Suwardih. 2006. Penangkaran dan Perbibitan Ayam Merawang di Bangka Belitung. Lokakarya Nasional. Inovasi Teknologi Dalam Mendukung Usaha Ternak Unggas Berdaya Saing. 7581. Semarang, 4 Agustus 2006.
He XM, Fang MX, Zhang ZT, Hu YS, Jia XZ, He DL, Liang SD, Nie QH and Zhang XQ. (2013). Characterization of chicken natural resistance-associated macrophage protein encoding genes (Nramp1 and Nramp2) and association with salmonellosis resistance. Genetics and Molecular Research, 12: 618-630.
Hu, G. S., Chang, G. B., Zhang, Y., Hong, J., Liu, Y., & Chen, G. H. (2011). Association analysis between polymorphisms of Nramp1 gene and immune traits in chicken. Journal of Animal and Veterinary Advances, 10(9), 1133-1136.
Handayani, I., Djaharuddin, I., Natzir, R., Arief, M., Ahmad, A., Hatta, M., ... & Massi, M. N. (2021). Contribution of NRAMP1 gene expression and protein level in pulmonary and latent TB infection in Indonesia. Journal of Applied Pharmaceutical Science, 11(8), 017-021.
Iskandar, S. O. F. J. A. N., & Susanti, T. R. I. A. N. A. (2007). Karakter dan manfaat ayam pelung di Indonesia. Wartazoa, 17(3), 128-136.
Janiszewski, L. N., Minson, M., Allen, M. A., Dowell, R. D., & Palmer, A. E. (2021). Characterization of global gene expression, regulation of metal ions, and infection outcomes in immune-competent 129S6 mouse macrophages. Infection and Immunity, 89(11).
Khan, M. M. H., Rafii, M. Y., Ramlee, S. I., Jusoh, M., Al Mamun, M., & Halidu, J. (2021). DNA fingerprinting, fixation-index (Fst), and admixture mapping of selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions using ISSR markers system. Scientific reports, 11(1), 14527.
Kramer, J., Malek, M., & Lamont, S. J. (2003). Association of twelve candidate gene polymorphisms and response to challenge with Salmonella enteritidis in poultry. Animal Genetics, 34(5), 339-348.
Li, T., Wang, L., Guo, C., Zhang, H., Xu, P., Liu, S., ... & Gao, Q. (2022). Polymorphisms of SLC11A1 (NRAMP1) rs17235409 associated with and susceptibility to spinal tuberculosis in a southern Han Chinese population. Infection, Genetics and Evolution, 98, 105202.
Li, X., Nie, C., Liu, Y., Chen, Y., Lv, X., Wang, L., ... & Qu, L. (2020). The genetic architecture of early body temperature and its correlation with Salmonella pullorum resistance in three chicken breeds. Frontiers in Genetics, 10, 1287.
Liu W, Kaiser MG, Lamont SJ. (2003). Natural resistanceassociated macrophage protein 1 gene polymorphisms and response to vaccine against or challenge with Salmonella enteritidis in young chicks. Poult. Sci. 82: 259-266..
Morin, P. A., Leduc, R. G., Archer, F. I., Martien, K. K., Huebinger, R., Bickham, J. W., & Taylor, B. L. (2009). Significant deviations from Hardy–Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Molecular Ecology Resources, 9(2), 498-504. https://doi.org/10.1111/j.1755-0998.2008.02502.x
Muhsinin, M., Ulupi, N., Gunawan, A., Wibawan, I. W. T., & Sumantri, C. (2016). Association of NRAMP1 polymorphisms with immune traits in Indonesian native chickens. Int J Poult Sci, 15, 401-406.
Nataamijaya, A. G. (2008). Karakteristik dan produktivitas ayam Kedu hitam. Bulletin Plasma Nutfah, 14: 85-89.
Nei M (1987). Molecular evolutionary genetics. Columbia University Press, New York, USA. https://doi.org/10.7312/ nei-92038
Peter, C., Bruford, M., Perez, T., Dalamitra, S., Hewitt, G., Erhardt, G., & Econogene Consortium. (2007). Genetic diversity and subdivision of 57 European and Middle‐Eastern sheep breeds. Animal genetics, 38(1), 37-44. https://doi.org/10.1111/j.1365-2052.2007.01561.x
Purwantini, D. (2010). An estimation of genetic variation in Indonesian local duck using microsatellite marker. Asian journal of poultry science, 4(4), 198-204. https://doi. org/10.3923/ajpsaj.2010.198.204
Sartika, T., & Iskandar, S. (2007). Mengenal Plasma Nutfah Ayam Indonesia. Balai Penelitian Ternak, Bogor, 140.
Seo, D., Bhuiyan, M. S. A., Sultana, H., Heo, J. M., & Lee, J. H. (2016). Genetic diversity analysis of South and East Asian duck populations using highly polymorphic microsatellite markers. Asian-Australasian Journal of Animal Sciences, 29(4), 471. https://doi. org/10.5713/ajas.15.0915
Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., dos Santos Rabaiolli, S. M., & Stefanel, C. M. (2020). Determining the polymorphism information content of a molecular marker. Gene, 726, 144175.
Tohidi, R., Idris, I., Panandam, J. M., & Hair-Bejo, M. (2011). Analysis of genetic variation of inducible nitric oxide synthase and natural resistance-associated macrophage protein 1 loci in Malaysian native chickens. African Journal of Biotechnology, 10(8), 1285-1289.
Vashchenko P, Saienko A, Sukhno V, Tsereniuk O, Babicz M, Shkavro N, Smołucha G, Łuszczewska-Sierakowska I. (2022). Association of NRAMP1 gene polymorphism with the productive traits of the Ukrainian Large White pig. Medycyna Weterynaryjna 78: 563-566.
Worku M. (2017). Expression of Natural Resistance Associate Macrophages Protein One (NRAMP1) in Ruminant Neutrophils. Agric. Res. & Tech. 12: 1-3.
Wu Y, Liu X, Hou S, Huang W (2008). Study on genetic diversity of six duck populations with microsatellite DNA. Asian-Aust. J. Anim. Sci., 21(6): 776-783. https://doi. org/10.5713/ajas.2008.70367
Yuan M, Zhang J, Gao, Yuan Z, Zhu Z, Wei Y, Wu T, Han J and Zhang Y. (2021). HMEJ-based safe-harbor genome editing enables efficient generation of cattle with increased resistance to tuberculosis. J. Biol. Chem. 296: 1-12.
License
Copyright (c) 2024 Maskur Maskur, Muhammad Muhsinin, Tapaul Rozi, Rahma Jan, L. Kasip
This work is licensed under a Creative Commons Attribution 4.0 International License.
Jurnal Biologi Tropis is licensed under a Creative Commons Attribution 4.0 International License.
The copyright of the received article shall be assigned to the author as the owner of the paper. The intended copyright includes the right to publish the article in various forms (including reprints). The journal maintains the publishing rights to the published articles.
Authors are permitted to disseminate published articles by sharing the link/DOI of the article at the journal. Authors are allowed to use their articles for any legal purposes deemed necessary without written permission from the journal with an acknowledgment of initial publication to this journal.
