Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus

Authors

  • Laily Isnaini Rahmawati SMPN 27 Kota Malang, Jl. Lesanpuro No.24b, Lesanpuro, Kedungkandang District, Malang City, East Java, 65138
  • Abdul Basith Study Program of Biology Education, University of KH. Abdul Wahab Hasbulloh, Jl. Garuda No.9, Tambak Rejo, Jombang District, Jombang Regency, East Java,61419, Indonesia ; Indonesian Genetic and Biodiversity Community, Jln. Ikan Mujair 1, Lowokwaru District, Malang City, East Java
  • Fitria Lestari Study Program of Biology Education, University of PGRI Silampari, Jln. Mayor Toha, Air Kuti, Lubuk Linggau Timur I District, Lubuklinggau City, South Sumatera, 31625

DOI:

https://doi.org/10.26740/jrba.v5n1.p37-42

Abstract

This study focused on the application of microsatellite markers at the INRA032 locus for genetic diversity assessment in buffalo (Bubalus bubalis) populations in Pacitan and Tuban Regencies, East Java, Indonesia. The total number of samples used was 16, each population represented by 8 samples. Genetic diversity assessment parameters include allele frequency, the Polymorphism Information Content (PIC) and heterozygosity. The results showed that based on the INRA032 locus, the Tuban buffalo population had a higher allele frequency range (0.08 to 0.33) than the Pacitan population (0.18 to 0.31). The average PIC value in both populations was 0.39, so it can be concluded that the INRA032 locus is informative enough to detect polymorphisms in both populations. The percentage heterozygosity of the Pacitan buffalo population is 88%, which is higher than the Tuban population at 50%, suggesting that the genetic diversity of the two populations is still quite high despite the decreasing trend in population numbers.

References

Afrida, I. R., Amin, M. & Ghofur. (2014). Pengembangan bahan ajar matakuliah genetika populasi berbasis penelitian keragaman genetik kerbau lokal Tana Toraja dan Lombok. Jurnal Kependidikan, 13(4), 337–347.

Amin, A. & Lestari, U. (2014). Identifikasi keragaman genetik kerbau lokal populasi Jawa Timur dan Nusa Tenggara Barat berbasis mikrosatelit sebagai model pengembangan konservasi kerbau secara ex situ. Prosiding Seminar Nasional XI Pendidikan Biologi FKIP UNS, 11(1), 528–533.

Amin, M. (2012). Genetic variation of local (Bubalus bubalis) buffalo in West Nusa Tenggara based on microsatellite loci. Proceeding of the 5th Indonesian Biotechnology Conference: An International Forum, 374–383.

Botstein, D., White, R. L., Skolnick, M. & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314–331.

BPS-Statistics of East Java. (2018). Populasi kerbau menurut Kabupaten/Kota di Jawa Timur tahun 2009-2017, (https://jatim.bps.go.id/statictable/2018/10/18/1298/populasi-kerbau-menurut-kabupaten-kota-di-jawa-timur-2009-2017-ekor-.html, accessed on November 8, 2022.

Brenig, B. & Schütz, E. (2016). Recent development of allele frequencies and exclusion probabilities of microsatellites used for parentage control in the German Holstein Friesian cattle population. BMC Genetics, 17(18), 1–9. https://doi.org/10.1186/s12863-016-0327-z.

Buitenhuis, A. J., Lund, M. S., Thomasen, J. R., Thomsen, B., Nielsen, V. H., Bendixen, C. & Guldbrandtsen, B. (2007). Detection of quantitative trait loci affecting lameness and leg conformation traits in Danish Holstein cattle. Journal of Dairy Science, 90(1), 472–481. https://doi.org/10.3168/jds.S0022-0302(07)72649-8.

Director General of Livestock and Animal Health. (2021). Livestock and animal health statistics 2021. Ministry of Agricultural Affairs of the Republic of Indonesia, Jakarta.

Gillespie, J. H. (2004). Population genetics: a concise guide (2 edition). Baltimore, Md.: The Johns Hopkins University Press.

Gunawan & Romjali, E. (2009). Program pengembangan perbibitan kerbau. Prosiding Seminar dan Lokakarya Nasional Kerbau, 3–10.

Hale, M. L., Burg, T. M., & Steeves, T. E. (2012). Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PloS one, 7(9), e45170. https://doi.org/10.1371/journal.pone.0045170.

Harder, B., Bennewitz, J., Reinsch, N., Thaller, G., Thomsen, H., Kühn, C., Schwerin, M., Erhardt, G., Förster, M., Reinhardt, F. & Kalm, E. (2006). Mapping of quantitative trait loci for lactation persistency traits in German Holstein dairy cattle. Journal of Animal Breeding and Genetics, 123(2), 89–96. https://doi.org/10.1111/j.1439-0388.2006.00577.x.

Kayang, B. B., Inoue-Murayama, M., Hoshi, T., Matsuo, K., Takahashi, H., Minezawa, M., Mizutani, M. & Ito, S. (2002). Microsatellite loci in japanese quail and cross-species amplification in chicken and guinea fowl. Genetics, Selection, Evolution, 34(2), 233–253. https://doi.org/10.1186/1297-9686-34-2-233.

Komariah, K., Burhanuddin, B. & Permatasari, N. (2019). Analisis potensi dan pengembangan kerbau lumpur di Kabupaten Serang. Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan, 6(3), 90–97.

Lathifah, A. S. (2016). Identifikasi variasi genetik kerbau Kudus berbasis mikrosatelit sebagai bahan ajar blended learning pada matakuliah TABM. Prosiding SNPBS (Seminar Nasional Pendidikan Biologi dan Saintek) Universitas Muhammadiyah Surakarta, 920–928.

Lestari, F. (2013). Identifikasi variasi genetik kerbau (Bubalus bubalis) lokal Sumatera Selatan berbasis mikrosatelit sebagai pengembangan media interaktif untuk pembelajaran Teknik Analisis Biologi Molekuler di Universitas Negeri Malang. Unpublished Thesis. Malang: State University of Malang.

Limiansi, K. (2015). Identifikasi variasi genetik kerbau (Bubalus bubalis) endemik lokal Sleman DIY berbasis mikrosatelit untuk pengembangan modul Teknik Analisis Biologi Molekuler di Universitas Negeri Yogyakarta. Unpublished Thesis. Malang: State University of Malang.

Liu, J-E, Qiao, C-L & Hou, X. (2000). A useful population genetics software package–GENEPOP (Version 3.1). Biodiversity Science, 08(2): 238–240.

MacHugh, D. E., Shriver, M. D., Loftus, R. T., Cunningham, P. & Bradley, D. G. (1997). Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics, 146(3), 1071–1086. https://doi.org/10.1093/genetics/146.3.1071.

Nuraini, H., Aditia, E. L. & Brahmantiyo, B. (2018). Meat Quality of Indonesian Local Cattle and Buffalo. In S. S. O., & S. J. Patil (Eds.), Bovine science–A key to sustainable development. IntechOpen. https://doi.org/10.5772/intechopen.79904.

Putman, A. I. & Carbone, I. (2014). Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecology and evolution, 4(22), 4399–4428. https://doi.org/10.1002/ece3.1305.

Sambrook, J., E. F. Fritsch & T. Maniatis. (1989). Molecular Cloning: A Laboratory Manual. 2nd ed. Plainview, N.Y.: Cold Spring Harbor Laboratory Press.

Serrote, C. M. L., Reiniger, L. R. S., Silva, K. B., Rabaiolli, S. M. D. S. & Stefanel, C. M. (2020). Determining the polymorphism information content of a molecular marker. Gene, 726(144175), 1–15. https://doi.org/10.1016/j.gene.2019.144175.

Sharma, R., Kumar, B., Arora, R., Ahlawat, S., Mishra, A. K. & Tantia, M. S. (2016). Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India. Meta gene, 8, 14–20. http://dx.doi.org/10.1016/j.mgene.2016.01.002.

Shete, S., Tiwari, H. & Elston, R. C. (2000). On estimating the heterozygosity and polymorphism information content value. Theoretical Population Biology, 57(3), 265–271. https://doi.org/10.1006/tpbi.2000.1452.

Sukri, A. (2014). Analisis filogenetik kerbau lokal lombok tengah (Bubalus bubalis) berdasarkan penanda DNA mikrosatelit. Jurnal Florea, 1(2), 52–55. http://doi.org/10.25273/florea.v1i2.392.

Sukri, A., Dewi, I. N., Primawati, S. B., Wangiyana, I. G. A. S, Muttaqin, Z. & Winaya, A. (2022). Revealing the genetic diversity of Sumbawa endemic horse using microsatellite-based DNA fingerprint. Biodiversitas, 23(8), 4153–4159. https://doi.org/10.13057/biodiv/d230837.

Vaiman, D., Mercier, D., Moazami-Goudarzi, K., Eggen, A., Ciampolini, R., Lépingle, A., Velmala, R., Kaukinen, J., Varvio, S. L. & Martin, P. (1994). A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism. Mammalian Genome, 5(5), 288–297. https://doi.org/10.1007/BF00389543.

Vanessa, R, Prastowo, S, Nugroho, T, Widyas, N, Susilowati, A. & Sutarno. (2018). Microsatellite selection candidate associated with reproduction trait in Indonesian Friesian Holstein using published studies. AIP Conference Proceedings 2014, 020055-1–02055-2. https://doi.org/10.1063/1.5054459.

Viryanski, D. (2019). Microsatellite markers–a tool for molecular characterization of cattle genetic resources. Bulgarian Journal of Agricultural Science, 25(1), 158–165.

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Published

2023-03-31

How to Cite

Rahmawati, L. I., Basith, A., & Lestari, F. (2023). Genetic Profile of Local Buffalo (Bubalus bubalis) Populations in Pacitan and Tuban, East Java, Indonesia Measured by the Molecular Marker of INRA032 Locus . Jurnal Riset Biologi Dan Aplikasinya, 5(1), 37–42. https://doi.org/10.26740/jrba.v5n1.p37-42

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