Genetic Diversity of Indonesian Swamp Buffalo Based on Microsatellite Markers
Abstract
Indonesia has high genetic resources of local swamp buffalo with good adaptation across regions. However, these animals decline in both population and genetic quality. This research was conducted to study the genetic diversity of Indonesian swamp buffalo. A total of 199 DNA samples (swamp buffalo) from seven provincial populations were used in this study. Genetics identification used three microsatellite markers (CSSM66, ILSTS61, and ILSTS17). Microsatellites were visualized by Polyacrylamide Gel Electrophoresis (PAGE) 10% with silver staining method. Microsatellite data were analyzed using GenAlEx 6.41, Cervus 3.0, and POPTREE2 software. The results showed that a total of 9 alleles were found from the three loci. ILSTS61 had a high PIC (Polymorphism Information Content) compared to the other loci. The high observed heterozygosity of ILSTS61 was found in swamp buffalo from Riau Province, while the Ho value of ILSTS17 ranged from 0.000 to 0.170. This study identified two clusters for Indonesian swamp buffalo, i.e., cluster I (Aceh, North Sumatra, and Riau) and cluster II (Banten, Central Java, West Nusa Tenggara, and South Sulawesi). The two major divergent directions are considered in Indonesia swamp buffaloes across the observed provinces.
References
Agung, P. P., F. Saputra, W. A. Septian, Lusiana, M. S. A. Zein, S. Sulandari, S. Anwar, A. S. Wulandari, S. Said, & B. Tappa. 2016. Study of genetic diversity among simmental cross cattle in West Sumatra based on microsatellite markers. Asian-Australas. J. Anim. Sci. 29:176-183. https://doi.org/10.5713/ajas.15.0155
Agung, P. P., F. Saputra, M. S. A Zein, A. S. Wulandari, W. P. B. Putra, S. Said, & J. Jakaria. 2019. Genetic diversity of Indonesian cattle breeds based on microsatellite markers. Asian-Australas. J. Anim. Sci. 32:467-476. https://doi.org/10.5713/ajas.18.0283
Anggraeni, A., C. Sumantri, L. Praharani, & E. Andreas. 2011. Genetic distance estimation of local swamp buffaloes through morphology analysis approach. Jurnal Ilmu Ternak dan Veteriner. 16:199-210. http://medpub.litbang.pertanian.go.id/index.php/jitv/article/view/614
Arthofer, W., C. Heussler, P. Krapf, B. C. Schlick-Steiner, & F. M. Steiner. 2018. Identifying the minimum number of microsatellite loci needed to assess population genetic structure: A case study in fly culturing. Fly 12:13-22. https://doi.org/10.1080/19336934.2017.1396400
Barker, J. S. F., S. S. Moore, D. J. S. Hetzel, D. Evans, S. G. Tan, & K. Byrne. 1997. Genetic diversity of Asian water buffalo (Bubalus bubalis): Microsatellite variation and a comparison with protein-coding loci. Anim. Genet. 28:103-115. https://doi.org/10.1111/j.1365-2052.1997.00085.x
Byun, S. O., Q. Fang, H. Zhou, & J. G. H. Hickford. 2009. An effective method for silver-staining DNA in large numbers of polyacrylamide gels. Anal. Biochem. 385:174-175. https://doi.org/10.1016/j.ab.2008.10.024
Colli, L., M. Milanesi, E. Vajana, D. Iamartino, L. Bomba, F. Puglisi, M. Del Corvo, E. L. Nicolazzi, S. S. E. Ahmed, J. R. V. Herrera et al. 2018. New insights on water buffalo genomic diversity and post-domestication migration routes from medium density SNP chip data. Front. Genet. 9:53 https://doi.org/10.3389/fgene.2018.00053
Jakaria, M. S. A. Zein, S. Sulandari, Subandriyo, & Muladno. 2012. The use of microsatellite markers to study genetic diversity in Indonesian sheep. J. Indonesian Trop. Anim. Agric. 37:1-9. https://doi.org/10.14710/jitaa.37.1.1-9
Kalinowski, S. T., M. L. Taper, & T. C. Marshall. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16:1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Kantanen, J., P. Løvendahl, E. Strandberg, E. Eythorsdottir, M. H. Li, A. Kettunen-Praebel, P. Berg, & T. Meuwissen. 2015. Utilization of farm animal genetic resources in a changing agroecological environment in the Nordic countries. Front. Genet. 5:1-9. https://doi.org/10.3389/fgene.2015.00052
Kathiravan, P., B. P. Mishra, R. S. Kataria, & D. K. Sadana. 2009. Evaluation of genetic architecture and mutation drift equilibrium of Marathwada buffalo population in Central India. Livest. Sci. 121:288-293. https://doi.org/10.1016/j.livsci.2008.06.023
Mishra, B. P., P. K. Dubey, B. Prakash, P. Kathiravan, S. Goyal, D. K. Sadana, G. C. Das, R. N. Goswami, V. Bhasin, B. K. Joshi, & R. S. Kataria. 2015. Genetic analysis of river, swamp and hybrid buffaloes of north-east India throw new light on phylogeography of water buffalo (Bubalus bubalis). J. Anim. Breed. Genet. 132:454-466. https://doi.org/10.1111/jbg.12141
Peakall, R., & P. E. Smouse. 2012. GenALEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinform. 28:2537-2539. https://doi.org/10.1093/bioinformatics/bts460
Pekkala, N., K. E. Knott, J. S. Kotiaho, K. Nissinen, & M. Puurtinen. 2014. The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients. Evol. Appl. 7:1107-1119. https://doi.org/10.1111/eva.12145
Praharani, L., & R. S. G. Sianturi. 2018. Inbreeding depression and alternative solution in buffaloes. Wartazoa 28:1-12. https://doi.org/10.14334/wartazoa.v28i1.1744
Rusdin, M., D. D. Solihin, A. Gunawan, C. Talib, & C. Sumantri. 2020. Genetic variation of eight indonesian swamp-buffalo populations based on cytochrome b gene marker. Trop. Anim. Sci. J. 43:1-10. https://doi.org/10.5398/tasj.2020.43.1.1
Saputra, F., Jakaria, & C. Sumantri. 2013. Genetic variation of mtDNA cytochrome oxidase subunit I (COI) in Local swamp buffaloes in Indonesia. Med. Pet. 36:165-170. https://doi.org/10.5398/medpet.2013.36.3.165
Seligmann, H. 2010. Positive correlations between molecular and morphological rates of evolution. J. Theor. Biol. 264:799-807. https://doi.org/10.1016/j.jtbi.2010.03.019
Takezaki, N., M. Nei, & K. Tamura. 2010. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with windows interface. Mol. Biol. Evol. 27:747-752. https://doi.org/10.1093/molbev/msp312
Wang, S., N. Chen, M. R. Capodiferro, T. Zhang, H. Lancioni, H. Zhang, Y. Miao, V. Chanthakhoun, M. Wanapat, M. Yindee, Y. Zhang, H. Lu, L. Caporali, R. Dang, Y. Huang, X. Lan, M. Plath, H. Chen, J. A. Lenstra, A. Achilli & C. Lei. 2017. Whole mitogenomes reveal the history of swamp buffalo: initially shaped by glacial periods and eventually modelled by domestication. Sci. Rep. 7: 4708. https://doi.org/10.1038/s41598-017-04830-2
Yue, X. P., R. Li, W. M. Xie, P. Xu, T. C. Chang, L. Liu, F. Cheng, R. F. Zhang, X. Y. Lan, H. Chen, & C. Z. Lei. 2013. Phylogeography and domestication of Chinese swamp buffalo. PLoS ONE 8:1-13. https://doi.org/10.1371/journal.pone.0056552
Zein, M., S. Sulandari, Muladno, Subandriyo, & Riwantoro. 2012. Diversitas genetik dan hubungan kekerabatan kambing lokal Indonesia menggunakan marker DNA mikrosatelit. Jurnal Ilmu Ternak dan Veteriner 17:25-35.
Zhang, Y., D. Vankan, Y. Zhang, & J. S. F. Barker. 2011. Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: Inferences on the region of domestication of the swamp buffalo. Anim. Genet. 42:366-377. https://doi.org/10.1111/j.1365-2052.2010.02166.x
Zhang, Y., Y. Lu, M. Yindee, K. Y. Li, H. Y. Kuo, Y. T. Ju, S. Ye, M. O. Faruqoe, Q. Li, Y. Wang et al. 2016. Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region. Mol. Ecol. 25:1530-1550. https://doi.org/10.1111/mec.13518
Authors
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
Authors submitting manuscripts should understand and agree that copyright of manuscripts of the article shall be assigned/transferred to Tropical Animal Science Journal. The statement to release the copyright to Tropical Animal Science Journal is stated in Form A. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA) where Authors and Readers can copy and redistribute the material in any medium or format, as well as remix, transform, and build upon the material for any purpose, but they must give appropriate credit (cite to the article or content), provide a link to the license, and indicate if changes were made. If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
Article Details
