Genetic Diversity of Various Goat Breeds in East Java Based on DNA Microsatellite Markers
Abstract
Information on genetic diversity using microsatellite markers was essential to formulate effective conservation and breeding strategies. This study aims to identify the genetic diversity and relationships between Kacang, Senduro, Peranakan Ettawa (PE), Boer, and Saanen goats in the East Java region, Indonesia, using 12 microsatellite markers. A total of 86 goat blood DNA samples, which consisted of Kacang (n=41), Senduro (n=23), Boer (n=13), PE (n=5), and Saanen (n=4), were used in this study. The DNA was extracted based on Genomic DNA Mini Kits protocols for analysis fragment in microsatellite DNA region using specific primer recommended by the ISAG/FAO. A total of 96 alleles were identified in this study. The observed heterozygosity ranged from 0.470±0.135 (Kacang) to 0.592±0.211 (PE) and the expected heterozygosity ranged from 0.589±0.251 (Saanen) to 0.762±0.084 (PE). F statistical analysis include inter-population inbreeding rate (Fis) 0.2583 (25.83%), inbreeding rate in population (Fit) 0.3238 (32.38%), and genetic differentiation (Fst) 0.0882 (8.82%). The 11 microsatellite markers were highly informative (PIC>0.5), except the INRA063 locus markers were quite informative (PIC 0.25-0.5). The research showed that Kacang, Senduro, and PE goats had a close genetic distance and formed a cluster. Kacang and Saanen goats showed a long genetic distance at 26.9%. In conclusion, the genetic relationship among goat breeds in East Java was divided into three clusters where Boer and Saanen goats formed their cluster.
References
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Câmara, T. S., J. F. Nunes, F. M. Diniz, G. R. Silva, & A. M. de Araújo. 2017. Genetic diversity and relatedness between canindé and British Alpine goat breeds in Northeastern Brazil accessed by microsatellite markers. Genet. Mol. Res. 16:gmr16019569. https://doi.org/10.4238/gmr16019569
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ISAG/FAO. 2011. Draft Guidelines on Molecular Genetic Characterization of Animal Genetic Resources. Commission on Genetic Resources for Food And Agriculture. Rome, Italy.
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Maletsanake, D., S. J. Nsoso, & P. M. Kgwatalala. 2013. Genetic variation from 12 microsatellite makers in an indigenous Tswana goat flock in South-eastern Botswana. Livestock Research for Rural Development 25:2013.
Manirakiza, J., G. Hatungumukama, B. Besbes, & J. Detilleux. 2020. Characteristics of smallholders’ goat production systems and effect of Boer crossbreeding on body measurements of goats in Burundi. Pastoralism 10:1-11. https://doi.org/10.1186/s13570-019-0157-5
Missohou, A., M. R. Poutya, A. Nenonene, G. K. Dayo, S. B. Ayssiwede, E. Talaki, & A. Fané. 2011. Genetic diversity and differentiation in nine West African local goat breeds assessed via microsatellite polymorphism. Small Rumin. Res. 99:20-24. https://doi.org/10.1016/j.smallrumres.2011.04.005
Murital, I., O. Afolayan, M. N. Bemji, O. Dadi, V. Landi, A. Martínez, & A. O. Adebambo. 2015. Genetic diversity and population structure of Nigerian indigenous goat using DNA microsatellite markers. Archivos de Zootecnia 64:93-98. https://doi.org/10.21071/az.v64i246.382
Nguluma, A. S., Y. Huang, Y. Zhao, L. Chen, G. Msalya, C. Lyimo, & S. W. Chenyambuga. 2018. Assessment of genetic variation among four populations of Small East African goats using microsatellite markers. S. Afr. J. Anim. Sci. 48:117-127. https://doi.org/10.4314/sajas.v48i1.14
Oliveira, J. C. V., M. N. Ribeiro, L. L. Rocha, M. A. Gomes-Filho, J. V. Delgado, A. M. Martinez, & L. T. Gama. 2010. Genetic relationships between two homologous goat breeds from Portugal and Brazil assessed by microsatellite markers. Small Rumin. Res. 93:79-87. https://doi.org/10.1016/j.smallrumres.2010.05.002
Pakpahan, S., W. T. Artama, R. Widayanti, & G. Suparta. 2015. Genetic variations and the origin of native Indonesian goat breeds based on mtDNA D-loop sequences. Asian J. Anim. Sci. 9:341-350. https://doi.org/10.3923/ajas.2015.341.350
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Parreira, B. & L. Chikhi. 2015. On some genetic consequences of social structure, mating systems, dispersal, and sampling. Proc. Natl. Acad. Sci. 112:E3318-E3326. https://doi.org/10.1073/pnas.1414463112
Pérez-Jiménez M, G. Besnard, G. Dorado, & P. Hernandez. 2013. Varietal tracing of virgin olive oils based on plastid DNA variation profiling. PLoS ONE 8:e70507. https://doi.org/10.1371/journal.pone.0070507
Puja, I. K., I. N. Sulabda, & I. N. Wandia. 2018. Microsatellite polymorphisms and its relationship with calving interval and gestation period in bali cattle. Adv. Anim. Vet. Sci. 6:197-200. https://doi.org/10.17582/journal.aavs/2018/6.5.197.200
Radhika, G., K. C. Raghavan, T. V. Aravindakshan, & V. Thirupathy. 2015. Genetic diversity and population structure analysis of native and crossbred goat genetic groups of Kerala, India. Small Rumin. Res. 131:50-57. https://doi.org/10.1016/j.smallrumres.2015.08.008
Saputra, F., J. Jakaria, A. Anggraeni, & C. Sumantri, C. 2020. Genetic diversity of Indonesian swamp buffalo based on microsatellite markers. Trop. J. Anim. Sci. 43:191-196. https://doi.org/10.5398/tasj.2020.43.3.191
Saputra, F., T. Sartika, A. Anggraeni, A. B. L. Ishak, K. Komarudin, & N. Pratiwi. 2021. Multivariate analysis of five chicken breed in Indonesia based on microsatellite allele frequency. Livestock and Animal Research. 19:48-53. https://doi.org/10.20961/lar.v19i1.43459
Seilsuth, S., J. H. Seo, H. S. Kong, & G. J. Jeon. 2016. Microsatellite analysis of the genetic diversity and population structure in dairy goats in Thailand. Asian-Australas J. Anim. Sci. 29:327. https://doi.org/10.5713/ajas.15.0270
Seo, J. H., J. H. Lee, & H. S. Kong. 2017. Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers. AsianAustralas. J. Anim. Sci. 30:136571. https://doi.org/10.5713/ajas.16.0514
Septian, W. A., & C. Sumantri. 2015. Genetic diversity of Bali Cattle based on microsatellite marker in Indonesian breeding centre. Med. Pet. 38:12-17. https://doi.org/10.5398/medpet.2015.38.1.12
Singh, G., Y. Thakur, A. Kour, V. Sankhyan, & S. Katoch. 2015. Genetic characterization of Gaddi goat breed of Western Himalayas using microsatellite markers. Vet. World. 8:527-531. https://doi.org/10.14202/vetworld.2015.527-531
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Authors
SusiloriniT. E., WulandariD., FurqonA., SeptianW. A., SaputraF., & SuyadiS. (2022). Genetic Diversity of Various Goat Breeds in East Java Based on DNA Microsatellite Markers. Tropical Animal Science Journal, 45(3), 247-254. https://doi.org/10.5398/tasj.2022.45.3.247
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