* Corresponding Author
Evaluation of Genetic Variation in Hybrid Catfish (Sangkuriang × Thai) Employing PCR-RAPD Markers
https://doi.org/10.22146/jfs.113208 Kurnia Anggraini Rahmi(1), Putriku Nadzira Sativa(2), Alimuddin Alimuddin(3*), Dinar Tri Soelistyowati(4)
(1) Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, West Java, Indonesia
(2) Undergraduate Study Program, Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, West Java, Indonesia
(3) Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, West Java, Indonesia
(4) Department of Aquaculture, Faculty of Fisheries and Marine Sciences, IPB University, Bogor, West Java, Indonesia
(*) Corresponding Author
Abstract
Hybridization is the process of crossing individuals with different genotypes to produce offspring with superior traits. In this study, Sangkuriang catfish were crossed with introduced Thai catfish to obtain heterosis in hybrid seeds. The objective was to analyze the genetic diversity of these hybrid seeds using the PCR-RAPD method. Specifically, the primers OPA-13, OPB-08, OPC-19, and OPD-02 were used. Crossbreeding involved Sangkuriang female and Thai male broodstock, with four pairs of broodfish used via a semi-natural spawning method. After spawning, hybrid seeds from each pair were reared separately in containers under uniform conditions for 1.5 months. DNA samples were then collected from the fin tissue of each replicate of the crosses, and were grouped according to size categories: large (7-8 cm), medium (5-6 cm), small (3-4 cm), and broodstock, with 30 samples per size category for each replicate. The results revealed a polymorphism percentage of 72.95-93.88%, heterozygosity values of 0.167-0.232, and an average genetic distance among hybrid seeds from the three size categories and broodstock ranging from 0.001-0.018.
Keywords
Full Text:
PDFReferences
Ahmed, A.M.M., & Talib, E.A.H. 2018. Effects of ovaprim hormone on induced breeding of Clarias gariepinus. Agricultural Extension Journal. 2 (2): 75-77. https://ssrn.com/abstract=3662949
Ajogbasile, F.V., A.T. Kayode, P.E. Oluniyi, K.O. Akano, J.N. Uwanibe, B.B. Adegboyega, C. Philip, O.G. John, P.J. Eromon, G. Emechebe, F. Finimo, N. Ogbulafor, N. Jiya, U. Okafor, J. Ambe, R.D. Wammanda, S. Oguche, O.A. Mokuolu, A. Sowunmi, O.A. Folarin & C.T. Happi. 2021. Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis. Malaria Journal. 20 (236): 1-9. https://doi.org/10.1186/s12936-021-03734-x
Amin, M., F.H. Taqwa, Y. Yulisman, R.C. Mukti, M.A. Rarassari & R.M. Antika. 2020. The effectiveness of utilization of local raw materials as feed to increase productivity of catfish (Clarias sp.) in Sakatiga Village, Indralaya District, Ogan Ilir Regency, South Sumatra. Journal of Aquaculture and Fish Health. 9 (3): 222-231. https://doi.org/10.20473/jafh.v9i3.17969
Andayani, N., J.C. Morales, M.R.J. Forstner, J. Supriatna & D.J. Melnick. 2001. Genetic variability in mtDNA of the silvery gibbon: Implications for the conservation of a critically endangered species. Conservation Biology. 15 (3): 1545-1548. http://people.se.cmich.edu/swans1bj/andayani_etal_01.pdf
Arifin, O.Z., I. Imron, A. Asependi, A. Hendri, N. Muslim & A. Yani. 2017. Hibridisasi intraspesifik antar dua populasi ikan gurami Galunggung (Osphronemus goramy, Lacepede, 1801). Jurnal Riset Akuakultur. 12 (4): 315-323. https://ejournal-balitbang.kkp.go.id/index.php/jra/article/view/5460/5445
Ath-thar, M.H.F., A. Ambarwati, D.T. Soelistyowati & A.H. Kristanto. 2018. Keragaman genotipe dan fenotipe ikan uceng Nemacheilus fasciatus (Valenciennes, 1846) asal Bogor, Temanggung, dan Blitar. Jurnal Riset Akuakultur. 13 (1): 1-10. http://dx.doi.org/10.15578/jra.13.1.2018.1-10
Banerjee, R., S. Chattopadhyay & A.K. Saha. 2016. Genetic diversity and relationship of mulberry genotypes revealed by RAPD and ISSR markers. Journal of Crop Improvement. 30 (4): 478-492. https://doi.org/10.1080/15427528.2016.1177803
Buwono, I.D., A.U. Lathifah & U. Subhan. 2018. Deteksi keragaman genotip hibrid ikan lele Sangkuriang, Mutiara transgenik dan non transgenik pada keturunan pertama. Jurnal Biologi Indonesia. 7 (2): 111-120. https://jurnal.unpad.ac.id/jpk/article/view/11368
Ellegren, H & N. Galtier. 2016. Determinants of genetic divervisty. Nature Reviews Genetics. 17 (7): 422-433. https://doi.org/10.1038/nrg.2016.58
Frankham, R., J.D. Ballou, K. Ralls, M.D.B. Eldridge, M.R. Dudash, C.B. Fenster, R.C. Lacy, & P. Sunnucks. 2017. Evolutionary genetics of small populations. In Genetic Management of Fragmented Animal and Plant Populations. Oxford University. Press Oxford. https://doi.org/10.1093/oso/9780198783398.003.0002
Hafidah, R., A. Yustiati, Y. Mulyani & I.B.B. Suryadi. 2021. Determination of genetic diversity of four guppy strains using the random amplified polymorphic. Asian Journal of Biochemistry, Genetics and Molecular Biology. 8 (1): 1-8. https://doi.org/10.9734/ajbgmb/2021/v8i130183
Hague, M.T.J & E.J. Routman. 2015. Does population size affect genetic diversity? A test with sympatric lizard species. Heredity. 116 (1): 92-98. https://doi.org/10.1038/hdy.2015.76
Hasan, I & M.M. Goswami. 2015. Genetic variation among catfish (Mystus cavasius) population assessed by randomly amplified polymorphic (RAPD) markers from Assam, India. International Journal of Fisheries and Aquatic Studies. 2 (4): 198-203. https://www.fisheriesjournal.com/vol2issue4/Pdf/2-4-19.1.pdf
Hayati, A., O. Carman & A. Alimuddin. 2021. Identifikasi kandidat marka molekuler pada ikan nilem (Osteochilus hasselti) rentan stres menggunakan teknik RAPD PCR. Jurnal Penelitian Belida Indonesia. 1 (1): 1–5.
Hayuningtyas, E.P & T. Kadarini. 2016. Keragaman genotipe tiga generasi ikan rainbow kurumoi (Melanotaenia parva) hasil domestikasi berdasarkan RAPD. Jurnal Riset Akuakultur. 11 (2): 107-114. https://ejournal-balitbang.kkp.go.id/index.php/jra/article/view/966/2411
Hayuningtyas, E.P., S. Sinansari, M.R. Fahmi, E. Kusrini & B. Nur. 2018. Karakter genotipe tiga populasi ikan rainbow ajamaru (Melanotaenia ajamaruensis) dari alam dan budidaya menggunakan RAPD. Jurnal Riset Akuakultur. 13 (2): 105-113. http://dx.doi.org/10.15578/jra.13.2.2018.105-113
Ikpeme, E.V., O.U. Udensi, U.B. Ekaluo, M.E. Kooffreh, C.M. Okolo, P.B. Ekpo & N.C. Ogbonna. 2015. Unveiling the genetic diversity in Clarias gariepinus (Burchell, 1822) using random amplified polymorphic DNA (RAPD) fingerprinting technique. Asian Journal of Animal Sciences. 9 (3): 187-197. https://doi.org/10.3923/ajas.2015.187.197
Iza, N. 2017. Frekuensi alel, heterozigositas dan migrasi alel pada populasi etnis Jawa dan Madura di Malang dan Madura, Jawa Timur, Indonesia. Jurnal Ilmiah Sains. 17 (1): 43-50. https://doi.org/10.35799/jis.17.1.2017.15289
KKP (Kementerian Kelautan dan Perikanan). 2024. Laporan Kinerja Direktorat Jenderal Perikanan Budi Daya Tahun 2024. Jakarta.
Kristanto, A.H., J. Subagja, W. Cahyanti & O.Z. Arifin. 2017. Evaluasi variasi fenotipe dan genotipe populasi ikan tambakan dari Kalimantan Tengah, Jawa Barat, dan Jambi dengan truss morfometrik dan random amplified polymorphic DNA (RAPD). Jurnal Riset Akuakultur. 12 (3): 203-211. https://doi.org/10.15578/jra.12.3.2017.203-211
Lubis, R.A., A. Alimuddin & N.B.P. Utomo. 2019. Enrichment of recombinant growth hormone in diet containing different levels of protein enhanced growth and meat quality of striped catfish (Pangasionodon hypophthalmus). BIOTROPIA. 26 (1): 1-8. https://doi.org/10.11598/btb.2019.26.1.710
Maryeni, S., R. Hertati & J. Juliana. 2022. Pemijahan ikan lele Sangkuriang (Clarias gariepinus) dengan dosis yang berbeda di Aquaculture Farm Rimbo Bujang Kabupaten Tebo Provinsi Jambi. SEMAH: Journal Pengelolaan Sumberdaya Perairan. 6 (1): 1-9. https://doi.org/10.36355/semahjpsp.v6i1.829
Mukai, Y & L.S. Lim. 2011. Larval rearing and feeding behavior of african catfish, Clarias gariepinus under dark conditions. Journal of Fisheries and Aquatic Sciences. 6 (3): 272-278. https://doi.org/10.3923/jfas.2011.272.278
Mulyadi, G.K., I.D. Buwono & U. Subhan. 2017. Analisis kekerabatan genetik hibrid ikan nilem (Osteochilus hasselti) dan ikan mas (Cyprinus carpio L.) menggunakan PCR-RAPD. Jurnal Perikanan dan Kelautan. 8 (1): 42–47. https://jurnal.unpad.ac.id/jpk/article/view/13884
Mulyani, Y., E.R. Sundari, N.N. Aidin, A. Lesmana & A. Aisyah. 2023. Genetic diversity analysis of Poeciliidae fish using RAPD-PCR method. Asian Journal of Fisheries and Aquatic Research. 24 (3): 44-51. https://doi.org/10.9734/ajfar/2023/v24i3636
Nei, M. 1972. Genetic distance between populations. The American Naturalist. 106 (949): 283-292. http://www.jstor.org/stable/2459777
Nugroho, E & S. Putera. 2018. Karakterisasi genetik ikan lele dumbo berdasarkan marker RAPD fingerprinting. Berita Biologi. 17 (1): 85–90. https://doi.org/10.14203/beritabiologi.v17i1.2869
Nugroho, E. 2013. Genetic variability of giant gouramy strain revealed by RAPD. Indonesian Aquaculture Journal. 8 (1): 107–111. http://dx.doi.org/10.15578/iaj.8.2.2013.107-111
Nugroho, E., H. Azrita, S. Syandri & R. Refilza. 2016. Evaluation of genetic divergence of kalui fish (Osphronemus goramy) strains from West Sumatra revealed by random amplified polymorphism DNA (RAPD) marker. Jurnal Riset Akuakultur. 11 (4): 313-319. https://ejournal-balitbang.kkp.go.id/index.php/jra/article/view/1403/2729
Nurnaningsih, N., I.W. Kantun & S. Wulandari. 2022. Analisis populasi ikan bawal hitam (Parastromateus niger Bloch, 1795) berdasarkan keragaman dan jarak genetik di WPPNRI 718. BAWAL Widya Riset Perikanan Tangkap. 14 (3): 149-159. http://dx.doi.org/10.15578/bawal.14.3.2022.149-159
Omer, O.M., A.E.W.H. Abdalla & Z.N. Mahmoud. 2020. Genetic diversity of two Tilapia species (Oreochromis niloticus and Sarotherodon galilaeus) using RAPD. The Open Biology Journal. 8 (1): 22-28. http://dx.doi.org/10.2174/1874196702008010022
Pranata, B., I. Lapadi, F.F. Simatauw, A.F. Wyrasti, F.I. Mansyur & A.B. Kusuma. 2024. Morfologi dan genetik ikan sidat (Anguilla marmorata) di Sungai Prafi Kabupaten Manokwari Provinsi Papua Barat. Jurnal Enggano. 9 (1): 11-23. https://doi.org/10.31186/jenggano.9.1.11-23
Safran, R & S.E. Kurnianto. 2017. Polimorfisme protein plasma darah pada kelinci Rex, Lokal, dan New Zealand White. Jurnal Veteriner. 18 (1): 144-153. https://doi.org/10.19087/jveteriner.2017.18.1.144
Saleky, D., R. Sianturi, M. Dailami & A.B. Kusuma. 2021. Kajian molekuler ikan Oreochromis spp. dari perairan daratan Merauke-Papua berdasarkan DNA mitokondria gen COI. Jurnal Perikanan Universitas Gadjah Mada. 23 (1): 37-43. https://doi.org/10.22146/jfs.61026
SNI (Standar Nasional Indonesia). 2000. Produksi benih ikan lele dumbo (Clarias gariepinus × C. fuscus) kelas benih sebar 01-6484.4-2000. Jakarta: Badan Standardisasi Nasional.
SNI (Standar Nasional Indonesia). 2014. Ikan lele dumbo (Clarias sp.) Bagian 3: Produksi induk 6484.3-2014. Jakarta: Badan Standardisasi Nasional.
Sunarma, A. 2016. Hibridisasi interpopulasi ikan lele afrika Clarias gariepinus yang diintroduksi di Indonesia. [Disertasi]. Bogor: IPB University.
Suprapto, R & B. Iswanto. 2022. Status genetik ikan lele mutiara berdasarkan sekuens gen COI. Media Akuakultur. 17 (2): 43–52. http://dx.doi.org/10.15578/ma.17.2.2022.43-52
Tamanna, F.M., J. Rashid & M.S. Alam. 2012. High levels of genetic variation revealed in wild and hatchery populations of the stripped dwarf catfish Mystus vittatus (Bloch) (Bagridae: Siluriformes) in Bangladesh by Random Amplified Polymorphic DNA techniques. International Journal of Adv Biol Res. 2: 322-327.
Ukat, Y.S.A., N.P.D. Kusuma & R.Y. Valentine. 2023. Teknik pembenihan ikan lele sangkuriang (Clarias gariepinus) di Munir Koi Ngrajek 3 Mungkid, Jawa Tengah. Fisheries: Jurnal Perikanan dan Ilmu Kelautan. 5 (2): 74–77.
Utomo, A.H.P., T.B. Pramono, H.T. Soedibya, P. Sukardi & H. Syakuri. 2020. Analysis of DNA polymorphism on different size of snakehead fish (Channa striata) using RAPD technique. SAINTEKS. 17 (2): 133-143. https://doi.org/10.30595/sainteks.v17i2.9376
Welsh, A.B. 2014. Genetic considerations in the restoration of small forest populations: perspectives from fish and wildlife genetics. Journal of Sustainable Forestry. 33 (1): S66-S92. https://doi.org/10.1080/10549811.2014.887475
Willi, Y., J. Van Buskirk, B. Schmid & M. Fischer. 2006. Genetic isolation of fragmented populations is exacerbated by drift and selection. Journal of Evolutionary Biology. 20 (2): 534-542. https://doi.org/10.1111/j.1420-9101.2006.01263.x
Xie, M., Y. Zhou, Y. Gong, M. Liu, P. Zhen, Z. Li, L. Zhou, J. Gui & Z. Wang. 2024. Growth superiority and genetic characterization of the hybrid from female ussuri catfish (Pseudobagrus ussuriensis) and male longsnout catfish (Leiocassis longirostris). Animals. 14 (24): 3617. https://doi.org/10.3390/ani14243617
How to Cite this Article:
Rahmi, K.A., P.N. Sativa, A. Alimuddin & D.T. Soelistyowati. 2026. Evaluation of genetic variation in hybrid catfish (Sangkuriang × Thai) employing PCR-RAPD markers. Jurnal Perikanan Universitas Gadjah Mada. 28 (1): 39-49. https://doi.org/10.22146/jfs.113208
DOI: https://doi.org/10.22146/jfs.113208
Article Metrics
Abstract views : 440
| 
views : 343
Refbacks
- There are currently no refbacks.
Copyright (c) 2026 Jurnal Perikanan Universitas Gadjah Mada
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
View My Stats