Volume 57 Issue 12 (December 2023) 1627 RESEARCH ARTICLE Indian Journal of Animal Research, Volume 57 Issue 12: 1627-1633 (December 2023) The Analysis of Genetic Variation in the Mitochondrial ND6 Gene and its Application for the Identification of Indonesian Catfish Species Rini Widayanti 1 , Alek Ibrahim 1 , Muhammad Hesham Maulana 1 , Korniawan Eko Sakti 1 , Danastri Hanida Nur Arifah 1 , Suhendra Pakpahan 2 10.18805/IJAR.BF-1495 ABSTRACT Background: Catfish is a freshwater and saltwater fish type with a wide distribution throughout the Indonesian archipelago. This study was conducted to analyze Indonesian catfish’s genetic diversity and evolutionary relationships based on the mitochondrial ND6 gene. Methods: Twenty-eight catfish samples were collected from nine rivers and one ocean in seven provinces of Indonesia. The MT-ND6 gene was amplified by using a set of primers (BaungND6F and BaungND6R). The MEGA X software was used to examine the MT- ND6 sequences for genetic variation and phylogenetic relation between Indonesian catfish populations. Result: There were 167 nucleotide site variations and thirty-two amino acid variations in the MT-ND6 gene. The genetic difference among populations ranges from 0.9 to 25% and the average evolutionary divergence in the overall populations was 14%, with catfish BB and PM having the closest genetic distance, while the farthest is BF to MP and BF to MS. In conclusion, the phylogenetic tree indicated that there were four distinct catfish clades in this study: MP, MS, KR, PM, BB and KS had been grouped with Hemibagrus nemurus (Bagridae family), EM had been grouped with Mystus vittatus (Bagridae family), BSBJ had been grouped with Pangasius pangasius (Pangasiidae family) and PD and BF had been grouped with Netuma thalassina (Ariidae family). Key words: Catfish, Genetic variation, Indonesian catfish, MT-ND6 gene, Phylogenetic study. INTRODUCTION Indonesia is a country that has abundant natural resources, which is called a mega biodiversity country (Pakpahan et al., 2016; Ibrahim et al., 2020). Water resources are an important part of Indonesia because they have abundant freshwater and saltwater fish (Allen and Adrim, 2003). Currently, nearly 40% of identified fish species are limited to freshwater habitats, which account for just 0.8% of the earth’s surface (Dudgeon et al., 2006). This fish is found in large rivers and flooded swamps. Indonesian catfish have high economic value and the population is classified as vulnerable to extinction (Aryani, 2015). The catfish group consists of about 3,000 species, 478 orders and 36 families of fish, including Bagridae, Siluridae, Pangasiidae, Akysidae, Schilbeidae, Sisoridae, Parakysidae, Ariidae, Plotosidae, Loricariidae, Chacidae, Clariidae, Kryptopterus and the others (Abell et al., 2008; Vitt, 2021; Wong et al., 2011; Widayanti et al., 2021; Ng and Kottelat, 2013). Indonesian catfish have different local names (common names) in several areas of Indonesia, such as Baon, Baong, Duri, Geso (Sumatra), Bawon (Betawi), Senggal, Singgah (Sunda), Tiken Bato (Kalimantan), Tagih, Tageh, Jendil and Baung fish (Java) (Widayanti et al. , 2021). In previous studies, catfish in Indonesia were grouped and classified into several genera and species, such as Silurichthys (Silurihthys ligneoulus from Kahayan River of Central Kalimantan) (Ng and Tan, 2011), Pangasius (Pangasius rheophilus from Berau and Kayan Rivers of East Kalimantan, Pangasius pangasius from Bengawan Solo River-Central Java) (Pouyaud and Teugels, 2000) , Mystus (Mystus singaringan from Musi River-South Sumatra), Barcoides (Barcoides macropterus from Musi River-South Sumatra) and Hemibagrus ( Hemibagrus nemurus from Musi and Penukal River-South Sumatra, Hemibagrus wyckii from Kampar Kanan River-Riau, Hemibagrus olyroides from Behau River-North Kalimantan, Hemibagrus bongan from Haloi River-West Kalimantan, Hemibagrus lacustrinus from Batang Ombilin River-West Sumatra, Hemibagrus planiceps from Cibogo River-West Java, Hemibagrus caventus from 1 Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna No. 2, Karangmalang, Yogyakarta 55281, Indonesia. 2 Museum Zoologicum Bogoriense, Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia. Corresponding Author: Alek Ibrahim, Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna No. 2, Karangmalang, Yogyakarta 55281, Indonesia. Email: alek.ibrahim@mail.ugm.ac.id How to cite this article: W idayanti, R., Ibrahim, A., Maulana, M.H., Sakti, K.E., Arifah, D.H.N. and Pakpahan, S. (2023). The Analysis of Genetic Variation in the Mitochondrial ND6 Gene and its Application for the Identification of Indonesian Catfish Species. Indian Journal of Animal Research. 57(12): 1627-1633. doi: 10.18805/IJAR.BF-1495. Submitted: 24-01-2022 Accepted: 28-04-2022 Online: 26-05-2022