Clarias magur (Hamilton, 1822), a popular Indian catfish, is of significant ecological and economic importance, and found across India, Nepal, Bhutan, and Bangladesh. The taxonomic characters of C. magur exhibit a high degree of homogeneity with the exotic African catfish C. gariepinus that has a widespread unauthorized presence in India. Only the shape of the supraoccipital process is considered a diagnostic morphological characteristic, but it is useful only in adults, and intermediate shapes and inter-species hybrids have also been reported, leading to widespread misidentification. Further, due to the decline of its wild populations, C. magur is classified as ‘Endangered’ by the IUCN (2022), and accurate species identification is essential for conservation and implementation of the ban on the exotic species. DNA barcoding based on the mitochondrial COI gene fails to distinguish the species from their hybrids, and NCBI/ BOLD databases too have sequences of misidentified species.
Here, we report multiplexed Sequence Characterised Amplified Region (SCAR) markers developed from the carefully identified specimens of the two species and their experimental hybrids. Seven multiplexed primer sets observed to produce diagnostic agarose gel profiles in the lab, were used to genotype 190 fish specimens being sold as “magur” in fish markets across 19 districts in seven Indian States (Maharashtra, Tamil Nadu, Odisha, West Bengal, Bihar, Uttar Pradesh, and Jharkhand) by isolating DNA from fin clips. The sampled fish were also photographed for visual identification based on the shape of the supraoccipital process.
Results reveal that multiplexed SCAR markers proved effective in distinguishing between C. magur, C. gariepinus, and their hybrid, overcoming limitations of traditional morphological methods. The study confirmed widespread sale of C. gariepinus in urban fish markets of India, and the 190 sampled fish being sold as magur or hybrid by the vendors were 82% gariepinus, 15.4% magur, and 2.6% hybrids.
One SCAR primer set that generates a single 449 bp band in C. magur, a 319 bp band in C. gariepinus and both bands in the hybrid proved to be most reliable for identification by a single PCR reaction. This genotyping kit to be produced by ICAR-CIFE, Mumbai in public private partnership mode will strengthen targeted conservation efforts and also enable aquaculturists to confirm the identity of magur brooders for better outcomes of induced breeding. The paper discusses the development of these molecular markers and presents evidence of their robustness.