Mitochondrial DNA reveals shallow population genetic structure in economically important Cyprinid fish Labeo rohita (Hamilton, 1822) from South and Southeast Asia

BackgroundAssessment of genetic diversity and population genetic structure is important for species that are economically important, threatened, and are at global conservation priority. Analysis of mitochondrial DNA is broadly used in species identification and population genetics studies due to the availability of sufficient reference data and better evolutionary dynamics for phylogeographic investigation. Labeo rohita (Rohu) is an economically important species cultured under carp polyculture systems in Asia. The present study explores the genetic diversity, phylogeography, and population structure of L. rohita from different countries using cytochrome oxidase subunit I (COI) gene.Methods and resultsA total of 17 L. rohita specimens were sampled from River Beas, India. For the genetic study, we amplified and sequenced COI mitochondrial DNA region. The obtained genetic data was combined with 268 COI records available in the NCBI and BOLD databases originating from multiple populations/countries across South and Southeast Asia. As a result, 33 haplotypes were identified that displayed low nucleotide (pi = 0.0233) and moderate haplotype diversity (Hd = 0.523). Tajima (D) was found to be negative (P > 0.05), whereas Fu's Fs showed a positive value (P > 0.05). The overall F-ST value between studied populations was 0.481 (P < 0.05).ConclusionAMOVA analysis indicated higher variation within than among the population examined. The neutrality tests suggested the presence of rare haplotypes and stable demography within studied populations of L. rohita. The Bayesian skyline plot indicated steady population growth until 1 Mya followed by population decline, whereas F-ST values indicated significant genetic differentiation. High heterogeneity was observed in the Pakistan population which could be indicative of long-term isolation and excessive culturing to meet market demands. The present results are the first global comparative analysis of L. rohita and pave the way forward for detailed genomic and ecological studies aimed at the development of improved stock and effective conservation plans. The study also makes recommendations to conserve the genetic integrity of wild species from aquaculture-reared fishes.

Automated summary

This study investigates the genetic diversity, phylogeography, and population structure of Labeo rohita (Rohu) from different countries using the COI gene of mitochondrial DNA. The results show low nucleotide diversity and moderate haplotype diversity in L. rohita populations. Significant genetic differentiation is observed among populations, with high heterogeneity in the Pakistan population. This study provides the first global comparative analysis of L. rohita and offers insights for future genomic and ecological studies, as well as recommendations for the conservation of wild species from aquaculture-reared fishes.