Genetic Diversity in Labeo rohita Population Based on Selected Mitochondrial and Nuclear DNA Markers

Abstract

The genetic diversity of Labeo rohita, a commercially important freshwater fish in South Asia, was examined at specific DNA regions of the mitochondrial cytochrome b gene (cytb), the control region (D-loop), and the nuclear myostatin gene (mstn). Despite the significance of L. rohita, no prior studies have employed a combination of cytb, the control region, and mstn markers for genetic analysis. This research addresses that gap by using these as molecular markers to assess population structure and genetic diversity. The findings provide valuable insights into the effective conservation and management of L. rohita populations. 250 Samples were collected from Padma, Jamuna, and Halda rivers, as well as from hatchery origin cultured stocks in Bangladesh. Following DNA extraction, PCR amplification, and sequencing of 200 fish samples, a total of 137 cytb, 162 D-loop, and 84 mstn sequences were analyzed after quality assessment. While cytb and D-loop sequences were analyzed for wild and cultured samples, mstn1 analysis was limited to wild samples only. The cytb gene region (616 bp) exhibited 11 haplotypes with 98.4% sequence conservation, while the control region (598 bp) displayed 50 haplotypes with greater variability. The mstn gene region (569 bp) showed 18 haplotypes with 98.41% conservation. Additionally, the mstn sequences have shown homozygous (A9/A9) and heterozygous (A9/A10) genotypes at its microsatellite loci. The A9 allele (with nine “A”s) was predominant (72%-89%) across all populations, with the highest occurrence of the homozygous A9A9 genotype in the Halda population (78%). Nucleotide polymorphisms were observed at 22 sites in the control region, 16 in the cytb gene, and 10 in the mstn gene. Notable regional variation was found, with specific haplotypes predominating in different populations, such as the haplotype HP04 of the control region found in 61.36% of the Halda River population. Based on the control region DNA sequences, the cultured population showed the highest haplotype (0.951) and nucleotide diversity (0.00778) among all, and the Halda population had the lowest. Similarly, for cytb, the cultured population exhibited the highest diversity, while the Padma population had the lowest. Among the wild populations, the mstn gene sequences showed the highest diversity in the Halda population, with the lowest in the Jamuna population. AMOVA and pairwise FST analyses revealed significant genetic differentiation, particularly between the Halda and other populations. Phylogenetic and haplotype network analyses identified two major genetic clusters, with distinct separations between populations, particularly between the Halda and Padna x populations in all study markers. The genetic statuses of three river populations of L. rohita have been compared and discussed. The causes of variation in genetic diversity may include differences in breeding practices, gene flow, and population history. Possibly, the cultured populations show higher diversity due to the mixing of different breeds in the hatchery. While the wild populations face anthropogenic and natural constraints. Additionally, varying mutation rates and population sizes may influence the observed differences in haplotype and nucleotide diversity. Overall, the findings highlight significant genetic differentiation and regional variations, and document the genetic isolation of the Halda population and the mixed genetic background of the cultured stocks. These results underscore the need for targeted conservation strategies to protect wild populations and sustainably manage cultured stocks. The study provides valuable insights for future research and fisheries management practices in Bangladesh and similar regions facing anthropogenic pressures