Abstract
Labeo fimbriatus is a medium carp species found throughout India's peninsular river basins and is regarded as a valuable aquaculture resource alongside Indian major carps due to its taste and nutritional value. This species has recently declined dramatically due to habitat degradation and overfishing. Because of its enormous economic importance, a selective breeding programme is likely to be in place to improve performance traits. Knowledge of genetic variation among the base population from which the broodstock will be selected is an important step in this process. A diverse genetic base of broodstock is required to achieve the best response to selection for long-term aquaculture management practices. Consequently, using mitochondrial DNA (ATPase 6 and Control region) and microsatellite markers, we have made the first step toward estimating the level of genetic variation and how it is distributed among the four populations of L. fimbriatus found in peninsular rivers in India. The ATPase 6 gene analysis in four populations revealed 15 haplotypes and 51 variable sites, in contrast to the Control region, which had 60 haplotypes together with 73 variable sites and a haplotype diversity of 0.941. Twelve microsatellite loci displayed estimated allele numbers (NA) ranging from 3 to 19, observed heterozygosity (HO), and expected heterozygosity (HE), respectively, of 0.705 to 0.753 and 0.657 to 0.914. Each marker type showed a significant FST value, indicating the presence of low to moderate genetic differentiation across entire wild populations. The Godavari, Kaveri, and Mahanadi populations formed one cluster according to the UPGMA, which was based on genetic distance matrix, while the Krishna population formed a separate cluster. The comparative genetic analysis of data from different markers utilized in the current study would enable the identification of the genetic stocks of L. fimbriatus and facilitate conservation measures and selective breeding.
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Data availability
The nucleotide sequences of present study are available in the GenBank repository (https://www.ncbi.nlm. nih.gov/genbank/) with the accession number KC734902-KC735069, KU541892-KU541949, and JQ838157-JQ838171.
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Acknowledgements
The authors are thankful to Indian Council of Agricultural Research (ICAR)—Central Institute of Freshwater Aquaculture (CIFA), for the laboratory facilities provided during the work.
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PD contributed to the conceptualization of this study. SKS, SPD, LS and PCD collected samples. SKS, BPS, SPD, and LS carried out the genomic DNA isolation; PCR carried out the genotyping and population genetic analysis. SKS and BPS compiled the results and prepared the first draft. PD, SPD, LS and PCD supervised the study and edited the final draft and gave final approval of this version to be published. All authors read and approved the final manuscript.
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All the experiments in the present study were carried out in accordance with the guidelines for control and supervision of experiments on animals by the Government of India and approved by Institutional Animal Ethics Committee (AEC).
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Swain, S.K., Sahu, B.P., Das, S.P. et al. Population genetic structure of fringe-lipped carp, Labeo fimbriatus from the peninsular rivers of India. 3 Biotech 12, 300 (2022). https://doi.org/10.1007/s13205-022-03369-y
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DOI: https://doi.org/10.1007/s13205-022-03369-y