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Development of novel microsatellite markers for population differentiation and detection of natural selection in wild populations of butter catfish, Ompok bimaculatus (Bloch, 1794)

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Abstract

Background

Butter catfish (Ompok bimaculatus) is a preferred species in South East Asia, with huge aquaculture potential. However, there is limited information about genetic stock composition due to insufficient markers. The goal of this study was to develop de novo microsatellite markers.

Methods and results

For sequencing, genomic SMRT bell libraries (1.5 Kbp size) were prepared for O. bimaculatus. A total of 114 SSR containing sequences were used for primer designing. Polymorphic loci were validated by genotyping 83 individuals from four distant riverine populations, viz., Brahmaputra, Bichiya, Gomti and Kaveri. A total of 30 microsatellite loci were polymorphic, of which five were found to be associated with functional genes and eight (four positive and four negative) loci were found to be under selection pressure. A total of 115 alleles were detected in all loci and PIC ranged from 0.539 to 0.927 and pair-wise FST values from 0.1267 to 0.26002 (p < 0.001), with an overall FST value of 0.17047, indicating the presence of population sub-structure. Cross-species transferability of 29 loci (96.67%) was successful in congener species, Ompok pabda.

Conclusion

The novel SSR markers developed in this study would facilitate stock characterization of natural populations, to be used in future selection breeding programs and planning conservation strategies in these species. Identified non-neutral markers will give insights into the effect of local adaptation on genetic differentiation in the natural population of this species.

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Acknowledgements

The authors are thankful to The Director, National Bureau of Fish Genetic Resources (NBFGR), Lucknow for facilitating the work. The present work is the part of ICAR-NBFGR Project FISHNBFGRSIL202000900224, funded by Indian Council of Agricultural Research, New Delhi. Thanks are due to Dr. Ratnesh Tripathi for his help in generating long read sequences. Mr. Kantharajan is acknowledged for his role in preparing location map.

Funding

This investigation was supported by ICAR-National Bureau of Fish Genetic Resources, Lucknow, India, under project No. FISHNBFGRSIL202000900224.

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Authors and Affiliations

  1. ICAR- National Bureau of Fish Genetic Resources (NBFGR), Canal Ring Road, PO-Dilkusha, 226002, Lucknow, Uttar Pradesh, India

    Sangeeta Mandal & Kuldeep K. Lal

  2. Fish Conservation Division, ICAR-National Bureau of Fish Genetic Resources, Canal Ring Road, PO-Dilkusha, 226002, Lucknow, Uttar Pradesh, India

    Labrechai Mog Chowdhury, Shradha Chaturvedi, Sangeeta Mandal, Rajesh Kumar, Rajeev K. Singh & Vindhya Mohindra

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  1. Labrechai Mog Chowdhury
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Contributions

Kuldeep K. Lal conceived the idea and designed the experiments. Investigation, data collection and analysis were performed by Labrechai Mog Chowdhury, Shradha Chaturvedi, Sangeeta Mandal, Rajesh Kumar, Rajeev K. Singh and Vindhya Mohindra. The first draft of the manuscript was written by Sangeeta Mandal, Shradha Chaturvedi, Labrechai Mog Chowdhury, Vindhya Mohindra and all authors commented on previous versions of the manuscript. All authors approved the manuscript.

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Correspondence to Sangeeta Mandal.

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The experiments were approved by Institute Animal Ethics Committee (IAEC), ICAR-NBFGR, Lucknow vide No. G/IAEC/2020/022 dated 09-02-2021.

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Chowdhury, L.M., Chaturvedi, S., Mandal, S. et al. Development of novel microsatellite markers for population differentiation and detection of natural selection in wild populations of butter catfish, Ompok bimaculatus (Bloch, 1794). Mol Biol Rep 50, 2435–2444 (2023). https://doi.org/10.1007/s11033-022-08105-6

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