IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0263540.html
   My bibliography  Save this article

Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon

Author

Listed:
  • Judith G Makombu
  • Evans K Cheruiyot
  • Francesca Stomeo
  • David N Thuo
  • Pius M Oben
  • Benedicta O Oben
  • Paul Zango
  • Eric Mialhe
  • Jules R Ngueguim
  • Fidalis D N Mujibi

Abstract

Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright’s Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.

Suggested Citation

  • Judith G Makombu & Evans K Cheruiyot & Francesca Stomeo & David N Thuo & Pius M Oben & Benedicta O Oben & Paul Zango & Eric Mialhe & Jules R Ngueguim & Fidalis D N Mujibi, 2022. "Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon," PLOS ONE, Public Library of Science, vol. 17(10), pages 1-17, October.
  • Handle: RePEc:plo:pone00:0263540
    DOI: 10.1371/journal.pone.0263540
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263540
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0263540&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0263540?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0263540. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.