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

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 g...

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Autores principales: Makombu, Judith G., Cheruiyot, Evans K., Stomeo, Francesca, Thuo, David N., Oben, Pius M., Oben, Benedicta O., Zango, Paul, Mialhe, Eric, Ngueguim, Jules R., Mujibi, Fidalis D. N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9529149/
https://www.ncbi.nlm.nih.gov/pubmed/36190939
http://dx.doi.org/10.1371/journal.pone.0263540
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author Makombu, Judith G.
Cheruiyot, Evans K.
Stomeo, Francesca
Thuo, David N.
Oben, Pius M.
Oben, Benedicta O.
Zango, Paul
Mialhe, Eric
Ngueguim, Jules R.
Mujibi, Fidalis D. N.
author_facet Makombu, Judith G.
Cheruiyot, Evans K.
Stomeo, Francesca
Thuo, David N.
Oben, Pius M.
Oben, Benedicta O.
Zango, Paul
Mialhe, Eric
Ngueguim, Jules R.
Mujibi, Fidalis D. N.
author_sort Makombu, Judith G.
collection PubMed
description 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.
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spelling pubmed-95291492022-10-04 Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon Makombu, Judith G. Cheruiyot, Evans K. Stomeo, Francesca Thuo, David N. Oben, Pius M. Oben, Benedicta O. Zango, Paul Mialhe, Eric Ngueguim, Jules R. Mujibi, Fidalis D. N. PLoS One Research Article 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. Public Library of Science 2022-10-03 /pmc/articles/PMC9529149/ /pubmed/36190939 http://dx.doi.org/10.1371/journal.pone.0263540 Text en © 2022 Makombu et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Makombu, Judith G.
Cheruiyot, Evans K.
Stomeo, Francesca
Thuo, David N.
Oben, Pius M.
Oben, Benedicta O.
Zango, Paul
Mialhe, Eric
Ngueguim, Jules R.
Mujibi, Fidalis D. N.
Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title_full Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title_fullStr Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title_full_unstemmed Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title_short Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon
title_sort species-informative snp markers for characterising freshwater prawns of genus macrobrachium in cameroon
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9529149/
https://www.ncbi.nlm.nih.gov/pubmed/36190939
http://dx.doi.org/10.1371/journal.pone.0263540
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