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...
| Autores principales: | , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/125118 |
| _version_ | 1855514418678333440 |
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| author | Makombu, J.G. Cheruiyot, E.K. Stomeo, Francesca Thuo, D.N. Oben, P.M. Oben, Benedicta O. Zango, P. Mialhe, E. Ngueguim, J.R. Mujibi, F.D.N. |
| author_browse | Cheruiyot, E.K. Makombu, J.G. Mialhe, E. Mujibi, F.D.N. Ngueguim, J.R. Oben, Benedicta O. Oben, P.M. Stomeo, Francesca Thuo, D.N. Zango, P. |
| author_facet | Makombu, J.G. Cheruiyot, E.K. Stomeo, Francesca Thuo, D.N. Oben, P.M. Oben, Benedicta O. Zango, P. Mialhe, E. Ngueguim, J.R. Mujibi, F.D.N. |
| author_sort | Makombu, J.G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| 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. |
| format | Journal Article |
| id | CGSpace125118 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| record_format | dspace |
| spelling | CGSpace1251182025-12-08T09:54:28Z Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon Makombu, J.G. Cheruiyot, E.K. Stomeo, Francesca Thuo, D.N. Oben, P.M. Oben, Benedicta O. Zango, P. Mialhe, E. Ngueguim, J.R. Mujibi, F.D.N. macrobrachium single nucleotide polymorphism genetic markers freshwater prawns and shrimps genetics animal breeding 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. 2022-10-03 2022-10-19T12:55:51Z 2022-10-19T12:55:51Z Journal Article https://hdl.handle.net/10568/125118 en Open Access Makombu, J.G., Cheruiyot, E.K., Stomeo, F., Thuo, D.N., Oben, P.M., Oben, B.O., Zango, P., Mialhe, E., Ngueguim, J.R., Mujibi, F.D.N. 2022. Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon. PLoS ONE 17(10):e0263540. |
| spellingShingle | macrobrachium single nucleotide polymorphism genetic markers freshwater prawns and shrimps genetics animal breeding Makombu, J.G. Cheruiyot, E.K. Stomeo, Francesca Thuo, D.N. Oben, P.M. Oben, Benedicta O. Zango, P. Mialhe, E. Ngueguim, J.R. Mujibi, F.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 | macrobrachium single nucleotide polymorphism genetic markers freshwater prawns and shrimps genetics animal breeding |
| url | https://hdl.handle.net/10568/125118 |
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