Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population
A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding...
| Autores principales: | , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/152344 |
| _version_ | 1855529062468943872 |
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| author | Mbanjo, Edwige Gaby Nkouaya Ogungbesan, Adebukola Agbona, Afolabi Akpotuzor, Patrick Toyinbo, Seyi Iluebbey, Peter Rabbi, Ismail Yusuf Peteti, Prasad Wages, Sharon A. Norton, Joanna Zhang, Xiaofei Bohorquez-Chaux, Adriana Mushoriwa, Hapson Egesi, Chiedozie Kulakow, Peter Parkes, Elizabeth |
| author_browse | Agbona, Afolabi Akpotuzor, Patrick Bohorquez-Chaux, Adriana Egesi, Chiedozie Iluebbey, Peter Kulakow, Peter Mbanjo, Edwige Gaby Nkouaya Mushoriwa, Hapson Norton, Joanna Ogungbesan, Adebukola Parkes, Elizabeth Peteti, Prasad Rabbi, Ismail Yusuf Toyinbo, Seyi Wages, Sharon A. Zhang, Xiaofei |
| author_facet | Mbanjo, Edwige Gaby Nkouaya Ogungbesan, Adebukola Agbona, Afolabi Akpotuzor, Patrick Toyinbo, Seyi Iluebbey, Peter Rabbi, Ismail Yusuf Peteti, Prasad Wages, Sharon A. Norton, Joanna Zhang, Xiaofei Bohorquez-Chaux, Adriana Mushoriwa, Hapson Egesi, Chiedozie Kulakow, Peter Parkes, Elizabeth |
| author_sort | Mbanjo, Edwige Gaby Nkouaya |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future. |
| format | Journal Article |
| id | CGSpace152344 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1523442025-12-08T10:29:22Z Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population Mbanjo, Edwige Gaby Nkouaya Ogungbesan, Adebukola Agbona, Afolabi Akpotuzor, Patrick Toyinbo, Seyi Iluebbey, Peter Rabbi, Ismail Yusuf Peteti, Prasad Wages, Sharon A. Norton, Joanna Zhang, Xiaofei Bohorquez-Chaux, Adriana Mushoriwa, Hapson Egesi, Chiedozie Kulakow, Peter Parkes, Elizabeth cassava biofortification breeding genetic markers population structure selection criteria A validated marker system is crucial to running an effective genomics-assisted breeding program. We used 36 Kompetitive Allele-Specific PCR (KASP) markers to genotype 376 clones from the biofortified cassava pipeline, and fingerprinted 93 of these clones with DArTseq markers to characterize breeding materials and evaluate their relationships. The discriminating ability of the 36-quality control (QC) KASP and 6602 DArTseq markers was assessed using 92 clones genotyped in both assays. In addition, trait-specific markers were used to determine the presence or absence of target genomic regions. Hierarchical clustering identified two major groups, and the clusters were consistent with the breeding program origins. There was moderate genetic differentiation and a low degree of variation between the identified groups. The general structure of the population was similar using both assays. Nevertheless, KASP markers had poor resolution when it came to differentiating the genotypes by seed sources and overestimated the prevalence of duplicates. The trait-linked markers did not achieve optimal performance as all markers displayed variable levels of false positive and/or false negative. These findings represent the initial step in the application of genomics-assisted breeding for the biofortified cassava pipeline, and will guide the use of genomic selection in the future. 2024 2024-09-23T14:18:04Z 2024-09-23T14:18:04Z Journal Article https://hdl.handle.net/10568/152344 en Open Access application/pdf MDPI Mbanjo, E.G.N.; Ogungbesan, A.; Agbona, A.; Akpotuzor, P.; Toyinbo, S.; Iluebbey, P.; Rabbi, I.Y.; Peteti, P.; Wages, S.A.; Norton, J.; Zhang, X.; Bohorquez-Chaux, A.; Mushoriwa, H.; Egesi, C.; Kulakow, P.; Parkes, E. (2024) Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population. Plants 13(16): 2328. ISSN: 2223-7747 |
| spellingShingle | cassava biofortification breeding genetic markers population structure selection criteria Mbanjo, Edwige Gaby Nkouaya Ogungbesan, Adebukola Agbona, Afolabi Akpotuzor, Patrick Toyinbo, Seyi Iluebbey, Peter Rabbi, Ismail Yusuf Peteti, Prasad Wages, Sharon A. Norton, Joanna Zhang, Xiaofei Bohorquez-Chaux, Adriana Mushoriwa, Hapson Egesi, Chiedozie Kulakow, Peter Parkes, Elizabeth Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title | Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title_full | Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title_fullStr | Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title_full_unstemmed | Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title_short | Validation of SNP markers for diversity analysis, quality control, and trait selection in a biofortified cassava population |
| title_sort | validation of snp markers for diversity analysis quality control and trait selection in a biofortified cassava population |
| topic | cassava biofortification breeding genetic markers population structure selection criteria |
| url | https://hdl.handle.net/10568/152344 |
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