Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm
Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically im...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/119861 |
| _version_ | 1855522081793376256 |
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| author | Silva, G. Bömer, M. Turaki, A.A. Nkere, C. Kumar, P. Lava Seal, S. |
| author_browse | Bömer, M. Kumar, P. Lava Nkere, C. Seal, S. Silva, G. Turaki, A.A. |
| author_facet | Silva, G. Bömer, M. Turaki, A.A. Nkere, C. Kumar, P. Lava Seal, S. |
| author_sort | Silva, G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam. |
| format | Journal Article |
| id | CGSpace119861 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1198612025-12-08T10:29:22Z Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm Silva, G. Bömer, M. Turaki, A.A. Nkere, C. Kumar, P. Lava Seal, S. yams dioscorea food security viruses west africa Viruses of the genus Badnavirus (family Caulimoviridae) are double-stranded DNA-reverse transcribing (dsDNA-RT) plant viruses and have emerged as serious pathogens of tropical and temperate crops globally. Endogenous badnaviral sequences are found integrated in the genomes of several economically important plant species. Infection due to activation of replication-competent integrated copies of the genera Badnavirus, Petuvirus and Cavemovirus has been described. Such endogenous badnaviral elements pose challenges to the development of nucleic acid-based diagnostic methods for episomal virus infections and decisions on health certification for international movement of germplasm and seed. One major food security crop affected is yam (Dioscorea spp.). A diverse range of Dioscorea bacilliform viruses (DBVs), and endogenous DBV (eDBV) sequences have been found to be widespread in yams cultivated in West Africa and other parts of the world. This study outlines the development of multiplex PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE) to assist in the detection and analysis of eDBVs, through the example of analysing yam germplasm from Nigeria and Ghana. Primers targeting the three most prevalent DBV monophyletic species groups in West Africa were designed to improve DGGE resolution of complex eDBV sequence fingerprints. Multiplex PCR-DGGE with the addition of a tailor-made DGGE sequence marker enables rapid comparison of endogenous badnaviral sequence diversity across germplasm, as illustrated in this study for eDBV diversity in yam. 2022 2022-06-16T11:01:07Z 2022-06-16T11:01:07Z Journal Article https://hdl.handle.net/10568/119861 en Open Access application/pdf Frontiers Media Silva, G., Bömer, M., Turaki, A.A., Nkere, C., Kumar, P.L. & Seal, S. (2022). Homing in on endogenous badnaviral elements: development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm. Frontiers in Plant Science, 13:846989, 1-16. |
| spellingShingle | yams dioscorea food security viruses west africa Silva, G. Bömer, M. Turaki, A.A. Nkere, C. Kumar, P. Lava Seal, S. Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title | Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title_full | Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title_fullStr | Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title_full_unstemmed | Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title_short | Homing in on endogenous badnaviral elements: Development of multiplex PCR-DGGE for detection and rapid identification of badnavirus sequences in yam germplasm |
| title_sort | homing in on endogenous badnaviral elements development of multiplex pcr dgge for detection and rapid identification of badnavirus sequences in yam germplasm |
| topic | yams dioscorea food security viruses west africa |
| url | https://hdl.handle.net/10568/119861 |
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