A protocol for detection of large chromosome variations in Banana using next generation sequencing
Core activities of genebank operations include the preservation of germplasm identity and maintenance of genetic integrity. Some organisms such as banana are maintained by tissue culture that can foster accumulation of somatic mutations and loss of genetic integrity. Such changes can be reflected in...
| Main Authors: | , , , , , , |
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| Format: | Book Chapter |
| Language: | Inglés |
| Published: |
Springer
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/119749 |
| _version_ | 1855513071386099712 |
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| author | Breton, Catherine Cenci, Alberto Sardos, Julie Chase, Rachel Ruas, Max Rouard, Mathieu Roux, Nicolas |
| author_browse | Breton, Catherine Cenci, Alberto Chase, Rachel Rouard, Mathieu Roux, Nicolas Ruas, Max Sardos, Julie |
| author_facet | Breton, Catherine Cenci, Alberto Sardos, Julie Chase, Rachel Ruas, Max Rouard, Mathieu Roux, Nicolas |
| author_sort | Breton, Catherine |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Core activities of genebank operations include the preservation of germplasm identity and maintenance of genetic integrity. Some organisms such as banana are maintained by tissue culture that can foster accumulation of somatic mutations and loss of genetic integrity. Such changes can be reflected in their genome structure and thus be revealed by sequencing methods. Here, we propose a protocol for the detection of large chromosomal gains and/or losses that was applied to in vitro banana accessions with different levels of ploidy. Mixoploidy was detected in triploid (3x) accessions with chromosomal regions being diploid (2x) and tetraploid (4x) and in diploid accessions (2x) where large deletions resulted in partial haploidy (1x). Such abnormal molecular karyotypes can potentially explain phenotypic aberrations observed in off type material. With the affordable cost of Next Generation Sequencing (NGS) technologies and the release of the presented bioinformatic pipeline, we aim to promote the application of this methodology as a routine operation for genebank management as an important step to monitor the genetic integrity of distributed material. Moreover, genebank users can be also empowered to apply the methodology and check the molecular karyotype of the ordered material. |
| format | Book Chapter |
| id | CGSpace119749 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1197492025-11-05T12:37:31Z A protocol for detection of large chromosome variations in Banana using next generation sequencing Breton, Catherine Cenci, Alberto Sardos, Julie Chase, Rachel Ruas, Max Rouard, Mathieu Roux, Nicolas aneuploidy somaclonal variation gene banks mutation aneuploidia variación somaclonal banco de genes Core activities of genebank operations include the preservation of germplasm identity and maintenance of genetic integrity. Some organisms such as banana are maintained by tissue culture that can foster accumulation of somatic mutations and loss of genetic integrity. Such changes can be reflected in their genome structure and thus be revealed by sequencing methods. Here, we propose a protocol for the detection of large chromosomal gains and/or losses that was applied to in vitro banana accessions with different levels of ploidy. Mixoploidy was detected in triploid (3x) accessions with chromosomal regions being diploid (2x) and tetraploid (4x) and in diploid accessions (2x) where large deletions resulted in partial haploidy (1x). Such abnormal molecular karyotypes can potentially explain phenotypic aberrations observed in off type material. With the affordable cost of Next Generation Sequencing (NGS) technologies and the release of the presented bioinformatic pipeline, we aim to promote the application of this methodology as a routine operation for genebank management as an important step to monitor the genetic integrity of distributed material. Moreover, genebank users can be also empowered to apply the methodology and check the molecular karyotype of the ordered material. 2022 2022-06-07T07:41:10Z 2022-06-07T07:41:10Z Book Chapter https://hdl.handle.net/10568/119749 en Open Access application/pdf Springer Breton, C.; Cenci, A.; Sardos, J.; Chase, R.; Ruas, M.; Rouard, M.; Roux, N. (2022) A protocol for detection of large chromosome variations in Banana using next generation sequencing. In: Jankowicz-Cieslak, J.; Ingelbrecht, I.L. (eds) Efficient screening techniques to identify mutants with TR4 resistance in banana. Berlin, Heidelberg (Germany): Springer. p. 129–148. ISBN: 978-3-662-64914-5 |
| spellingShingle | aneuploidy somaclonal variation gene banks mutation aneuploidia variación somaclonal banco de genes Breton, Catherine Cenci, Alberto Sardos, Julie Chase, Rachel Ruas, Max Rouard, Mathieu Roux, Nicolas A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title | A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title_full | A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title_fullStr | A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title_full_unstemmed | A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title_short | A protocol for detection of large chromosome variations in Banana using next generation sequencing |
| title_sort | protocol for detection of large chromosome variations in banana using next generation sequencing |
| topic | aneuploidy somaclonal variation gene banks mutation aneuploidia variación somaclonal banco de genes |
| url | https://hdl.handle.net/10568/119749 |
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