Management and Use of Genetic Resources for Climate Smart Crop Improvement: Overview of the Tailor-Made Training (TMT) Course
DOI :
https://doi.org/10.56027/JOASD.202024Mots-clés :
Plant Genetic Resources, Management, policies, Sequencing, BioinformaticsRésumé
Via a close cooperation between Dutch and Tunisian research organizations and leveraging the possibilities provided by the Dutch Orange Knowledge Fund, a tailor-made training course on management and use of genetic resources for climate smart crop improvement took place in Tunisia from April 15-26 2024. The course consisted of two modules: one focused on Plant Genetic Resources Management and the other on Sequencing and Bioinformatics. The module on PGR management covered key topics including food security and Biodiversity, PGR management, and PGR policies, whereas the module on Sequencing and Bioinformatics provided up to date information on DNA sequencing methods, genome assembly, genotyping, diversity assessment and genome-wide association studies. The course was structured with a combination of lectures and practical assignments. Additionally, two full-day field visits were integrated into the program, providing participants with valuable information and practical knowledge in on farm management techniques. In total, the course was attended by 26 participants.
Références
Beavis, W., & Mahama, A. A. (2023). Multi Environment Trials: Linear Mixed Models. In Quantitative Genetics for Plant Breeding. Iowa State University Digital Press.
Breese, E.L. (1989). Regeneration and multiplication of germplasm resources in seed genebanks: the scientific background. IBPGR, Rome, Italy, pp. 69.
Brush, S.B. (2005). Genes in the field: on farm conservation of crop diversity. Lewis Publ., Boca Raton, USA.
Chung, Y. S., Choi, S. C., Jun, T. H., & Kim, C. (2017). Genotyping-by-sequencing: a promising tool for plant genetics research and breeding. Horticulture Environment and Biotechnology, 58(5), 425–431. https://doi.org/10.1007/S13580-017-0297-8/METRICS
Churchill, G. A., & Doerge, R. W. (1994). Empirical threshold values for quantitative trait mapping. Genetics, 138(3), 963–971. https://doi.org/10.1007/s11703-007-0022-y
COGENT (2018). A global strategy for the conservation and use of coconut genetic resources 2018-2028. (R. Bourdeix and A. Prades, compilers), Bioversity International, Montpellier, France.
Cronn, R., Knaus, B. J., Liston, A., Maughan, P. J., Parks, M., Syring, J. V., & Udall, J. (2012). Targeted enrichment strategies for next-generation plant biology. American Journal of Botany, 99(2), 291–311. https://doi.org/10.3732/ajb.1100356
Crop Genebank Knowledge Base. https://cropgenebank.sgrp.cgiar.org/index.php/home-mainmenu-71/about-this-site
Cross, R.J., & Wallace, A.R. (1994). Loss of genetic diversity from heterogeneous self-pollinating genebank accessions. Theor. Appl. Genet., 88, 885-890.
De Boef, W.S., Subedi, A., Peroni, N., Thijssen, M., &O’Keeffe, E. (2013). Community Biodiversity Management. Routledge Ltd., Oxon., UK.
Delahaye, C., & Nicolas, J. (2021). Sequencing DNA with nanopores: Troubles and biases. PLoS ONE, 16(10). https://doi.org/10.1371/JOURNAL.PONE.0257521
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE, 6(5), e19379. https://doi.org/10.1371/journal.pone.0019379
FAO (2011). Introduction tothe International Treaty on Plant Genetic Resources for Food and Agriculture. http://www.fao.org/3/a-i2631e.pdf
Gale, J.S., & Lawrence, M.J. (1984). The decay of variability. In Crop Genetic Resources: Conservation and Evaluation (J.H.W. Holden & J.T. Williams, Eds.), George Allen & Unwin Ltd., Hert., UK, pp. 77-101.
Geibelid, J., Reimer, C., Weigendid, S., Weigend, A., Pookid, T., &Simianer, H. (2021). How array design creates SNP ascertainment bias. https://doi.org/10.1371/journal.pone.0245178
Giani, A. M., Gallo, G. R., Gianfranceschi, L., &Formenti, G. (2020). Long walk to genomics: History and current approaches to genome sequencing and assembly. Computational and Structural Biotechnology Journal, 18, 9–19. https://doi.org/10.1016/J.CSBJ.2019.11.002
Goodwin, S., McPherson, J. D., & Richard McCombie, W. (2016). Coming of age: ten years of next-generation sequencing technologies. https://doi.org/10.1038/nrg.2016.49
Heywood, V.H., & Dulloo, M.E. (2005). In situ conservation of wild plants: a critical review of best practisers. IPGRI Tech. Bull., 11, IPGRI, Rome, Italy.
Hu, T., Chitnis, N., Monos, D., & Dinh, A. (2021). Next-generation sequencing technologies: An overview. Human Immunology, 82(11), 801–811. https://doi.org/10.1016/j.humimm.2021.02.012 Ikegawa, S. (2012). A Short History of the Genome-Wide Association Study: Where We Were and Where We Are Going. Genomics & Informatics, 10(4), 220. https://doi.org/10.5808/GI.2012.10.4.220
Kapli, P., Yang, Z., & Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 21(7), 428–444. https://doi.org/10.1038/s41576-020-0233-0
Li, H., & Durbin, R. (2024). Genome assembly in the telomere-to-telomere era. Nature Reviews Genetics. https://doi.org/10.1038/s41576-024-00718-w
Miller, M. R., Dunham, J. P., Amores, A., Cresko, W. A., & Johnson, E. A. (2007). Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Research, 17(2), 240–248. https://doi.org/10.1101/GR.5681207
PacBio. (2024). Long-read sequencing myths: debunked. Part 1- HiFi sequencing. https://www.pacb.com/blog/long-read-sequencing-myths-debunked-part-1-hifi-sequencing
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945–959. https://doi.org/10.1111/j.1471-8286.2007.01758.x
Sims, D., Sudbery, I., Ilott, N. E., Heger, A., & Ponting, C. P. (2014). Sequencing depth and coverage: Key considerations in genomic analyses. Nature Reviews Genetics, 15(2), 121–132. https://doi.org/
Sohn, J., & Nam, J.-W. (2016). The present and future of de novo whole-genome assembly. Briefings in Bioinformatics, bbw096. https://doi.org/10.1093/bib/bbw096
Song, L., Huang, W., Kang, J., Huang, Y., Ren, H., & Ding, K. (2017). Comparison of error correction algorithms for Ion Torrent PGM data: application to hepatitis B virus. Scientific Reports 2017 7:1, 7(1), 1–11. https://doi.org/10.1038/s41598-017-08139-y
Thomas, D. C., Haile, R. W., & Duggan, D. (2005). Recent Developments in Genomewide Association Scans: A Workshop Summary and Review. The American Journal of Human Genetics, 77(3), 337–345. https://doi.org/10.1086/432962
Wilson, E.O. (1988). Biodiversity. National Acad. of Sc., Washington D.C. Natl. Acad. Press, USA. https://doi.org/10.17226.989.
Yu, J., Pressoir, G., Briggs, W. H., Vroh Bi, I., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., Kresovich, S., & Buckler, E. S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics, 38(2), 203–208. https://doi.org/10.1038/ng1702
Zhang, J., Liu, F., Reif, J. C., & Jiang, Y. (2021). On the use of GBLUP and its extension for GWAS with additive and epistatic effects. G3 Genes|Genomes|Genetics, 11(7). https://doi.org/10.1093/g3journal/jkab122
Téléchargements
Fichiers supplémentaires
Publié-e
Comment citer
Numéro
Rubrique
Licence
(c) Tous droits réservés JOURNAL OF OASIS AGRICULTURE AND SUSTAINABLE DEVELOPMENT 2024

Cette œuvre est protégée sous licence Creative Commons Attribution - Partage dans les Mêmes Conditions 4.0 International.
https://creativecommons.org/licenses/by-sa/4.0/
Plum Analytics
Artifact Widget
