The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
2024
Salojaervi, J. | Rambani, A. | Yu, Z. | Guyot, Romain | Strickler, S. | Lepelley, M. | Wang, C. | Rajaraman, S. | Rastas, P. | Zheng, C. F. | Munoz, D. S. | Meidanis, J. | Paschoal, A. R. | Bawin, Y. | Krabbenhoft, T. J. | Wang, Z. Q. | Fleck, S. J. | Aussel, R. | Bellanger, L. | Charpagne, A. | Fournier, C. | Kassam, M. | Lefebvre, G. | Metairon, S. | Moine, D. | Rigoreau, M. | Stolte, J. | Hamon, Perla | Couturon, Emmanuel | Dubreuil Tranchant, Christine | Mukherjee, M. | Lan, T. Y. | Engelhardt, J. | Stadler, P. | de Lemos, S. M. C. | Suzuki, S. I. | Sumirat, U. | Wai, C. M. | Dauchot, N. | Orozco-Arias, S. | Garavito, A. | Kiwuka, C. | Musoli, P. | Nalukenge, A. | Guichoux, Erwan | Reinout, H. | Smit, M. | Carretero-Paulet, L. | Guerreiro, O. | Braghini, M. T. | Padilha, L. | Sera, G. H. | Ruttink, T. | Henry, R. | Marraccini, P. | van de Peer, Y. | Andrade, A. | Domingues, D. | Giuliano, G. | Mueller, L. | Pereira, L. F. | Plaisance, S. | Poncet, Valérie | Rombauts, S. | Sankoff, D. | Albert, V. A. | Crouzillat, D. | Kochko, Alexandre De | Descombes, P. | Nanyang Technological University [Singapour] (NTU) | Helsingin yliopisto = Helsingfors universitet = University of Helsinki | Cornell University [Ithaca] (CU) | Diversité, adaptation, développement des plantes (UMR DIADE) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [Occitanie])-Université de Montpellier (UM) | Institut de Recherche pour le Développement (IRD) | Biodiversité, Gènes & Communautés (BioGeCo) ; Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
法语. Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred similar to 30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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