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The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

TitleThe genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Publication TypeArticolo su Rivista peer-reviewed
Year of Publication2024
AuthorsSalojärvi, J., Rambani A., Yu Z., Guyot R., Strickler S., Lepelley M., Wang C., Rajaraman S., Rastas P., Zheng C., Muñoz 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., Métairon S., Moine D., Rigoreau M., Stolte J., Hamon P., Couturon E., Tranchant-Dubreuil C., Mukherjee M., Lan T., Engelhardt J., Stadler P., De Lemos S.M. Correia, Suzuki S.I., Sumirat U., Wai C.M., Dauchot N., Orozco-Arias S., Garavito A., Kiwuka C., Musoli P., Nalukenge A., Guichoux E., Reinout H., Smit M., Carretero-Paulet L., Filho O.G., Braghini M.T., Padilha L., Sera G.H., Ruttink T., Henry R., Marraccini P., Van De Peer Y., Andrade A., Domingues D., Giuliano Giovanni, Mueller L., Pereira L.F., Plaisance S., Poncet V., Rombauts S., Sankoff D., Albert V.A., Crouzillat D., de Kochko A., and Descombes P.
JournalNature Genetics
Date PublishedJan-04-2024
Keywordsallopolyploidy, article, Breeding, Coffea, Coffea arabica, Coffea canephora, Coffee, controlled study, Cultivar, Diploidy, Domestication, Genetic Variation, Genome, haploidy, nonhuman, polyploidy, population genomics

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 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. © The Author(s) 2024.


cited By 0

Short TitleNat Genet
Citation KeySalojärvi2024721