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

2024; Nature Portfolio; Volume: 56; Issue: 4 Linguagem: Inglês

10.1038/s41588-024-01695-w

1546-1718

Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan R. Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidânis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J. Krabbenhoft, Zhen Qin Wang, Steven J. Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Grégory Lefebvre, Sylviane Métairon, D Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant‐Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter F. Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Wai, Nicolas Dauchot, Simón Orozco-Arias, Andréa Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero‐Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lílian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert J Henry, Pierre Marraccini, Yves Van de Peer, Alan Carvalho Andrade, Douglas Silva Domingues, Giovanni Giuliano, Lukas A. Mueller, Luiz Filipe Protásio Pereira, Stéphane Plaisance, Valérie Poncet, Stéphane Rombauts, David Sankoff, Victor A. Albert, Dominique Crouzillat, Alexandre de Kochko, Patrick Descombes,

CRISPR and Genetic Engineering

Abstract 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 .