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

Author(s):Show less -

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

• Document type: Journal article
• Source: Nature Genetics; v. 56, n. 4, p. 27-pg., 2024-04-01.

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 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. (AU)

• FAPESP's process: 17/01455-2 - Biochemical and molecular basis of the metabolic network of diterpenes, bioactive and natural compounds in coffee
• Grantee: Suzana Tiemi Ivamoto
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/10896-0 - Can hexanoic acid signaling modulate the transcriptome, metabolome and pathogen development in coffee trees?
• Grantee: Douglas Silva Domingues
• Support Opportunities: Research Grants - Young Investigators Grants