sequencing of the Robusta genome in 2014. Albert and collaborators’ current work also presents a highly improved version of the Robusta genome, as well as new sequence of Arabica’s other progenitor species, Coffea eugenioides.
While breeders have tried replicating this crossbreeding to boost pathogen defense, the new Arabica reference genome allowed the present researchers to pinpoint a novel region harboring members of the RPP8 resistance gene family as well as a general regulator of resistance genes, CPR1.
“These results suggest a novel target locus for potentially improving pathogen resistance in Arabica,” Salojärvi says.
The genome provided other new findings as well, like which wild varieties are closest to modern, cultivated Arabica coffee. They also found that the Typica variety, an early Dutch cultivar originating from either India or Sri Lanka, is likely the parent of the Bourbon variety, principally cultivated by the French.
“Our work has not been unlike reconstructing the family tree of a very important family,” Albert says.
Reference: “The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars” by Jarkko Salojärvi, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, Sitaram Rajaraman, Pasi Rastas, Chunfang Zheng, Daniella Santos Muñoz, João Meidanis, Alexandre Rossi Paschoal, Yves Bawin, Trevor J. Krabbenhoft, Zhen Qin Wang, Steven J. Fleck, Rudy Aussel, Laurence Bellanger, Aline Charpagne, Coralie Fournier, Mohamed Kassam, Gregory Lefebvre, Sylviane Métairon, Déborah Moine, Michel Rigoreau, Jens Stolte, Perla Hamon, Emmanuel Couturon, Christine Tranchant-Dubreuil, Minakshi Mukherjee, Tianying Lan, Jan Engelhardt, Peter Stadler, Samara Mireza Correia De Lemos, Suzana Ivamoto Suzuki, Ucu Sumirat, Ching Man Wai, Nicolas Dauchot, Simon Orozco-Arias, Andrea Garavito, Catherine Kiwuka, Pascal Musoli, Anne Nalukenge, Erwan Guichoux, Havinga Reinout, Martin Smit, Lorenzo Carretero-Paulet, Oliveiro Guerreiro Filho, Masako Toma Braghini, Lilian Padilha, Gustavo Hiroshi Sera, Tom Ruttink, Robert Henry, Pierre Marraccini, Yves Van de Peer, Alan Andrade, Douglas Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stephane Plaisance, Valerie Poncet, Stephane Rombauts, David Sankoff, Victor A. Albert, Dominique Crouzillat, Alexandre de Kochko and Patrick Descombes, 15 April 2024, Nature Genetics.
DOI: 10.1038/s41588-024-01695-w
Nestlé Research funded the majority of the research. The large international team was co-led by Albert, whose work was supported by the National Science Foundation, and contributions from many other organizations. Other UB contributors include Trevor Krabbenhoft, PhD, and Zhen Wang, PhD, both assistant professors of biological sciences; PhD student Steven Fleck; PhD graduate Minakshi Mukherjee; and former research scientist Tianying Lan – all from the Department of Biological Sciences.