The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
- Author
- 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 (UGent) , Robert Henry, Pierre Marraccini, Yves Van de Peer (UGent) , Alan Andrade, Douglas Domingues, Giovanni Giuliano, Lukas Mueller, Luiz Filipe Pereira, Stephane Plaisance, Valerie Poncet, Stephane Rombauts (UGent) , David Sankoff, Victor A. Albert, Dominique Crouzillat, Alexandre de Kochko and Patrick Descombes
- Organization
- Project
- 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.
- Keywords
- Genetics, RESYNTHESIZED BRASSICA-NAPUS, PHYLOGENETIC ANALYSIS, RESISTANCE, ARABIDOPSIS, EVOLUTION, GENES, POLYPLOIDY, EXPRESSION, INFERENCE, PROVIDES
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Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HVKANDH9F3AYC8RFV1VW1R81
- MLA
- Salojärvi, Jarkko, et al. “The Genome and Population Genomics of Allopolyploid Coffea Arabica Reveal the Diversification History of Modern Coffee Cultivars.” NATURE GENETICS, vol. 56, no. 4, 2024, pp. 721–31, doi:10.1038/s41588-024-01695-w.
- APA
- Salojärvi, J., Rambani, A., Yu, Z., Guyot, R., Strickler, S., Lepelley, M., … Descombes, P. (2024). The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. NATURE GENETICS, 56(4), 721–731. https://doi.org/10.1038/s41588-024-01695-w
- Chicago author-date
- Salojärvi, Jarkko, Aditi Rambani, Zhe Yu, Romain Guyot, Susan Strickler, Maud Lepelley, Cui Wang, et al. 2024. “The Genome and Population Genomics of Allopolyploid Coffea Arabica Reveal the Diversification History of Modern Coffee Cultivars.” NATURE GENETICS 56 (4): 721–31. https://doi.org/10.1038/s41588-024-01695-w.
- Chicago author-date (all authors)
- Salojärvi, Jarkko, 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. 2024. “The Genome and Population Genomics of Allopolyploid Coffea Arabica Reveal the Diversification History of Modern Coffee Cultivars.” NATURE GENETICS 56 (4): 721–731. doi:10.1038/s41588-024-01695-w.
- Vancouver
- 1.Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, et al. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. NATURE GENETICS. 2024;56(4):721–31.
- IEEE
- [1]J. Salojärvi et al., “The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars,” NATURE GENETICS, vol. 56, no. 4, pp. 721–731, 2024.
@article{01HVKANDH9F3AYC8RFV1VW1R81,
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.}},
articleno = {{s41588-024-01695-w}},
author = {{Salojärvi, Jarkko and Rambani, Aditi and Yu, Zhe and Guyot, Romain and Strickler, Susan and Lepelley, Maud and Wang, Cui and Rajaraman, Sitaram and Rastas, Pasi and Zheng, Chunfang and Muñoz, Daniella Santos and Meidanis, João and Paschoal, Alexandre Rossi and Bawin, Yves and Krabbenhoft, Trevor J. and Wang, Zhen Qin and Fleck, Steven J. and Aussel, Rudy and Bellanger, Laurence and Charpagne, Aline and Fournier, Coralie and Kassam, Mohamed and Lefebvre, Gregory and Métairon, Sylviane and Moine, Déborah and Rigoreau, Michel and Stolte, Jens and Hamon, Perla and Couturon, Emmanuel and Tranchant-Dubreuil, Christine and Mukherjee, Minakshi and Lan, Tianying and Engelhardt, Jan and Stadler, Peter and Correia De Lemos, Samara Mireza and Suzuki, Suzana Ivamoto and Sumirat, Ucu and Wai, Ching Man and Dauchot, Nicolas and Orozco-Arias, Simon and Garavito, Andrea and Kiwuka, Catherine and Musoli, Pascal and Nalukenge, Anne and Guichoux, Erwan and Reinout, Havinga and Smit, Martin and Carretero-Paulet, Lorenzo and Filho, Oliveiro Guerreiro and Braghini, Masako Toma and Padilha, Lilian and Sera, Gustavo Hiroshi and Ruttink, Tom and Henry, Robert and Marraccini, Pierre and Van de Peer, Yves and Andrade, Alan and Domingues, Douglas and Giuliano, Giovanni and Mueller, Lukas and Pereira, Luiz Filipe and Plaisance, Stephane and Poncet, Valerie and Rombauts, Stephane and Sankoff, David and Albert, Victor A. and Crouzillat, Dominique and de Kochko, Alexandre and Descombes, Patrick}},
issn = {{1061-4036}},
journal = {{NATURE GENETICS}},
keywords = {{Genetics,RESYNTHESIZED BRASSICA-NAPUS,PHYLOGENETIC ANALYSIS,RESISTANCE,ARABIDOPSIS,EVOLUTION,GENES,POLYPLOIDY,EXPRESSION,INFERENCE,PROVIDES}},
language = {{eng}},
number = {{4}},
pages = {{s41588-024-01695-w:721--s41588-024-01695-w:731}},
title = {{The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars}},
url = {{http://doi.org/10.1038/s41588-024-01695-w}},
volume = {{56}},
year = {{2024}},
}
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