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

Salojärvi Jarkko, Rambani Aditi, Yu Zhe, Guyot Romain, Strickler Susan R., Lepelley Maud, Wang Cui, Rajaraman Sitaram, Rastas Pasi, Zheng Chunfang, Santos Muñoz Daniella, Meidanis João, Rossi Paschoal Alexandre, Bawin Yves, Krabbenhoft Trevor J., Wang Zhen Qin, Fleck Steven J., Aussel Rudy, Bellanger Laurence, Charpagne Aline, Fournier Coralie, Kassam Mohamed, Lefebvre Gregory, Métairon Sylviane, Descombes Patrick, Rigoreau Michel, Stolte Jens, Hamon Perla, Couturon Emmanuel, Tranchant-Dubreuil Christine, Mukherjee Minakshi, Lan Tianying, Engelhardt Jan, Stadler Peter, De Lemos Samara Mireza Correia, Ivamoto Suzuki Suzana, Sumirat Ucu, Wai Ching Man, Dauchot Nicolas, Orozco-Arias Simon, Garavito Giovanny, Kiwuka Catherine, Musoli Pascal, Nalukenge Anne, Guichoux Erwan, Reinout Havinga, Smit Martin, Carretero-Paulet Lorenzo, Guerreiro Filho Oliveiro, Toma Braghini Masako, Padilha Lilian, Hiroshi Sera Gustavo, Ruttink Tom, Henry Robert, Marraccini Pierre, et al.. 2024. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nature Genetics, 56 : 721-731.

Url - jeu de données - Entrepôt autre : https://zenodo.org/doi/10.5281/zenodo.5136526 / Url - jeu de données - Entrepôt autre : https://genomevolution.org/coge/ / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA698600 / Url - jeu de données - Entrepôt autre : https://bioinformatics.psb.ugent.be/orcae/overview/Coara / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/JAZHSI000000000.1/

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : 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.

Mots-clés Agrovoc : Coffea arabica, Coffea canephora, Coffea eugenioides, polyploïdie, génome, variété, variation génétique, génétique des populations, dynamique des populations, génomique, adaptation aux changements climatiques, expression des gènes, phytogénétique, amélioration des plantes

Mots-clés libres : Coffea arabica, Genome sequencing, Genome informatics, Genomics, Plant Breeding, Plant genetics, Plant hybridization

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement européennes : European Research Council, European Commission

Agences de financement hors UE : Academy of Finland, Ghent University

Programme de financement européen : H2020

Projets sur financement : (EU) Replaying the 'genome duplication' tape of life: The importance of polyploidy for adaptation in a changing environment, (EU) Promoting a Plant Genetic Resource Community for Europe

Auteurs et affiliations

• Salojärvi Jarkko, Nanyang Technological University (SGP) - auteur correspondant
• Rambani Aditi, Cornell University (USA)
• Yu Zhe, University of Ottawa (CAN)
• Guyot Romain, IRD (FRA)
• Strickler Susan R., Boyce Thompson Institute for Plant Research (USA)
• Lepelley Maud, Nestlé (FRA)
• Wang Cui, University of Helsinki (FIN)
• Rajaraman Sitaram, University of Helsinki (FIN)
• Rastas Pasi, University of Helsinki (FIN)
• Zheng Chunfang, University of Ottawa (CAN)
• Santos Muñoz Daniella, University of Ottawa (CAN)
• Meidanis João, UNICAMP (BRA)
• Rossi Paschoal Alexandre, UTFPR (BRA)
• Bawin Yves, ILVO (BEL)
• Krabbenhoft Trevor J., University at Buffalo (USA)
• Wang Zhen Qin, University at Buffalo (USA)
• Fleck Steven J., University at Buffalo (USA)
• Aussel Rudy, Aix-Marseille université (FRA)
• Bellanger Laurence, Nestlé (FRA)
• Charpagne Aline, Nestlé (CHE)
• Fournier Coralie, Nestlé (CHE)
• Kassam Mohamed, Nestlé (CHE)
• Lefebvre Gregory, Nestlé (CHE)
• Métairon Sylviane, Nestlé (CHE)
• Descombes Patrick, Nestlé (CHE) - auteur correspondant
• Rigoreau Michel, Nestlé (FRA)
• Stolte Jens, Nestlé (CHE)
• Hamon Perla, IRD (FRA)
• Couturon Emmanuel, IRD (FRA)
• Tranchant-Dubreuil Christine, IRD (FRA)
• Mukherjee Minakshi, University at Buffalo (USA)
• Lan Tianying, University at Buffalo (USA)
• Engelhardt Jan, University of Leipzig (DEU)
• Stadler Peter, University of Leipzig (DEU)
• De Lemos Samara Mireza Correia, USP (BRA)
• Ivamoto Suzuki Suzana, UEL (BRA)
• Sumirat Ucu, ICCRI (IDN)
• Wai Ching Man, University of Illinois (USA)
• Dauchot Nicolas, University of Namur (BEL)
• Orozco-Arias Simon, UAM (COL)
• Garavito Giovanny, Universidad Nacional de Colombia (COL)
• Kiwuka Catherine, NARO (UGA)
• Musoli Pascal, NARO (UGA)
• Nalukenge Anne, NARO (UGA)
• Guichoux Erwan, INRAE (FRA)
• Reinout Havinga, Hortus Botanicus Amsterdam (NLD)
• Smit Martin, Hortus Botanicus Amsterdam (NLD)
• Carretero-Paulet Lorenzo, University of Almeria (ESP)
• Guerreiro Filho Oliveiro, IAC [Instituto Agronomico] (BRA)
• Toma Braghini Masako, IAC [Instituto Agronomico] (BRA)
• Padilha Lilian, EMBRAPA (BRA)
• Hiroshi Sera Gustavo, IAPAR (BRA)
• Ruttink Tom, ILVO (BEL)
• Henry Robert, University of Queensland (AUS)
• Marraccini Pierre, CIRAD-BIOS-UMR DIADE (FRA) ORCID: 0000-0001-7637-6811
• et al.

Source : Cirad-Agritrop (https://agritrop.cirad.fr/609262/)

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