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

SALOJÄRVI.; RAMBANI, A.; YU, Z.; GUYOT, R.; STRICKLER, S.; LEPELLEY, M.; WANG, C.; RAJARAMAN, S.; RASTAS, P.; ZHENG, C.; MUÑOZ, D. S.; MEIDANIS, J.; PASCHOAL, A. R.; BAWIN, Y.; KRABBENHOFT, T. J.; WANG, Z. Q.; FLECK, S. J.; AUSSEL, R.; BELLANGER, L.; CHARPAGNE, A.; FOURNIER, C.; KASSAM, M.; LEFEBVRE, G.; MÉTAIRON, S.; MOINE, D.; RIGOREAU, M.; STOLTE, J.; HAMON, P.; COUTURON, E.; TRANCHANT-DUBREUIL, C.; MUKHERJEE, M.; LAN, T.; ENGELHARDT, J.; STADLER, P.; LEMOS, S. M. C. DE; SUZUKI, S. I.; SUMIRAT, U.; WAI, C. M.; DAUCHOT, N.; OROZCO-ARIAS, S.; GARAVITO, A.; KIWUKA, C.; MUSOLI, P.; NALUKENGE, A.; GUICHOUX, E.; REINOUT, H.; SMIT, M.; CARRETERO-PAULET, L.; GUERREIRO FILHO, O.; BRAGHINI, M. T.; PADILHA, L.; SERA, G. H.; RUTTINK, T.; HENRY, R.; MARRACCINI, P.; PEER, Y. V. DE; ANDRADE, A. C.; DOMINGUES, D.; GIULIANO, G.; MUELLER, L.; PEREIRA, L. F. P.; PLAISANCE, S.; PONCET, V.; ROMBAUTS, S.; SANKOFF, D.; ALBERT, V. A.; CROUZILLAT, D.; KOCHKO, A. DE; DESCOMBES, P.; JARKKO SALOJÄRVI, NANYANG TECHNOLOGICAL UNIVERSITY; ADITI RAMBANI, CORNELL UNIVERSITY; ZHE YU, UNIVERSITY OF OTTAWA; ROMAIN GUYOT, UNIVERSITÉ DE MONTPELLIER; SUSAN STRICKLER, CORNELL UNIVERSITY; MAUD LEPELLEY, SOCIÉTÉ DES PRODUITS NESTLÉ SA; CUI WANG, UNIVERSITY OF HELSINKI; SITARAM RAJARAMAN, UNIVERSITY OF HELSINKI; PASI RASTAS, UNIVERSITY OF HELSINKI; CHUNFANG ZHENG, UNIVERSITY OF OTTAWA; DANIELLA SANTOS MUÑOZ, UNIVERSITY OF OTTAWADAVID; JOÃO MEIDANIS, UNIVERSIDADE DE CAMPINAS; ALEXANDRE ROSSI PASCHOAL, UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ; YVES BAWIN, FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; TREVOR J. KRABBENHOFT, UNIVERSITY AT BUFFALO; ZHEN QIN WANG, UNIVERSITY AT BUFFALO; STEVEN J. FLECK, UNIVERSITY AT BUFFALO; RUDY AUSSEL, AIX MARSEILLE UNIVERSITÉ; LAURENCE BELLANGER, SOCIÉTÉ DES PRODUITS NESTLÉ SA; ALINE CHARPAGNE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; CORALIE FOURNIER, SOCIÉTÉ DES PRODUITS NESTLÉ SA; MOHAMED KASSAM, SOCIÉTÉ DES PRODUITS NESTLÉ SA; GREGORY LEFEBVRE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; SYLVIANE MÉTAIRON, SOCIÉTÉ DES PRODUITS NESTLÉ SA; DÉBORAH MOINE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; MICHEL RIGOREAU, SOCIÉTÉ DES PRODUITS NESTLÉ SA; JENS STOLTE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; PERLA HAMON, UNIVERSITÉ DE MONTPELLIER; EMMANUEL COUTURON, UNIVERSITÉ DE MONTPELLIER; CHRISTINE TRANCHANT-DUBREUIL, UNIVERSITÉ DE MONTPELLIER; MINAKSHI MUKHERJEE, UNIVERSITY AT BUFFALO; TIANYING LAN, UNIVERSITY AT BUFFALO; JAN ENGELHARDT, UNIVERSITY OF LEIPZIG; PETER STADLER, UNIVERSITY OF LEIPZIG; SAMARA MIREZA CORREIA DE LEMOS, UNIVERSIDADE ESTADUAL DE SÃO PAULO; SUZANA IVAMOTO SUZUKI, UNIVERSIDADE ESTADUAL DE LONDRINA; UCU SUMIRAT, INDONESIAN COFFEE AND COCOA RESEARCH INSTITUTE; CHING MAN WAI, UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN; NICOLAS DAUCHOT, UNIVERSITY OF NAMUR; SIMON OROZCO-ARIAS, UNIVERSIDAD AUTÓNOMA DE MANIZALES; ANDREA GARAVITO, UNIVERSIDAD DE CALDAS; CATHERINE KIWUKA, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; PASCAL MUSOLI, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; ANNE NALUKENGE, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; ERWAN GUICHOUX, INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE; HAVINGA REINOUT, HORTUS BOTANICUS AMSTERDAM; MARTIN SMIT, HORTUS BOTANICUS AMSTERDAM; LORENZO CARRETERO-PAULET, UNIVERSIDAD DE ALMERÍA; OLIVEIRO GUERREIRO FILHO, INSTITUTO AGRONÔMICO; MASAKO TOMA BRAGHINI, INSTITUTO AGRONÔMICO; LILIAN PADILHA, CNPCA; GUSTAVO HIROSHI SERA, INSTITUTO DE DESENVOLVIMENTO RURAL DO PARANÁ; TOM RUTTINK, FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; ROBERT HENRY, UNIVERSITY OF QUEENSLAND; PIERRE MARRACCINI, UNIVERSITÉ DE MONTPELLIER; YVES VAN DE PEER, UNIVERSITY OF PRETORIA; ALAN CARVALHO ANDRADE, CNPCA; DOUGLAS DOMINGUES, UNIVERSIDADE ESTADUAL DE SÃO PAULO; GIOVANNI GIULIANO, ITALIAN NATIONAL AGENCY FOR NEW TECHNOLOGIES; LUKAS MUELLER, CORNELL UNIVERSITY; LUIZ FILIPE PROTASIO PEREIRA, CNPCA; STEPHANE PLAISANCE, VIB NUCLEOMICS CORE; VALERIE PONCET, UNIVERSITÉ DE MONTPELLIER; STEPHANE ROMBAUTS, CENTER FOR PLANT SYSTEMS BIOLOGY; DAVID SANKOFF, UNIVERSITY OF OTTAWA; VICTOR A. ALBERT, UNIVERSITY AT BUFFALO; DOMINIQUE CROUZILLAT, SOCIÉTÉ DES PRODUITS NESTLÉ SA; ALEXANDRE DE KOCHKO, UNIVERSITÉ DE MONTPELLIER; PATRICK DESCOMBES, SOCIÉTÉ DES PRODUITS NESTLÉ SA.

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

2024

SALOJÄRVI. | RAMBANI, A. | YU, Z. | GUYOT, R. | STRICKLER, S. | LEPELLEY, M. | WANG, C. | RAJARAMAN, S. | RASTAS, P. | ZHENG, C. | MUÑOZ, D. S. | MEIDANIS, J. | PASCHOAL, A. R. | BAWIN, Y. | KRABBENHOFT, T. J. | WANG, Z. Q. | FLECK, S. J. | AUSSEL, R. | BELLANGER, L. | CHARPAGNE, A. | FOURNIER, C. | KASSAM, M. | LEFEBVRE, G. | MÉTAIRON, S. | MOINE, D. | RIGOREAU, M. | STOLTE, J. | HAMON, P. | COUTURON, E. | TRANCHANT-DUBREUIL, C. | MUKHERJEE, M. | LAN, T. | ENGELHARDT, J. | STADLER, P. | LEMOS, S. M. C. DE | SUZUKI, S. I. | SUMIRAT, U. | WAI, C. M. | DAUCHOT, N. | OROZCO-ARIAS, S. | GARAVITO, A. | KIWUKA, C. | MUSOLI, P. | NALUKENGE, A. | GUICHOUX, E. | REINOUT, H. | SMIT, M. | CARRETERO-PAULET, L. | GUERREIRO FILHO, O. | BRAGHINI, M. T. | PADILHA, L. | SERA, G. H. | RUTTINK, T. | HENRY, R. | MARRACCINI, P. | PEER, Y. V. DE | ANDRADE, A. C. | DOMINGUES, D. | GIULIANO, G. | MUELLER, L. | PEREIRA, L. F. P. | PLAISANCE, S. | PONCET, V. | ROMBAUTS, S. | SANKOFF, D. | ALBERT, V. A. | CROUZILLAT, D. | KOCHKO, A. DE | DESCOMBES, P. | JARKKO SALOJÄRVI, NANYANG TECHNOLOGICAL UNIVERSITY; ADITI RAMBANI, CORNELL UNIVERSITY; ZHE YU, UNIVERSITY OF OTTAWA; ROMAIN GUYOT, UNIVERSITÉ DE MONTPELLIER; SUSAN STRICKLER, CORNELL UNIVERSITY; MAUD LEPELLEY, SOCIÉTÉ DES PRODUITS NESTLÉ SA; CUI WANG, UNIVERSITY OF HELSINKI; SITARAM RAJARAMAN, UNIVERSITY OF HELSINKI; PASI RASTAS, UNIVERSITY OF HELSINKI; CHUNFANG ZHENG, UNIVERSITY OF OTTAWA; DANIELLA SANTOS MUÑOZ, UNIVERSITY OF OTTAWADAVID; JOÃO MEIDANIS, UNIVERSIDADE DE CAMPINAS; ALEXANDRE ROSSI PASCHOAL, UNIVERSIDADE TECNOLÓGICA FEDERAL DO PARANÁ; YVES BAWIN, FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; TREVOR J. KRABBENHOFT, UNIVERSITY AT BUFFALO; ZHEN QIN WANG, UNIVERSITY AT BUFFALO; STEVEN J. FLECK, UNIVERSITY AT BUFFALO; RUDY AUSSEL, AIX MARSEILLE UNIVERSITÉ; LAURENCE BELLANGER, SOCIÉTÉ DES PRODUITS NESTLÉ SA; ALINE CHARPAGNE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; CORALIE FOURNIER, SOCIÉTÉ DES PRODUITS NESTLÉ SA; MOHAMED KASSAM, SOCIÉTÉ DES PRODUITS NESTLÉ SA; GREGORY LEFEBVRE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; SYLVIANE MÉTAIRON, SOCIÉTÉ DES PRODUITS NESTLÉ SA; DÉBORAH MOINE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; MICHEL RIGOREAU, SOCIÉTÉ DES PRODUITS NESTLÉ SA; JENS STOLTE, SOCIÉTÉ DES PRODUITS NESTLÉ SA; PERLA HAMON, UNIVERSITÉ DE MONTPELLIER; EMMANUEL COUTURON, UNIVERSITÉ DE MONTPELLIER; CHRISTINE TRANCHANT-DUBREUIL, UNIVERSITÉ DE MONTPELLIER; MINAKSHI MUKHERJEE, UNIVERSITY AT BUFFALO; TIANYING LAN, UNIVERSITY AT BUFFALO; JAN ENGELHARDT, UNIVERSITY OF LEIPZIG; PETER STADLER, UNIVERSITY OF LEIPZIG; SAMARA MIREZA CORREIA DE LEMOS, UNIVERSIDADE ESTADUAL DE SÃO PAULO; SUZANA IVAMOTO SUZUKI, UNIVERSIDADE ESTADUAL DE LONDRINA; UCU SUMIRAT, INDONESIAN COFFEE AND COCOA RESEARCH INSTITUTE; CHING MAN WAI, UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN; NICOLAS DAUCHOT, UNIVERSITY OF NAMUR; SIMON OROZCO-ARIAS, UNIVERSIDAD AUTÓNOMA DE MANIZALES; ANDREA GARAVITO, UNIVERSIDAD DE CALDAS; CATHERINE KIWUKA, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; PASCAL MUSOLI, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; ANNE NALUKENGE, NATIONAL AGRICULTURAL RESEARCH ORGANIZATION; ERWAN GUICHOUX, INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE; HAVINGA REINOUT, HORTUS BOTANICUS AMSTERDAM; MARTIN SMIT, HORTUS BOTANICUS AMSTERDAM; LORENZO CARRETERO-PAULET, UNIVERSIDAD DE ALMERÍA; OLIVEIRO GUERREIRO FILHO, INSTITUTO AGRONÔMICO; MASAKO TOMA BRAGHINI, INSTITUTO AGRONÔMICO; LILIAN PADILHA, CNPCA; GUSTAVO HIROSHI SERA, INSTITUTO DE DESENVOLVIMENTO RURAL DO PARANÁ; TOM RUTTINK, FLANDERS RESEARCH INSTITUTE FOR AGRICULTURE; ROBERT HENRY, UNIVERSITY OF QUEENSLAND; PIERRE MARRACCINI, UNIVERSITÉ DE MONTPELLIER; YVES VAN DE PEER, UNIVERSITY OF PRETORIA; ALAN CARVALHO ANDRADE, CNPCA; DOUGLAS DOMINGUES, UNIVERSIDADE ESTADUAL DE SÃO PAULO; GIOVANNI GIULIANO, ITALIAN NATIONAL AGENCY FOR NEW TECHNOLOGIES; LUKAS MUELLER, CORNELL UNIVERSITY; LUIZ FILIPE PROTASIO PEREIRA, CNPCA; STEPHANE PLAISANCE, VIB NUCLEOMICS CORE; VALERIE PONCET, UNIVERSITÉ DE MONTPELLIER; STEPHANE ROMBAUTS, CENTER FOR PLANT SYSTEMS BIOLOGY; DAVID SANKOFF, UNIVERSITY OF OTTAWA; VICTOR A. ALBERT, UNIVERSITY AT BUFFALO; DOMINIQUE CROUZILLAT, SOCIÉTÉ DES PRODUITS NESTLÉ SA; ALEXANDRE DE KOCHKO, UNIVERSITÉ DE MONTPELLIER; PATRICK DESCOMBES, SOCIÉTÉ DES PRODUITS NESTLÉ SA.

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.

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