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

J. Salojaervi; A. Rambani; Z. Yu; Romain Guyot; S. Strickler; M. Lepelley; C. Wang; S. Rajaraman; P. Rastas; C. F. Zheng; D. S. Munoz; J. Meidanis; A. R. Paschoal; Y. Bawin; T. J. Krabbenhoft; Z. Q. Wang; S. J. Fleck; R. Aussel; L. Bellanger; A. Charpagne; C. Fournier; M. Kassam; G. Lefebvre; S. Metairon; D. Moine; M. Rigoreau; J. Stolte; Perla Hamon; Emmanuel Couturon; Christine Dubreuil Tranchant; M. Mukherjee; T. Y. Lan; J. Engelhardt; P. Stadler; S. M. C. de Lemos; S. I. Suzuki; U. Sumirat; C. M. Wai; N. Dauchot; S. Orozco-Arias; A. Garavito; C. Kiwuka; P. Musoli; A. Nalukenge; Erwan Guichoux; H. Reinout; M. Smit; L. Carretero-Paulet; O. Guerreiro; M. T. Braghini; L. Padilha; G. H. Sera; T. Ruttink; R. Henry; P. Marraccini; Y. van de Peer; A. Andrade; D. Domingues; G. Giuliano; L. Mueller; L. F. Pereira; S. Plaisance; Valérie Poncet; S. Rombauts; D. Sankoff; V. A. Albert; D. Crouzillat; Alexandre De Kochko; P. Descombes

doi:10.1038/s41588-024-01695-w

Back

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

Journal article

Open access

Peer reviewed

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

J. Salojaervi, A. Rambani, Z. Yu, Romain Guyot, S. Strickler, M. Lepelley, C. Wang, S. Rajaraman, P. Rastas, C. F. Zheng, …

Nature Genetics, Vol.56(4), pp.721-731

15/04/2024

DOI: https://doi.org/10.1038/s41588-024-01695-w

Abstract

ETHIOPIE

MONDE

ZONE TROPICALE

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.

Files and links (2)

url

Find in HALView

url

https://doi.org/10.1038/s41588-024-01695-wView

Published (Version of record) Open

Metrics

1 Record Views

See more details

Details

Title: The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Creators - without role: J. Salojaervi - Nanyang Technological University
A. Rambani - Cornell University
Z. Yu - University of Ottawa
Romain Guyot - Université de Montpellier, Diversité, Adaptation et Développement des plantes - DIADE
S. Strickler - Cornell University
M. Lepelley - Nestlé
C. Wang - University of Helsinki
S. Rajaraman - University of Helsinki
P. Rastas - University of Helsinki
C. F. Zheng - University of Ottawa
D. S. Munoz - University of Ottawa
J. Meidanis - Universidade Estadual de Campinas (UNICAMP)
A. R. Paschoal - Universidade Tecnológica Federal do Paraná
Y. Bawin - Vlaams Instituut voor Biotechnologie
T. J. Krabbenhoft - University at Buffalo, State University of New York
Z. Q. Wang - University at Buffalo, State University of New York
S. J. Fleck - University at Buffalo, State University of New York
R. Aussel - Nestlé
L. Bellanger - Nestlé
A. Charpagne - Nestlé
C. Fournier - Nestlé
M. Kassam - Nestlé
G. Lefebvre - Nestlé
S. Metairon - Nestlé
D. Moine - Nestlé
M. Rigoreau - Nestlé
J. Stolte - Nestlé
Perla Hamon - Institut de Recherche pour le Développement
Emmanuel Couturon - Institut de Recherche pour le Développement
Christine Dubreuil Tranchant - Université de Montpellier, Diversité, Adaptation et Développement des plantes - DIADE
M. Mukherjee - University at Buffalo, State University of New York
T. Y. Lan - University at Buffalo, State University of New York
J. Engelhardt - Leipzig University
P. Stadler - Leipzig University
S. M. C. de Lemos - Universidade Estadual Paulista (Unesp)
S. I. Suzuki - Universidade Estadual de Londrina
U. Sumirat - Indonesian Coffee and Cocoa Research Institute
C. M. Wai - University of Illinois Urbana-Champaign
N. Dauchot - University of Namur
S. Orozco-Arias - Universidad Autonoma de Manizales
A. Garavito - University of Caldas
C. Kiwuka - National Agricultural Research Organisation
P. Musoli - National Agricultural Research Organisation
A. Nalukenge - National Agricultural Research Organisation
Erwan Guichoux - UMR BIOdiversity, GEnes & Communities
H. Reinout
M. Smit
L. Carretero-Paulet - University of Almería
O. Guerreiro
M. T. Braghini
L. Padilha
G. H. Sera - Instituto Agronômico do Paraná
T. Ruttink - Ghent University
R. Henry - Agriculture and Food
P. Marraccini - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
Y. van de Peer - Ghent University
A. Andrade - Brazilian Agricultural Research Corporation
D. Domingues - Universidade Estadual Paulista (Unesp)
G. Giuliano - ENEA Casaccia Research Centre
L. Mueller - Cornell University
L. F. Pereira - Brazilian Agricultural Research Corporation
S. Plaisance
Valérie Poncet - Institut de Recherche pour le Développement
S. Rombauts - Ghent University
D. Sankoff - University of Ottawa
V. A. Albert - University at Buffalo, State University of New York
D. Crouzillat - Nestlé
Alexandre De Kochko - Institut de Recherche pour le Développement
P. Descombes - Nestlé
Publication Details: Nature Genetics, Vol.56(4), pp.721-731
Identifiers: 9940204709311
Academic Unit: Diversité, Adaptation et Développement des plantes - DIADE
Language: English
Resource Type: Journal article
Local Fields: hal-04611385