The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
-
Published:2024-04
Issue:4
Volume:56
Page:721-731
-
ISSN:1061-4036
-
Container-title:Nature Genetics
-
language:en
-
Short-container-title:Nat Genet
Author:
Salojärvi JarkkoORCID, Rambani Aditi, Yu Zhe, Guyot RomainORCID, Strickler Susan, Lepelley Maud, Wang CuiORCID, Rajaraman SitaramORCID, Rastas PasiORCID, Zheng Chunfang, Muñoz Daniella Santos, Meidanis JoãoORCID, Paschoal Alexandre RossiORCID, Bawin Yves, Krabbenhoft Trevor J.ORCID, Wang Zhen Qin, Fleck Steven J.ORCID, Aussel Rudy, Bellanger Laurence, Charpagne Aline, Fournier CoralieORCID, Kassam Mohamed, Lefebvre Gregory, Métairon SylvianeORCID, Moine Déborah, Rigoreau Michel, Stolte Jens, Hamon Perla, Couturon Emmanuel, Tranchant-Dubreuil Christine, Mukherjee MinakshiORCID, Lan Tianying, Engelhardt JanORCID, Stadler PeterORCID, Correia De Lemos Samara MirezaORCID, Suzuki Suzana IvamotoORCID, Sumirat Ucu, Wai Ching ManORCID, Dauchot NicolasORCID, Orozco-Arias SimonORCID, Garavito AndreaORCID, Kiwuka Catherine, Musoli Pascal, Nalukenge Anne, Guichoux Erwan, Reinout Havinga, Smit Martin, Carretero-Paulet Lorenzo, Filho Oliveiro GuerreiroORCID, Braghini Masako Toma, Padilha LilianORCID, Sera Gustavo Hiroshi, Ruttink TomORCID, Henry Robert, Marraccini PierreORCID, Van de Peer YvesORCID, Andrade AlanORCID, Domingues DouglasORCID, Giuliano GiovanniORCID, Mueller Lukas, Pereira Luiz Filipe, Plaisance StephaneORCID, Poncet ValerieORCID, Rombauts StephaneORCID, Sankoff DavidORCID, Albert Victor A.ORCID, Crouzillat DominiqueORCID, de Kochko AlexandreORCID, Descombes PatrickORCID
Abstract
AbstractCoffea 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.
Publisher
Springer Science and Business Media LLC
Reference122 articles.
1. Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). 2. Van de Peer, Y., Ashman, T.-L., Soltis, P. S. & Soltis, D. E. Polyploidy: an evolutionary and ecological force in stressful times. Plant Cell 33, 11–26 (2021). 3. Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019). 4. Sun, H. et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat. Genet. 54, 342–348 (2022). 5. Athiyannan, N. et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 54, 227–231 (2022).
Cited by
9 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|