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

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dc.citation.journaltitleNATURE GENETICS
dc.creatorSALOJÄRVI, J.
dc.creatorRAMBANI, A.
dc.creatorYU, Z.
dc.creatorGUYOT, R.
dc.creatorSTRICKLER, S.
dc.creatorLEPELLEY, M.
dc.creatorWANG, C.
dc.creatorRAJARAMAN, S.
dc.creatorRASTAS, P.
dc.creatorZHENG, C.
dc.creatorMUÑOZ, D. S.
dc.creatorMEIDANIS, J.
dc.creatorPASCHOAL, A. R.
dc.creatorBAWIN, Y.
dc.creatorKRABBENHOFT, T. J.
dc.creatorWANG, Z. Q.
dc.creatorFLECK, S. J.
dc.creatorAUSSEL, R.
dc.creatorBELLANGER, L.
dc.creatorGUERREIRO FILHO, O.
dc.creatoret.al
dc.date.accessioned2026-05-05T17:57:23Z
dc.date.issued2024
dc.description.resumoCoffea 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.
dc.format.extent721-731
dc.format.issue56
dc.identifier.citationSalojärvi, J., Rambani, A., Yu, Z. et al. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 56, 721–731 (2024). https://doi.org/10.1038/s41588-024-01695-w
dc.identifier.doihttp://dx.doi.org/10.1038/s41588-024-01695-w
dc.identifier.urihttps://repositorio.iac.sp.gov.br/handle/iac/187
dc.subjectGenome informatics, Genomics, Plant breeding, Plant genetics, Plant hybridization
dc.titleThe genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

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