A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scalabrin Simone, Toniutti Lucile, Di Gaspero Gabriele, Scaglione Davide, Magris Gabriele, Vidotto Michele, Pinosio Sara, Cattonaro Frederica, Magni Federica, Jurman Irena, Cerutti Mario, Suggi Liverani Furio, Navarini Luciano, Del Terra Lorenzo, Pellegrino Gloria, Ruosi Manuela Rosanna, Vitulo Nicola, Valle Giorgio, Pallavicini Alberto, Graziosi Giorgio, Klein Patricia E., Bentley Nolan, Murray Seth C., Solano William, Al Hakimi Amin, Schilling Timothy, Montagnon Christophe, Morgante Michele, Bertrand Benoît. 2020. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm. Scientific Reports, 10:4642, 13 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
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Abstract : The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

Mots-clés Agrovoc : Coffea arabica, Polyploïdie, Dynamique des populations, Bioinformatique

Mots-clés libres : Polyploidization, Coffea arabica, Plant sciences, Computational biology and informatics, Evolution

Classification Agris : F30 - Plant genetics and breeding
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

  • Scalabrin Simone, IGA Technology (ITA) - auteur correspondant
  • Toniutti Lucile, World Coffee Research (FRA) - auteur correspondant
  • Di Gaspero Gabriele, Università Di Udine (ITA)
  • Scaglione Davide, IGA Technology (ITA)
  • Magris Gabriele, Università Di Udine (ITA)
  • Vidotto Michele, IGA Technology (ITA)
  • Pinosio Sara, Università Di Udine (ITA)
  • Cattonaro Frederica, IGA Technology (ITA)
  • Magni Federica, IGA Technology (ITA)
  • Jurman Irena, Università Di Udine (ITA)
  • Cerutti Mario, Luigi Lavazza S.p.A. (ITA)
  • Suggi Liverani Furio, Illycaffé (ITA)
  • Navarini Luciano, Illycaffé (ITA)
  • Del Terra Lorenzo, Illycaffé (ITA)
  • Pellegrino Gloria, Luigi Lavazza S.p.A. (ITA)
  • Ruosi Manuela Rosanna, Luigi Lavazza S.p.A. (ITA)
  • Vitulo Nicola, Universita di Verona (ITA)
  • Valle Giorgio, Università degli Studi-Padova (ITA)
  • Pallavicini Alberto, Universita Degli Studi di Trieste (ITA)
  • Graziosi Giorgio, Universita Degli Studi di Trieste (ITA)
  • Klein Patricia E., Texas A & M University (USA)
  • Bentley Nolan, Texas A & M University (USA)
  • Murray Seth C., Texas A & M University (USA)
  • Solano William, CATIE (CRI)
  • Al Hakimi Amin, Sana'a University (YEM)
  • Schilling Timothy, WCR (USA)
  • Montagnon Christophe, World Coffee Research (FRA)
  • Morgante Michele, Università Di Udine (ITA)
  • Bertrand Benoît, CIRAD-BIOS-UMR IPME (FRA)

Source : Cirad-Agritrop (

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