A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for 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, Kotch George, Bertrand Benoît, Morgante Michele. 2021. A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for extremely low genetic variation in wild and cultivated germplasm. In : 28th Conference of Association for the Science and Information on Coffee - Books of abstracts. ASIC. Montpellier : ASIC, Résumé, p. 102. Conference of Association for the Science and Information on Coffee (ASIC 2021). 28, Montpellier, France, 28 Juin 2021/1 Juillet 2021.

Résumé : RATIONALE - 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. METHODS - We studied an individual of C. arabica 'Bourbon Vermelho'. A BAC library of 175,872 BAC clones was constructed and sequenced using an Illumina HiSeq2000. Each BAC pool was assembled independently with the tool ABySS and scaffolded with SSPACE. Genotyping by sequencing (GBS) was conducted using the restriction enzyme PstI followed by single-end sequencing on an Illumina HiSeq2000. SNP calling was performed using Stacks. Principal Component Analysis was performed using the R package ade4. A hierarchical study of the diversity has been conducted using a model-based clustering procedure with admixture as implemented in STRUCTURE. RESULTS - 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 eugenioides 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. CONCLUSIONS & PERSPECTIVES - 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.

Auteurs et affiliations

• Scalabrin Simone, IGA Technology (ITA)
• Toniutti Lucile, CIRAD-BIOS-UMR AGAP (GLP)
• 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, Università Di Udine (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, Texas A & M University (USA)
• Al Hakimi Amin, Sana'a University (YEM)
• Schilling Timothy, WCR (USA)
• Montagnon Christophe, RD2 Vision (FRA)
• Kotch George, World Coffee Research (FRA)
• Bertrand Benoît, CIRAD-BIOS-UMR DIADE (FRA) ORCID: 0000-0003-1969-3479
• Morgante Michele, Università Di Udine (ITA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/600751/)

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