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03 13, 2020;10 (1): 4642.

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.

Simone Scalabrin, Lucile Toniutti, Gabriele Di Gaspero, Davide Scaglione, Gabriele Magris, Michele Vidotto, Sara Pinosio, Federica Cattonaro, Federica Magni, Irena Jurman, Mario Cerutti, Furio Suggi Liverani, Luciano Navarini, Lorenzo Del Terra, Gloria Pellegrino, Manuela Rosanna Ruosi, Nicola Vitulo, Giorgio Valle, Alberto Pallavicini, Giorgio Graziosi, Patricia E Klein, Nolan Bentley, Seth Murray, William Solano, Amin Al Hakimi, Timothy Schilling, Christophe Montagnon, Michele Morgante, Benoit Bertrand
Author Information
  1. Simone Scalabrin: IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy.
  2. Lucile Toniutti: World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France. lucile@worldcoffeeresearch.org.
  3. Gabriele Di Gaspero: Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.
  4. Davide Scaglione: IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy.
  5. Gabriele Magris: Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.
  6. Michele Vidotto: IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy.
  7. Sara Pinosio: Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.
  8. Federica Cattonaro: IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy.
  9. Federica Magni: IGA Technology Services S.r.l., via Jacopo Linussio 51, I-33100, Udine, Italy.
  10. Irena Jurman: Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.
  11. Mario Cerutti: Luigi Lavazza S.p.A., Innovation Center, I-10156, Torino, Italy.
  12. Furio Suggi Liverani: Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy.
  13. Luciano Navarini: Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy.
  14. Lorenzo Del Terra: Illycaffè S.p.A., Research & Innovation, via Flavia 110, I-34147, Trieste, Italy.
  15. Gloria Pellegrino: Luigi Lavazza S.p.A., Innovation Center, I-10156, Torino, Italy.
  16. Manuela Rosanna Ruosi: Luigi Lavazza S.p.A., Innovation Center, I-10156, Torino, Italy.
  17. Nicola Vitulo: Department of Biotechnology, University of Verona, Verona, Italy.
  18. Giorgio Valle: CRIBI, Università degli Studi di Padova, viale G. Colombo 3, I-35121, Padova, Italy.
  19. Alberto Pallavicini: Department of Life Sciences, University of Trieste, I-34148, Trieste, Italy.
  20. Giorgio Graziosi: Department of Life Sciences, University of Trieste, I-34148, Trieste, Italy.
  21. Patricia E Klein: Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA.
  22. Nolan Bentley: Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA.
  23. Seth Murray: Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA.
  24. William Solano: CATIE, Turrialba, Costa Rica.
  25. Amin Al Hakimi: Faculty of Agriculture, Sana'a University, Sana'a, Yemen.
  26. Timothy Schilling: World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France.
  27. Christophe Montagnon: World Coffee Research, 5 avenue du grand chêne, 34270, Saint-Mathieu-de-Tréviers, France.
  28. Michele Morgante: Istituto di Genomica Applicata, via Jacopo Linussio 51, I-33100, Udine, Italy.
  29. Benoit Bertrand: CIRAD, IPME, 34 398, Montpellier, France.
PMID: 32170172 DOI: 10.1038/s41598-020-61216-7

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.

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MeSH Term

Coffea
Costa Rica
Crops, Agricultural
Genome Size
Genome, Plant
Polymorphism, Single Nucleotide
Tetraploidy
Whole Genome Sequencing
Yemen
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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