Three founding ancestral genomes involved in the origin of sugarcane

Pompidor Nicolas, Charron Carine, Hervouet Catherine, Bocs Stéphanie, Droc Gaëtan, Rivallan Ronan, Manez Aurore, Mitros Therese, Swaminathan Kankshita, Glaszmann Jean-Christophe, Garsmeur Olivier, D'Hont Angélique. 2021. Three founding ancestral genomes involved in the origin of sugarcane. Annals of Botany, 14 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Abstract : Background and Aims: Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods: To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results: The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions: This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

Mots-clés Agrovoc : Génome, Saccharum, Diversité génétique (comme ressource), Variation génétique, Saccharum officinarum, Saccharum spontaneum, Hybridation interspécifique, Polyploïdie

Mots-clés libres : Saccharum, Sugarcane, Polyploidy, Hybridization, Founding ancestral genome, Diversity

Classification Agris : F30 - Plant genetics and breeding

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

Auteurs et affiliations

  • Pompidor Nicolas, CIRAD-BIOS-UMR AGAP (FRA)
  • Charron Carine, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-0281-9936
  • Hervouet Catherine, CIRAD-BIOS-UMR AGAP (FRA)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Rivallan Ronan, CIRAD-BIOS-UMR AGAP (FRA)
  • Manez Aurore, CIRAD-BIOS-UMR AGAP (FRA)
  • Mitros Therese, UC (USA)
  • Swaminathan Kankshita, University of Illinois (USA)
  • Glaszmann Jean-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9918-875X
  • Garsmeur Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8869-3689
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA) - auteur correspondant

Source : Cirad-Agritrop (

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