The complex polyploid genome architecture of sugarcane

Healey Adam, Garsmeur Olivier, Lovell John, Shengquiang S., Sreedasyam Avinash, Jenkins Jerry, Plott C.B., Piperidis George, Pompidor Nicolas, Llaca V., Metcalfe Daniel J., Dolezel Jaroslav, Cápal P., Carlson J.E., Hoarau Jean-Yves, Hervouet Catherine, Zini Cyrille, Diévart Anne, Lipzen Anna, Williams M., Boston L.B., Webber J., Keymanesh K., Tejomurthula S., Rajasekar S., Suchecki R., Furtado Agnelo, May G., Parakkal P., Simmons B.A., Barry K., Henry Robert, Grimwood Jane, Aitken Karen S., Schmutz J., D'Hont Angélique. 2024. The complex polyploid genome architecture of sugarcane. Nature, 628 : 804-810.

Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/JAQSUU000000000.1/ / Url - jeu de données - Entrepôt autre : https://doi.org/10.6084/m9.figshare.22138004 / Url - jeu de données - Entrepôt autre : http://sugarcane-genome.cirad.fr / Type d'url non précisé : https://github.com/a-healey/r570scripts

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Economie-gestion; Psychologie-éthologie-ergonomie

Résumé : Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Mots-clés Agrovoc : Saccharum officinarum, génome, Saccharum, Saccharum spontaneum, polyploïdie, carte génétique, amélioration des plantes, résistance aux maladies, diversité génétique (comme ressource)

Mots-clés géographiques Agrovoc : France

Mots-clés libres : Agriculture, Genome evolution, Genome informatics, Plant genetics, Polyploidy in plants

Agences de financement européennes : European Regional Development Fund

Agences de financement hors UE : Office of Science User Facilities, International Consortium for Sugarcane Biotechnology

Projets sur financement : (UE) Plants as a Tool for Sustainable Global Development

Auteurs et affiliations

• Healey Adam, HudsonAlpha Biotechnology Institute (USA) - auteur correspondant
• Garsmeur Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8869-3689
• Lovell John, HudsonAlpha Biotechnology Institute (USA)
• Shengquiang S., Lawrence Berkeley National Laboratory (USA)
• Sreedasyam Avinash, HudsonAlpha Biotechnology Institute (USA)
• Jenkins Jerry, HudsonAlpha Biotechnology Institute (USA)
• Plott C.B., HudsonAlpha Institute for Biotechnology (USA)
• Piperidis George, SRA (AUS)
• Pompidor Nicolas, CIRAD-BIOS-UMR AGAP (FRA)
• Llaca V., Corteva Agriscience (USA)
• Metcalfe Daniel J., CSIRO (AUS)
• Dolezel Jaroslav, Institute of Experimental Botany (CZE)
• Cápal P., Czech Academy of Sciences (CZE)
• Carlson J.E., Lawrence Berkeley National Laboratory (USA)
• Hoarau Jean-Yves, CIRAD-BIOS-UMR AGAP (REU) ORCID: 0000-0001-9734-4165
• Hervouet Catherine, CIRAD-BIOS-UMR AGAP (FRA)
• Zini Cyrille, Université de Montpellier (FRA)
• Diévart Anne, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9460-4638
• Lipzen Anna, Lawrence Berkeley National Laboratory (USA)
• Williams M., HudsonAlpha Institute for Biotechnology (USA)
• Boston L.B., HudsonAlpha Institute for Biotechnology (USA)
• Webber J., HudsonAlpha Institute for Biotechnology (USA)
• Keymanesh K., Lawrence Berkeley National Laboratory (USA)
• Tejomurthula S., Lawrence Berkeley National Laboratory (USA)
• Rajasekar S., University of Arizona (USA) - auteur correspondant
• Suchecki R., CSIRO (AUS)
• Furtado Agnelo, University of Queensland (AUS)
• May G., Corteva Agriscience (USA)
• Parakkal P., Corteva Agriscience (USA)
• Simmons B.A., University of Queensland (AUS)
• Barry K., Lawrence Berkeley National Laboratory (USA)
• Henry Robert, University of Queensland (AUS)
• Grimwood Jane, HudsonAlpha Biotechnology Institute (USA)
• Aitken Karen S., CSIRO (AUS)
• Schmutz J., HudsonAlpha Institute for Biotechnology (USA) - auteur correspondant
• D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/609082/)

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