The complex polyploid genome architecture of sugarcane

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 worldwide 1 . While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens,...

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Published in:	Nature (London) Vol. 628; no. 8009; pp. 804 - 810
Main Authors:	Healey, A. L., Garsmeur, O., Lovell, J. T., Shengquiang, S., Sreedasyam, A., Jenkins, J., Plott, C. B., Piperidis, N., Pompidor, N., Llaca, V., Metcalfe, C. J., Doležel, J., Cápal, P., Carlson, J. W., Hoarau, J. Y., Hervouet, C., Zini, C., Dievart, A., Lipzen, A., Williams, M., Boston, L. B., Webber, J., Keymanesh, K., Tejomurthula, S., Rajasekar, S., Suchecki, R., Furtado, A., May, G., Parakkal, P., Simmons, B. A., Barry, K., Henry, R. J., Grimwood, J., Aitken, K. S., Schmutz, J., D’Hont, A.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 25-04-2024 Nature Publishing Group
Subjects:	14/32 45 45/23 45/91 631/114/2785 631/208/212/2304 631/449/2491 631/449/2491/3933 706/1143 Adaptation Agricultural production Agricultural sciences agriculture Agriculture, economy and politics Assembly Biochemistry, Molecular Biology Biodiversity Bioinformatics Biotechnology Brown rust Chromosomes Chromosomes, Plant - genetics Complexity Computer Science Crops Cultivars DNA sequence Domestic species Domestication Environmental conditions Gene sequencing Genes Genetic diversity Genetic variation Genetics genome evolution genome informatics Genome, Plant - genetics Genomes Genomics Geopolitics Haplotypes Haplotypes - genetics Humanities and Social Sciences Hybridization Hybridization, Genetic - genetics Hybrids Interspecific hybridization Life Sciences multidisciplinary Nucleotide sequence Plant Breeding plant genetics Plants genetics Polyploidy polyploidy in plants Population genetics Populations and Evolution Representations Reproductive cycle Saccharides Saccharum - genetics Science Science (multidisciplinary) Sugar Sugarcane Whole genome sequencing Genome informatics Agriculture Genome evolution Polyploidy in plants Plant genetics
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Summary:	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 worldwide 1 . While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued 2 . 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. We build a polyploid reference genome for hybrid sugarcane cultivar R570, improving on its current ‘mosaic monoploid’ representation, enabling fine-grain description of genome architecture and the exploration of candidate genes underlying the Bru1 brown rust resistance locus.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF) AC02-05CH11231 USDOE Office of Science (SC), Biological and Environmental Research (BER)
ISSN:	0028-0836 1476-4687
DOI:	10.1038/s41586-024-07231-4