Genomic Strategies for Sugarcane Improvement

The global imperative to meet rising demand for sugar and bioenergy has driven adoption of genomic strategies to overcome the intrinsic complexity of sugarcane’s polyploid genome. Recent advances combine high-resolution genome assemblies, long-read sequencing, transcriptome profiling and high-throughput genotyping to dissect genetic diversity, pinpoint alleles of agronomic importance and accelerate breeding cycles. Polyploid reference genomes and BAC-based monoploid assemblies now provide foundational frameworks, while genome-wide association studies and quantitative trait loci mapping guide marker-assisted selection for traits such as disease resistance, tillering and ratooning. Integration of allelic dosage analysis and comparative genomics with sorghum has illuminated gene content, structural variation and transposable element dynamics, underpinning efforts to enhance yield, stress resilience and biofuel traits. These genomic resources and analytic tools promise to transform traditional breeding approaches, enabling precise selection and transgenic interventions tailored to diverse environments and sustainable production goals.

Research from Nature Portfolio

Recent research has culminated in a highly contiguous reference genome for a modern hybrid cultivar, capturing all twelve chromosome haplotypes in an 8.7 Gb assembly and revealing causal genes underlying brown rust resistance. A BAC-based monoploid sequence exploited sorghum colinearity to generate a 382 Mb gene-rich assembly, predicting over 25 000 protein-coding genes and mapping chromosomal rearrangements between progenitor species. A methodological framework for quantitative SNP allelic dosage analysis in autopolyploid sugarcane has established a basis for high-density genetic mapping and improved understanding of genome structure.

Genomic Strategies for Sugarcane Improvement publication trend

The graph below shows the total number of articles in genomic strategies for sugarcane improvement across all publications each year (not limited to Nature Index journals).

Technical terms

Polyploidy: The state of having multiple complete sets of chromosomes.

Monoploid: A genome representation comprising a single set of chromosomes in a polyploid organism.

Quantitative trait locus (QTL): A genomic region associated with variation in a quantitative trait.

Genotyping-by-sequencing (GBS): A reduced-representation sequencing method for simultaneous discovery and genotyping of genetic variants.

Genome-wide association study (GWAS): An approach that correlates genetic variation across the genome with phenotypic traits.

Allelic dosage: The number of copies of a given allele present at a locus in a polyploid genome.

References

1. The complex polyploid genome architecture of sugarcane. Nature (2024).
2. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications (2018).
3. SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Scientific Reports (2013).
4. Mapping of QTLs and Screening Candidate Genes Associated with the Ability of Sugarcane Tillering and Ratooning. International Journal of Molecular Sciences (2023).
5. Sugarcane Ratooning Ability: Research Status, Shortcomings, and Prospects. Biology (2021).
6. Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.). Frontiers in Plant Science (2018).