Sugarcane, a globally important crop, presents a unique challenge to plant scientists due to its incredibly complex genome. Now, researchers have developed a new approach to unraveling this genetic intricacy – a “multiscale pangenome graph” – offering a powerful tool for improving crop yields and understanding the plant’s evolution. The findings, published on , in the journal Science, represent a significant step forward in the field of genomics, particularly for polyploid organisms like sugarcane.
Sugarcane’s genome is complicated by its high ploidy level – meaning it has multiple sets of chromosomes. This makes traditional genome sequencing and analysis difficult. The team, led by researchers focusing on the Saccharum genus, tackled this challenge by integrating nine different genome assemblies into a single, unified reference using a graph-based approach. This isn’t simply a matter of stitching together sequences. it’s about creating a framework that accurately represents the vast diversity within the sugarcane genome.
The resulting pangenome graph allows scientists to represent the collective genetic information of multiple sugarcane varieties and their wild relatives. According to the study, each set of homo(eo)logous chromosomes – encompassing both homologous and homeologous relationships – contains between 47 and 57 haplotypes, and approximately 74,000 to 271,000 gene alleles. This level of detail provides an unprecedented view of the genetic variation within the species.
But the innovation doesn’t stop at simply mapping the genome. The multiscale pangenome graph also facilitates “multiomics exploration,” meaning researchers can integrate data from various biological levels – including genomics, epigenomics, and other ‘omics’ technologies – to gain a more holistic understanding of how genes function and interact. This integrated approach is crucial for understanding complex traits like sugar content and disease resistance.
The practical implications of this research are substantial. The researchers used the pangenome to analyze 417 sugarcane accessions with mixed ploidy levels. This analysis revealed instances of “convergent selection,” where different sugarcane varieties independently evolved similar genetic adaptations. Identifying these consistently selected genes can pinpoint traits that are particularly important for sugarcane performance.
One specific gene identified through this process is a homolog of the Andropogoneae TB1 gene, which is linked to tillering – the process by which plants produce multiple shoots. The researchers suggest this gene is a promising target for gene editing, with the potential to increase cane yield. The pangenome also supports dosage-informed genome-wide association studies, improving the accuracy of identifying genetic factors associated with desirable traits.
Specifically, the study highlighted the identification of sugar-associated loci, including SaIRX10 and SaBAK5, and leaf-angle-associated loci. By considering the number of copies of each gene (dosage), the researchers were able to improve the accuracy of their genetic associations, leading to a better understanding of the genetic basis of these traits.
The development of this analytical framework isn’t limited to sugarcane. The researchers believe their approach can be applied to other polyploid genomes, which are notoriously difficult to study. Polyploidy – having more than two sets of chromosomes – is common in many important crop plants, including wheat, potatoes, and cotton. A standardized framework for pangenome graph evaluation is currently being developed, as noted in a publication, to further refine these methods.
The creation of this unified reference genome represents a significant investment in sugarcane research. By providing a comprehensive and accurate representation of the sugarcane genome, this work lays the foundation for future studies aimed at improving this vital crop. The ability to dissect the genetic basis of complex traits will ultimately lead to the development of sugarcane varieties with higher yields, improved disease resistance, and enhanced sugar content, benefiting both farmers and consumers.
This research underscores the power of advanced genomic technologies in addressing challenges in agriculture. As the global population continues to grow, the need for efficient and sustainable crop production becomes increasingly urgent. Tools like the multiscale pangenome graph are essential for unlocking the genetic potential of our crops and ensuring food security for the future.
