Exploring morphological, transcriptomic, and metabolomic differences between two sister lines with contrastive resistance to orange rust disease in sugarcane

Authors: ZHOU, YUPENG - University Of Florida; MIHAIL, EDVIN - University Of Florida; LUO, ZILIANG - University Of Florida; Sood, Sushma; Islam, Md; WANG, JIANPING - University Of Florida

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2025
Publication Date: 4/8/2025
Citation: Zhou, Y., Mihail, E.S., Luo, Z., Sood, S.G., Islam, M.S., Wang, J. 2025. Exploring morphological, transcriptomic, and metabolomic differences between two sister lines with contrastive resistance to orange rust disease in sugarcane. International Journal of Molecular Sciences. 26.3490. https://doi.org/10.3390/ijms26083490.
DOI: https://doi.org/10.3390/ijms26083490

Interpretive Summary: Sugarcane, one of Florida's most important economic crops, has been affected by orange rust (OR) disease and has resulted in significant yield loss. Developing resistant cultivars is the most valuable in terms of efficiency, financially, and also environmentally friendly. The molecular mechanisms underlying the resistance to OR disease in sugarcane are still obscure. Morphological and anatomical observations revealed that the resistant line (540) had significantly smaller stomatal size and lower stomatal density than the susceptible line (664). The transcriptomic analyses showed that resistant line 540 has increased cell surface modification activity, suggesting possible increased surface receptors. Transcriptome analysis revealed key genes involved in the biosynthesis of anti-fungal molecules. Transcriptomic-metabolomic joint analysis suggested that the resistance line 540 has increased biosynthesis of phenylpropanoid derivatives with purported antioxidant and anti-fungal capabilities. Genes, pathways, and some single nucleotide polymorphism identified in this study will provide fundamental information and resources to advance the knowledge of sugarcane molecular genetic mechanisms to OR disease and breeding programs in developing cultivars with improved resistance to OR.

Technical Abstract: Sugarcane (Saccharum spp.) hybrid, one of the most important crops in Florida, has been affected by orange rust (OR) disease caused by Puccinia kuehnii since 2007 and has resulted in significant yield loss. Developing resistant cultivars to this disease has become an important goal in sugarcane breeding programs. However, the specific genes and molecular mechanisms underlying the resistance to OR disease in sugarcane are still not clear. In this study, we selected two sugarcane sister lines with different genotypes in a major quantitative trait loci (QTL) region controlling OR disease resistance and showing contrastive resistant responses to the disease. Morphological and anatomical observations revealed that the resistant line (540) had significantly smaller stomatal size and lower stomatal density than the susceptible line (664). The transcriptomic analyses showed that resistant line 540 has increased cell surface modification activity, suggesting possible increased surface receptors. Diferentially expressed gene and coexpression analysis also revealed key genes involved in the biosynthesis of anti-fungal molecules such as hordatines, arabidopyrones, and alkaloids. It also showed a strong increase in RNA expression, playing a role in transcriptional regulation. Transcriptomic-metabolomic joint analysis suggested that line 540 has increased bio-synthesis of phenylpropanoid derivatives with purported antioxidant and anti-fungal capabilities, especially those deriving from ferulate. Genes, pathways, and some single nucleotide polymorphism identified in this study will provide fundamental information and resources to advance the knowledge of sugarcane molecular genetic mechanisms to OR disease and breeding programs in developing cultivars with improved resistance to OR.