Location: Sugarcane Field Station
2025 Annual Report
Objectives
1. Identify pathogenic variation in sugarcane pathogens that are endemic and emerging within the United States. 1. A: Identify variation in sugarcane pathogens that are endemic and detect emerging pathogens in Florida. 1. B: Characterization of endophytes of sugarcane during disease development. 2. Screen germplasms of sugarcane and related grasses for resistance to major diseases such as brown rust, orange rust, leaf scald, sugarcane mosaic, smut, and ratoon stunting diseases. 2. A: Screen sugarcane clones for brown rust, orange rust, leaf scald, sugarcane mosaic, smut, and ratoon stunting diseases. 2. B: Molecular approach to develop disease-resistant cultivars
Approach
Natural infections of sugarcane clones in Stage IV, small and large seed increases at ten commercial production locations across the sugarcane production region in FL will be surveyed in the spring and fall for all the economically important diseases. Unusual disease symptoms or disease outbreaks on previously disease-resistant cultivars will be investigated as possible emerging pathogens or new pathogenic races\strains of an endemic pathogen. Studies by light, confocal laser scanning microscope, or/and electron microscopy will be conducted to determine if there is any cytological structural difference in the interaction between orange rust race and host. Microbial diversity of a sugarcane variety susceptible to leaf scald and mosaic caused by Xanthomonas albilineans and Sugarcane mosaic virus, respectively. Sugarcane clones in the Stage 3 increase and Stage 4 of the Canal Point Sugarcane Cultivar Development Program will be screened for their reactions to leaf scald, mosaic, ratoon stunt, and smut diseases in artificial inoculation tests. Incidence of Sugarcane yellow leaf virus and ratoon stunt will be determined in the sugarcane clones of small and large seed increases to provide stakeholder status of these diseases in seed canes. Genome-wide markers for mapping genes controlling particular disease resistance in sugarcane will allow finding candidate resistance genes and gene variations. A database to select the reliable and low dosage SNPs for R-gene; SNP array development to realize high throughput genotyping of mapping populations for rapid identification of markers linked to disease resistance in sugarcane; identify haplotype variation associated with diseases (Brown and orange rust, Leaf scald, Smut, and Ratoon Stunting Disease) resistance.
Progress Report
ARS researchers at Canal Point, Florida believe sugarcane is a vital economic driver in Florida, creating 12,500 jobs and contributing a remarkable $3.3 billion to the state's economy. As the nation’s leading producer of sugarcane, Florida supplies over 50% of the total sugar output in the USA. The success of sugarcane cultivars is heavily dependent on disease resistance. Sugarcane stakeholders grow disease resistant Canal Point released cultivars on almost 100% of acreage, however, emerging pathogens and variations in existing ones threaten these cultivars. Therefore, researchers at the Agricultural Research Service (ARS) in Canal Point, Florida, are committed to developing and releasing disease-resistant cultivars that empower stakeholders to boost profits by minimizing losses from diseases and reducing reliance on chemical controls. To combat these challenges, our researchers are proactively conducting comprehensive surveys for new diseases, running critical trials to understand both the pathogens involved and the diseases they cause, and meticulously screening sugarcane clones to identify the most resilient varieties. Objective 1 Sub-objective 1A: ARS researchers are exploring the variation in leaf scald pathogen isolates through advanced PCR techniques using numerous primer pairs targeting the five housekeeping genes (gyrB, abc, rpoD, atpD and glnA) and the complete ITS sequence of the 16S–23S rRNA region combinations. By collecting numerous isolates from a range of sugarcane varieties across multiple locations and different seasons. Leaf scald is a unique disease with several types of symptoms and phases. The two common chronic symptoms are white streak and chlorosis. ARS researchers found that white streaks symptoms can be found in every season, but the chlorosis of sugarcane leaves is prevalent during cold winter. Plants recover from these symptoms during the grand growth. Recent surveys have uncovered the prevalence of the sugarcane mild mosaic virus (SCMMV) in parental and advanced lines at the Sugarcane Field Station indicating an urgent need for vigilance. This discovery, along with our identification of a new disease characterized by unique chlorotic streak symptoms caused by Ethiopian maize associated virus (EaMv), underscores the importance of our efforts in monitoring pathogens. Association of EaMv with sugarcane mosaic virus creates severe symptoms of both pathogens. Several sugarcane yellow leaf viruses (SCYLV) genotypes have been reported in sugarcane-producing countries. ARS researchers surveyed sugarcane varieties in the small and large seed increase plantings at the growers' farms at ten locations in 2024. We found that two different genotypes of SCYLV (Brazilian and Cuban) were present in the sugarcane varieties in these locations. We didn't find the Reunion genotype of SCYLV in Florida varieties.Sub-objective 1B: Harnessing cooperative plant-microbe interactions holds the key to enhancing plant health. Through understanding plant microbiota, we can address critical plant health challenges and predict future crop defenses. ARS researchers investigating microbiota’s role in developing leaf scald and mosaic diseases. By inoculating sugarcane clones with the sugarcane mosaic virus (strain E) and Xanthomonas albilineans, we are collecting invaluable data that will reveal key differences in the microbiome (bacterial, fungal, and viral) between control and inoculated plants through metagenomic sequencing. Our collaboration with CIRAD in France furthers our commitment to groundbreaking research in this field. Objective 2 Sub-objective 2A The economic implications of disease-related losses in sugarcane are profound. To counter this, the Canal Point Sugarcane Breeding and Cultivar Development Programs (CP programs) are diligently screening their germplasm for resistance. ARS researchers are gathering critical data on disease reactions from both natural infections and inoculated trials to ensure that only the resistant clones are advanced and released. This ongoing selection process is essential, as pathogens continuously evolve. With over 10,000 clones assessed for natural disease reactions and inoculation data from breeding stages III and IV, we will advance and release high-yielding and disease-resistant clones that will benefit Florida's sugarcane industry. Sub-objective 2B Our extensive sugarcane germplasm collections not only have diversity but also contain numerous valuable alleles for disease resistance. By identifying all resistance genes and allele variants within these collections, breeders can significantly enhance their efforts. ARS researchers have meticulously selected 167 hybrids of Saccharum spp. and 25 wild accessions. A trial involving these 190 accessions is planted at Canal point with two replications. DNA was extracted and accessions were genotyped using selected disease resistance gene probe sequences. Data from genotyping will be aligned against sugarcane reference genome to identify SNPs. Additionally, we are analyzing samples from the world collection of sugarcane and related grasses to assess germplasm against various pathogens. The ongoing collection of samples from parental lines at Canal Point will further our understanding of pathogen prevalence. These efforts will ensure a profitable future for Florida's sugarcane industry. Three biparental populations expected to segregate for response to orange rust were transplanted in FY25 to enable experiments to map molecular markers linked with sugarcane orange rust resistance. Another biparental population was re-planted in FY25 in order to facilitate orange rust phenotyping and resistance mapping.
Accomplishments
1. Release of disease resistant germplasm. ARS researchers at Canal Point, Florida believe sugarcane is an economically important crop in Florida with a positive impact of $3.3 billion in Florida’s economy and provides approximately 20% of the total sugar consumed in the USA. Plant diseases cause significant losses in crop production that lead not only to lower yields and economic losses but also to loss of cultivar diversity, mitigation costs due to control measures, and downstream impacts on employment. Therefore, developing disease resistance is critical for sugarcane production in Florida. Researchers from the Agricultural Research Service (ARS) at Canal Point, Florida released eight high yielding disease resistant sugarcane cultivars for commercial production: seven (CP 14-4570, CP 17-1470, CP 17-1966, CP 17-2134, CP 17-2360, CP 17-2411, and CP 17-2435) for organic soils and one (CP 16-4524) for mineral soil. Disease resistant clones were selected in Stages 1, 2, 3, and 4 to advance to the next stage of the CP program.
2. Surveys of sugarcane for new endemic and emerging diseases. Pathogens continuously evolve to overcome host resistance by acquiring genetic or pathogenic variations. The losses from a new disease or a different pathogenic strain of an endemic disease resulted in several hundred million dollars in a single year. Since sugarcane is a perennial crop, it is harvested three to four times once planted. Farms infected with a new disease need to be plowed out and planted with resistant cultivars, increasing the cost of production. Therefore, rapid identification and detection of emerging pathogens are essential to developing resistant cultivars and limiting losses from new diseases. ARS researchers at Canal Point, Florida surveyed sugarcane collections at Canal Point and growers’ farms to find new endemic or emerging diseases. They found sugarcane infected with an Ethiopian virus associated with maize (EaMv); this is the first report of EaMV infection in sugarcane. The coinfection of this virus and sugarcane mosaic virus causes maize lethal necrosis. Therefore, the coinfection of EaMV and SCMMV in sugarcane can be detrimental. Fortunately, the cultivars released from the ARS program are resistant to SCMMV.
3. Genotyping of sugarcane germplasm for disease resistance. ARS researchers at Canal Point, Florida believe to overcome the threats from pathogen evolution and exotic pathogens, the crop improvement heavily relies on genetic diversity to find new sources of resistance, which is essential for developing superior disease resistant cultivars. This process involves identifying and incorporating genetic material from cultivated varieties, wild relatives, and germplasm collections. Therefore, ARS researchers genotyped a genetically diverse germplasm collection consisting of 192 accessions using selected disease resistance gene probe sequences. The alleles associated with disease resistance will contribute to the development of disease resistant cultivars and in marker-assisted selection of resistant cultivars. Marker-assisted selection of resistance will reduce the time and efforts required for phenotypic selection of disease resistance.
Review Publications
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.
Islam, M.S., Qin, L., Mccord, P.H., Sood, S.G., Zhang, M. 2024. Marker trait association and candidate gene identification for brown rust disease in sugarcane. Crop Science. 1:14. https://doi.org/10.1002/csc2.21388.
Coto Arbelo, O., Davidson, W.R., Islam, M.S., Sandhu, H., Zhao, D., Sood, S.G., Momotaz, A., Baltazar, M. 2025. Registration of ‘CP 16-1883’ a new sugarcane cultivar released for Florida muck soils. Journal of Plant Registrations. 19;e20416. https://doi.org/10.1002/plr2.20416.
Davidson, W.R., Gordon, V.S., Islam, M.S., Mccord, P.H., Sandhu, H.S., Zhao, D., Sood, S.G., Comstock, J.C., Maninder, S.P., Baltazar, M. 2024. Registration of ‘CP 10-1620’ sugarcane. Journal of Plant Registrations. 18:363-373. https://doi.org/10.1002/plr2.20365.