Location: Sugarcane Field Station
2024 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
Sugarcane is an economically important crop in Florida, generating 12,500 jobs and positively impacting Florida’s economy by $3.3 billion. Florida produces more than 50% of the total sugar produced in the USA from sugarcane. Disease resistance plays an essential role in the success of cultivars, but emerging pathogens and pathogenic variability in endemic pathogens threaten commercial cultivars. ARS researchers at Canal Point, Florida release disease resistant cultivars for the stakeholders in Florida to increase profit by mitigating losses from diseases and their chemical control. They survey for new diseases, perform trials to understand the pathogens and diseases they cause, and screen sugarcane clones to select resistant cultivars.
Objective 1
Sub-objective 1A. Variation in leaf scald pathogen isolates by PCR using different primer combinations. Several isolates were collected from several varieties and locations. Pathogenicity trials for these isolates were set up. The pathogenicity trials will be repeated. The isolates with different virulence will be sent for the whole genome sequencing. Whole genome sequencing is delayed a year because of not getting the expected results of a pathogenicity trial. ARS researchers surveyed for the new diseases in several fields throughout the sugarcane growing area. They found sugarcane mild mosaic virus (SCMMV) in the Canal Point parental lines. They also surveyed SCMMV in the sugarcane germplasms at Canal Point and the world collection of sugarcane and related grasses at Miami. The virus is more prevalent than reported previously. ARS researchers found a disease with unique mosaic symptoms and sent the samples to APHIS at Beltsville for high-throughput next-generation sequencing. High-throughput next-generation sequencing data revealed that the samples were infected with an Ethiopian maize-associated umbra-like virus. The virus is found to be associated with the maize lethal necrosis in Ethiopia.
Sub-objective 1B. Cooperative plant-microbe interactions can promote the recruitment of beneficial microorganisms and limit the development of pathogens. Plant microbiota are critical in addressing plant health challenges by predicting future plant defense and crop resistance. ARS researchers planted a trial to test how the microbiota plays a role in leaf scald and mosaic disease development. ARS researchers have inoculated the clones with sugarcane mosaic virus (strain E causes mosaic disease in Florida) and Xanthomonas albilineans (causes leaf scald disease). ARS researchers collected samples from leaves, stalks, and roots to evaluate the differences in the microbiome (bacterial, fungal, and viral) between control and inoculated plants by metagenomic sequencing. The project collaborators at CIRAD, France, completed the processing of the sample for metagenomics.
Objective 2
Sub-objective 2A. Economic losses caused by diseases are significant. Thus, the Canal Point Sugarcane Breeding and Cultivar Development Programs (CP programs) screen its germplasm for resistance to these diseases. ARS researchers obtained disease reaction data by natural infection and inoculated trials, ensuring that resistant or tolerant clones are advanced and released. Because pathogenic changes occur over time, selecting disease-resistant cultivars is an ongoing process in the CP programs. ARS researchers obtained natural disease reaction data for more than 10,000 clones in the different stages of the CP program and inoculated trial data in breeding Stages III and IV to advance and release disease-resistant or tolerant clones from the program. ARS researchers advanced and released high-yielding and disease-resistant or tolerant clones.
Sub-objective 2B. Sugarcane germplasm collections have great diversity and probably many valuable alleles for disease resistance. For breeders to use these germplasm accessions, it will be very informative to determine all the resistance gene and allele versions within the accessions of the sugarcane germplasm collections. ARS researchers selected 150 CP breeding parental lines frequently used in the last ten years and 40 wild accessions and collected their DNA for further studies. A trial consisting of 190 accessions was planted and evaluated for resistance to the natural infection of diseases. ARS researchers collected samples from the world collection of sugarcane and related grasses to evaluate the germplasm for pathogens (bacterial, fungal, and viral). Samples from 2024 parental lines at Canal Points were collected to identify pathogens.
Accomplishments
1. Emergence of Ethiopian maize associated umbra-like virus. Emergence of Ethiopian maize-associated umbra-like virus. Researchers from the Agricultural Research Service (ARS), in collaboration with researchers from the Animal and Plant Health Inspection Service (APHIS), have discovered a new mosaic disease in sugarcane at the Sugarcane Field Station in Canal Point, Florida. The disease is caused by an Ethiopian maize-associated umbra-like virus, marking the first time this disease and its pathogen have been found in sugarcane in the western hemisphere. This virus is also linked to maize lethal necrosis in Ethiopia. Maize lethal necrosis disease can devastate maize production, causing yield losses of up to 100% in some areas. In sugarcane, mixed infection of the emerging virus, Sugarcane mild mosaic virus, Sugarcane yellow leaf virus, and sugarcane mosaic virus led to a more than 50% reduction in biomass. Emerging plant diseases are of global concern and take a heavy toll on crop production. Rapid detection and selection of resistance against the emerging pathogen is essential to limit the losses from the new diseases.
2. Prevalence of sugarcane mild mosaic virus. A recent survey by ARS researchers at Canal Point, Florida, found that Sugarcane mild mosaic virus (SCMMV) is more prevalent and present in many commercial sugarcane cultivars. SCMMV and Sugarcane bacilliform virus (SCBV) mixed infections were associated with mosaic patterns, retarded growth, narrow leaves, and withering of shoots. SCBV is also prevalent in Florida. Knowledge and understanding of these diseases will aid in selecting resistant cultivars for the Florida sugarcane industry.
3. Release of disease resistant germplasm to stakeholders for commercial evaluations. ARS researchers at Canal Point, Florida,released seven cultivars for organic (muck) and two cultivars for mineral (sand) soils for the commercial evaluations by sugarcane stakeholders. 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 and worldwide.
Review Publications
Sood, S.G., Momotaz, A., Coto Arbelo, O., Baltazar, M., Davidson, W.R., Islam, M.S., Sandhu, H., Zhao, D., Rounds, E. 2024. Registration of ‘CP 15-2516’ for organic soils in Florida. Journal of Plant Registrations. 3:1-12. https://doi.org/10.1002/plr2.20360.
Lesmes, R., Zhao, D., Sood, S.G., Momotaz, A., Davidson, W.R., Islam, M.S., Baltazar, M., Gordon, V.S., Mccord, P.H., Coto Arbelo, O., Sandhu, H. 2024. Registration of ‘CP 13-1954’ sugarcane for Florida organic soils. Journal of Plant Registrations. 18:352-362. https://doi.org/10.1002/plr2.20364.
Momotaz, A., Coto Arbelo, O., Gordon, V.S., Wesley, B.L., Sood, S.G., Zhao, D. 2024. Genetic variability and clustering pattern of sugarcane (Saccharum spp.) germplasms with respect to sucrose and related traits. International Journal of Plant Biology. 15:203-216. https://doi.org/10.3390/ijpb15020017.
Islam, M.S., Sandhu, H.S., Zhao, D., Sood, S.G., Momotaz, A., Coto Arbelo, O., Baltazar, M., Davidson, W.R., Rounds, E. 2024. Registration of ‘CP 15-1407’ sugarcane for muck soils. Journal of Plant Registrations. 1-11. https://doi.org/10.1002/plr2.20363.
Cardenas, D.E., Carrillo, T.Y., Sood, S.G., Hincapie, M.A., Tapia, J., Wang, J., Rott, P.C., Cano, L.M. 2024. A diagnostic guide for orange rust disease in sugarcane. Plant Health Progress. 0:1-41. https://doi.org/10.1094/PHP-02-24-0013-DG.