Location: Sugarcane Field Station
2022 Annual Report
Objectives
1. Identify disease resistant sugarcane and energy cane clones for high yielding commercial production.
2. Develop methodologies to efficiently screen germplasm for resistance and to identify new molecular markers associated with resistance.
3. Identify pathogenic variation in sugarcane pathogens that are endemic and emerging within the United States.
Approach
Objective 1: Sugarcane clones in the cultivar development program for both sucrose and bio-energy will be screened for their disease reaction in artificial inoculation tests separate from the cultivar development plots with the major pathogens and ratings will be determined based on incidence and severity of disease.
Objective 2: For Sugarcane Yellowleaf Virus (SCYLV) existing markers will be tested against our known historical clones having both resistance and susceptible reaction. Two new populations will be screened for SCYLV resistance and genotyping by sequencing (GBS) to identify new markers. For ratoon stunt disease and smut two populations will be screened for disease reaction and GBS to identify markers. For orange rust we will test published markers and perform fine mapping using a larger population and whole genome sequencing of the parents and bulked progeny to identify markers for screening the whole population.
Objective 3: Orange rust spores have been collected over the last two years from different cultivars and locations in Florida and stored for determining possible pathogenic variation. Specifically, cultivars CP 80-1743 (the susceptible cultivar first observed with orange rust in Florida), CL 85-1040 (susceptible) and two cultivars CP 88-1762 and CP 89-2143 that were originally resistant but became susceptible will be used to evaluate pathogenic variation. The whorl inoculation technique (Sood et al. 2009) that is routinely used to evaluate brown and orange rust reactions will be used to evaluate variation between the isolates. The whorl technique has been shown to give consistent results, as seen by the sample data in Table 2 of the Appendix. These will be used along with the new collections described. Sentinel plots of orange rust susceptible and resistant sugarcane cultivars will be planted at 5 different locations and from grower’s fields where the “breaking down” of resistance is reported. Fields will be observed monthly from March to July when orange rust is most prevalent. Orange rust pustules that develop on previously resistant cultivars will be collected and compared using the whorl inoculation techniques to isolate the collected spores from different cultivars differing in susceptibility over several years. Mass rust spore collections from the field will be inoculated on plants of the same cultivar twice as a means to help purify the isolate. Variation in symptom development of isolates on specific cultivars will be used to identify pathogenic differences. Unfortunately, pathogen variation will be limited to isolates from Florida because isolates from outside the state are prohibited from introduction.
Progress Report
This is the final report for the project 6030-22000-011-000D, which terminated in March 2022 and replaced by the project 6030-22000-012-000D.
Economic losses caused by brown and orange rusts, leaf scald, sugarcane mosaic virus, ratoon stunt disease (RSD), and smut are substantial. 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 of these diseases by natural infection and inoculated trials ensuring the development of resistant or disease tolerant clones. Because pathogenic changes occur over time, selecting disease-resistant cultivars is an ongoing process in the CP programs. Twenty-five disease resistant and high-yielding CP cultivars were released for commercial production in Florida in the last five years. In addition, RSD and sugarcane yellow leaf disease were surveyed yearly in the primary and secondary sugarcane seed-cane increase trials. The data from these trials were provided to stakeholders to obtain the disease-free seed material. Molecular markers to screen for disease resistance are essential to save time and effort. Thus ARS researchers, in collaboration with a scientist at the University of Florida at Gainesville, identified quantitative trait loci associated with the disease resistance to orange rust, brown rust, ratoon stunt disease, and yellow leaf virus (SCYLV) and developed diagnostic markers to screen sugarcane clones for orange rust resistance. This marker has been used in selecting orange rust resistance in the CP program. Pathogens mutate to overcome disease resistance; monitoring the disease and evaluating pathogens is necessary to limit the economic losses; therefore, the researchers collected orange rust spores from different cultivars and other varieties to evaluate variation. Researchers monitored orange rust at different locations on the Growers' farms to find pathogenic variations. The two isolates of Puccinia kuehnii collected from sugarcane cultivars CL 85-1040 and CP 89-2143 showed pathogenic variation. The collaborators and ARS scientists created a draft genome using these two isolates. In addition, pathogenic variation in the sugarcane mosaic virus was discovered in the eight species of the Poaceae family. In 2022, under Objective 1, ARS researchers obtained disease reaction of 1500 clones in Stage II for brown and orange rust, 86 clones in Stage III increase (CP 18 Series), and 26 clones in Stage IV (CP 17 Series) for ratoon stunt, leaf scald, mosaic and smut. Advanced clones with acceptable resistance levels to later stages of the programs. Released high-yielding and disease-resistant or tolerant clones for commercial cultivation. Regarding Objective 2, RNA-sequencing data were obtained from orange rust resistant and susceptible lines to identify the candidate genes associated with orange rust resistance. A population required for the fine mapping to find orange rust resistant genes, these two lines were planted in the parental crossing lines; however, due to the lack of flowering, crosses were not made. Collected leaf scald, ratoon stunt disease, and smut inoculations data from the field and pot trials of a population originating from a cross of CP 72-2086 and CP 01-2390. Substantial progress is made under Objective 3. With the help of collaborators, ARS researchers discovered genetic variation in sugarcane mosaic virus (SCMV) at Canal Point, Florida, and assessed the virulent pattern of the SCMV genetic strains from Sugarcane, St. Augustine, and Columbus grass. The information will help in developing mosaic-resistant cultivars. The isolate from St. Augustine grass and sugarcane can cross infect each other; SCMV has been a threat to lawns in South Florida and can re-emerge as a threat to sugarcane as a different pathogenic strain. ARS researcher collected orange rust spores from different cultivars and other varieties and monitored orange rust at different locations at the growers' farms. Variations in orange rust have been evaluated.
Accomplishments
1. Disease resistant cultivars for commercial production. Sugarcane is a genetically complex polyploid clonally propagated and has multi-year crop cycles. The major diseases in Florida are brown and orange rusts, leaf scald, sugarcane mosaic virus, ratoon stunt disease (RSD), and smut. These diseases could cause 10 to 60% yield losses in the susceptible cultivars under stressed conditions. Therefore, the local sugarcane industry must cultivate high-yielding disease-resistant cultivars for sustainable and profitable sugar production. Sugarcane growers in Florida rely entirely on the improved Canal Point (CP) sugarcane cultivars. The development of the disease resistant cultivars starts with the crossing and subsequent selection of resistant clones at every stage of the development and takes more than ten years. In 2021, Florida Sugarcane Variety Committee released five new cultivars which are resistant and tolerant to the diseases mentioned earlier, CP 14-1377, CP14-1490, CP14-1934, CP13-4474, and CP13-4513, developed by the scientists at the ARS Canal Point, in collaboration with the University of Florida and the Florida Sugar Cane League. The first three cultivars are released to cultivate on the Florida muck soils, and the other two are for production on the Florida sand soils. The CP cultivars have significantly contributed to sustainable sugarcane production in Florida and provided approximately 20% of the sugar consumed in the United States.
2. Molecular markers for the disease resistance and high yields. Molecular markers are essential for the accurate and fast detection of disease resistance and yield parameters in marker-assisted sugarcane breeding. Molecular markers are assets to screen disease resistance for RSD and yellow leaf since these diseases do not exhibit external symptoms. In addition, for mosaic and leaf scald, symptoms of these two diseases become latent during unfavorable conditions for the pathogens. QTLs associated with resistance to orange rust, brown rust, RSD, and SCYLV resistance have been identified. A diagnostic marker for orange rust resistance has been developed to screen germplasm. Other sugarcane-producing countries have used this marker to identify orange rust resistance germplasms. ARS and collaborators research identified 217 non-redundant markers and 225 candidate genes significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement.
3. Pathogenic variation. Pathogenic variability in endemic pathogens and emerging pathogens could cause tremendous losses to sugarcane production. Therefore, monitoring and evaluating pathogens' variability is essential for the sugarcane industry. With the help of collaborators, ARS researchers discovered genetic variation in Sugarcane mosaic virus (SCMV) at Canal Point, Florida, and assessed the virulent pattern of the SCMV genetic strains from Sugarcane, St. Augustine, and Columbus grass. This information will help in developing mosaic-resistant cultivars. The isolate from St. Augustine grass and sugarcane can cross infect each other; SCMV has been a threat to lawns in South Florida and can re-emerge as a threat to sugarcane as a different pathogenic strain. Monitoring and evaluating pathogenic variations in the orange rust pathogen, P. kuehnii, will help in the sustainable management of orange rust. Chemical control of orange rust is not economical.
Review Publications
Sood, S.G., Momotaz, A., Davidson, W.R., Islam, M.S., Sandhu, H.S., Zhao, D., Baltazar, M., Gordon, V.S., Mccord, P.H., Coto Arbelo, O. 2022. Registration of ‘CP 12-1753’ sugarcane. Journal of Plant Registrations. 16:44-53. https://doi.org/10.1002/plr2.20178.
Islam, M.S., Sandhu, H.S., Zhao, D., Sood, S.G., Momotaz, A., Davidson, W.R., Baltazar, M., Gordon, V.S., Mcccord, P.H., Coto Arbelo, O. 2022. Registration of ‘CP 13-1223’ sugarcane for Florida organic soils. Journal of Plant Registrations. 16:54-63. https://doi.org/10.1002/plr2.20186.
Momotaz, A., Davidson, W.R., Islam, M.S., Sandhu, H.S., Zhao, D., Sood, S.G., Baltazar, M., Coto Arbelo, O., Gordon, V.S., Mccord, P.H. 2022. Registration of 'CP 13-4100' sugarcane. Journal of Plant Registrations. 16:34-43. https://doi.org/10.1002/plr2.20173.
Sandhu, H.S., Zhao, D., Davidson, W.R., Gordon, V.S., Islam, M.S., Mccord, P.H., Sood, S.G., Baltazar, M., Coto Arbelo, O., Momotaz, A. 2022. Registration of 'CP 12-1417' sugarcane. Journal of Plant Registrations. 16:64-72. https://doi.org10.1002/plr2.20192.
Sood, S.G., Davidson, W.R., Baltazar, M. 2021. Survey of Sugarcane yellow leaf virus in Canal Point breeding and cultivar development program. Agronomy. 11(10):1948. https://doi.org/10.3390/agronomy11101948.
Islam, M.S., Mccord, P.H., Olatoye, M.O., Qin, L., Sood, S.G., Lipka, A.E., Todd, J.R. 2021. Experimental evaluation of genomic selection prediction for rust resistance in sugarcane. The Plant Genome. 14(3). Article e20148. https://doi.org/10.1002/tpg2.20148.
