Location: Sugarcane Research
2020 Annual Report
Objectives
Objective 1: Identify germplasm of hybrid sugarcane and wild relatives of sugarcane for resistance to economically limiting diseases that breeders can use for parental clones.
Sub-objective 1.A. Classify available clones from different taxa for disease resistance.
Sub-objective 1.B. Identify DNA markers that are closely linked to genes for disease resistance.
Objective 2: Determine molecular and biological characteristics of economically important sugarcane pathogens that can be applied to effective diagnostic protocols.
Objective 3: Develop useful methods to monitor potential emergence of exotic pathogens and identify genetic diversity among pathogen populations that affect sugarcane.
Sub-objective 3.A. Characterize races, strains, or other biotypes of endemic pathogens and determine their distribution.
Sub-objective 3.B. Monitor the Louisiana sugarcane industry for the emergence of new pathogens.
Approach
To identify and develop parental germplasm with resistance to the economically limiting diseases affecting sugarcane in the United States, highly domesticated and wild clones of sugarcane and near relatives will be evaluated for disease resistance following either natural infections or artificial inoculation. To identify molecular markers that are linked to genes for disease resistance, Random Amplification of Polymorphic DNA (RAPD), Amplified fragment length polymorphism (AFLP), and Simple Sequence Repeats (SSR) markers in combination with the bulk segregant analysis (BSA) will be used to screen potential DNA markers for resistance to smut and other important diseases. Variations among the DNA sequences of polymorphic DNA fragments will be analyzed and used to design new pairs of specific primers to develop SCAR (Sequenced Characterized Amplified Region) and or single-nucleotide polymorphism (SNP) markers. Genotypic and phenotypic expressions of variability within populations of pathogens will be used to identify the genetic variability among pathogen populations and determine the distribution of races, strains, or biotypes. The domestic sugarcane industry will be monitored for the introduction of exotic pathogens.
Progress Report
To consolidate and strengthen complementary efforts in sugarcane research, National Program (NP) directed ARS researchers at Houma, Louisiana, to merge this project with NP 305 titled “New Crop Production and Protection Practices to Increase Sugarcane Ratoon Longevity and Maximize Economic Sustainability”. Therefore, this is the final report for project 6052-22000-018-00D which terminated in January 2020. As a result of the consolidation, only milestones for the first three years of this project were addressed prior to the consolidation. Some continuing field experiments with FY 2020 milestones were incorporated into the new consolidated project, 6052-21000-017-00D.
ARS researchers at Houma, Louisiana, made progress on the three objectives and sub-objectives. The availability of productive sugarcane cultivars for planting in Louisiana is limited. Objective 1, results of experiments and disease resistance trials by ARS researchers at Houma, Louisiana, have contributed to the release of four commercial cultivars, namely, HoCP 11-537, Ho 11-573, L 11-183, Ho 12-615, L 12-201, and Ho 13-739. The diversity of well adapted cultivars available to growers also lessens the vulnerability of the industry to the introduction of a new disease or new biotype of a disease already present in the industry. Cultivars advanced through the breeding program were evaluated by ARS researchers at Houma, Louisiana, for susceptibility to mosaic caused by two viruses, Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV); Sugarcane yellow leaf caused by Sugarcane yellow leaf virus (SCYLV); leaf scald caused by the bacterium Xanthomonas albilineans; smut caused by Sporosorium scitamineum; and two rust diseases, brown rust caused by Puccinia melanocephala, and orange rust caused by P. kuehnii. Cultivars released during this time period were resistant or moderately resistant to these economically important diseases. Disease management practices were developed by ARS researchers at Houma, Louisiana, for cultivars that have superior agronomic characteristics, but may be some level of susceptible to a pathogens. A series of field experiments were conducted by ARS researchers at Houma, Louisiana, between 2016 and 2019 to determine the susceptibility of the newly released varieties to ratoon stunt caused by Leifsonia xyli subsp. xyli, a bacterium that lives in the water vessels of the sugarcane stalk. Effective cultural practices were recommended by ARS researchers at Houma, Louisiana, for controlling ratoon stunt for those culitvars with high levels of susceptibility. This project provides the basis for continued development of disease management practices into the new project.
Objective 2, studies of the seed transmissibility of systemic pathogens were completed by ARS researchers at Houma, Louisiana. In the United States, exotic germplasm of sugarcane (Saccharum spp.) is mainly received as vegetative cuttings because the extensive actions required to meet existing Animal and Plant Health Inspection Service (APHIS) permit conditions make the importation of sugarcane seed impractical. While taking precautions against foreign pathogens is reasonable, disallowing seed exchange limits us from acquiring new germplasm that could potentially enhance the sugarcane industry. In order to ascertain the risk of introducing foreign pathogens, ARS researchers at Houma, Louisiana, investigated seed transmissibility of SCMV and SCYLV in sugarcane. Seedlings grown from seeds obtained from virus-infected female plants, tested negative for both viruses. These data are consistent with previously conducted research by our group, which revealed no seed transmission of viral sugarcane pathogens. This work contributed to the adoption of a practical permit requirement for the importation of biological seed of sugarcane.
Objective 3, the potential for new biotypes of endemic pathogens to emerge in the sugarcane industry and for exotic pathogens to be introduced was demonstrated. Between 2017 and 2019, leaf samples from sugarcane plants showing mosaic symptoms were collected by ARS researchers at Houma, Louisiana, at numerous locations within the Louisiana sugarcane industry. Virus isolates associated with the diseased plants were identified using reverse transcriptase-polymerase chain reaction (RT-PCR) to distinguish between SCMV and SrMV. Only SrMV was associated with these samples. In yield loss trials, the SrMV caused reduced yields in susceptible commercial sugarcane (Saccharum spp.) cultivars. A phylogenetic analysis was performed using the RT-PCR product sequences of 74 SrMV isolates. Isolates were assigned to five groups based on sequence similarity. A mixture of four isolates was used to inoculate 41 sugarcane clones. Isolates recovered from clones expressing symptoms indicated that one of the isolates caused the majority of infections. Twenty SrMV isolates from among the five groups were selected for high throughput sequencing to obtain full genomic sequences. Analysis of these sequences will continue in the newly initiated project. Orange rust caused by Puccinia kuehnii was first found in domestic sugarcane in Florida in 2007. ARS researchers at Houma, Louisiana, subsequently observed the spread of orange rust into Louisiana in 2012, and Texas in 2017. In Louisiana and Texas, highly susceptible near-release breeding varieties are no longer advanced and susceptible released varieties have been removed from lists of recommended varieties. Susceptibility to orange rust must be considered when introducing new sugarcane varieties.
Accomplishments
Review Publications
Grisham, M.P., Warnke, K.Z., Maggio, J.R., Davidson, W., Haudenshield, J.S., Hartman, G.L., Hernandez, E., Scott, Jr., A.W., Comstock, J.C., Mccord, P.H. 2020. First report of Puccinia kuehnii causing orange rust of sugarcane in Texas, USA. Plant Disease. https://doi.org/10.1094/PDIS-10-19-2117-PDN.
Rice, J.L., Hoy, J.W., Hale, A.L., Todd, J.R., Grisham, M.P., Kimbeng, C.A., Pontif, M.J. 2019. Evaluation of susceptibility to mosaic in Louisiana's sugarcane breeding program. Journal of the American Society of Sugar Cane Technologists. 39:1-11.
