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United States Department of Agriculture

Agricultural Research Service

2008 Annual Report

1a.Objectives (from AD-416)
The long-term objective of this project is to reduce the impact of diseases on the productivity of the domestic sugarcane (Saccharum hybrids) industry by providing assistance to sugarcane breeders in identifying parental clones with resistance, improving the efficiency of selection for disease resistance traits, and providing the industry the information needed to guard against more virulent strain shifts and/or new pathogens. Our primary objectives will be to identify and develop germplasm with resistance to the major diseases affecting sugarcane, to identify the genetic variability among endemic pathogen populations, and to monitor the Louisiana sugarcane industry for the emergence of new pathogens. Disease resistant germplasm will be sought from among different taxa of Saccharum and related genera. Molecular markers that are linked to genes for disease resistance will be identified. Molecular approaches will be used to enhance the studies of host and pathogen genetics.

1b.Approach (from AD-416)
To identify and develop germplasm with resistance to the major diseases affecting sugarcane in the United States, highly domesticated and wild clones of sugarcane and near relatives will be evaluated for resistance to the major sugarcane diseases following either natural and infections or artificial inoculation. To identify molecular markers that are linked to genes for disease resistance, polymerase chain reaction (PCR) based methods such as AFLP, SSR, or TRAP will be used to identify genetic markers closely linked to the resistance genes. Priority will be given to finding markers for smut, then ratoon stunting disease (RSD) and mosaic. 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 other biotypes. The domestic sugarcane industry will be monitored for the introduction of exotic pathogens.

3.Progress Report
The following addresses National Program 303 Component III, Plant Disease Resistance; Problem Statement, Disease Resistance in New Germplasm and Varieties: • Greenhouse trials were continued to test a collection of 86 varieties and off spring from crosses involving wild sugarcane relatives that are being used in the Sugarcane Research Unit's (SRU) breeding program for the major diseases affecting sugarcane (mosaic, smut, leaf scald, and RSD). Inoculations for RSD and mosaic were evaluated in early FY 2008. Inoculations and evaluations for leaf scald and smut were made in FY 2008 on plants established in FY 2007. • One hundred ninety candidate varieties that are being tested for possible release into commercial production in the next five years were screened through artificial inoculation for smut, leaf scald, and RSD. In other ARS breeding trials and nurseries, candidate varieties were observed for natural infection by pathogens that cause mosaic, rust, smut and leaf scald diseases. Pathology recommendations were made at variety advancement and variety release meetings. • Simple sequence repeats (SSR) are small segments of deoxyribose nucleic acid (DNA) that can be used as genetic markers to identify varieties of sugarcane. The unique markers of a variety are inherited by the off spring from these crosses. Using an additional 66 SSR markers, 277 of the original 286 progeny from the selfing of the sugarcane variety LCP 85-384 were verified as true selfs. The progeny were multiplied and screened in greenhouse and field tests for susceptibility to RSD, mosaic, smut, and rust. Only two out of 277 were susceptible to smut by inoculated test in the greenhouse; however, approximately 5% of the progeny were susceptible to natural inoculation in the field. Susceptibility to RSD ranged from resistance to highly susceptible. The 25 most susceptible and the 25 most resistant were identified for future genetic analysis. Natural infection by brown rust was recorded.

The following addresses National Program 303 Component I, Disease Diagnosis: Detection, Identification, and Characterization of Plant Disease Pathogens: • In the FY 2008 survey of sugarcane plants expressing mosaic symptoms, strain I of SrMV remained the predominant strain of virus causing mosaic. Strains H and M were also identified among the diseased plants; however, no isolate of SCMV was found. • Although sugarcane orange rust was detected in Florida, the disease was not observed in Louisiana.


Practical methods of detecting the bacterium that causes RSD, primarily those based on immunoassays, have required the use of stalk tissue from plants older than 6 months where concentrations of the disease-causing bacteria are high enough to be detected by these methods. A technique known as quantitative, real-time polymerase chain reaction (PCR) was recently developed to increase detection sensitivity and to quantify the lower levels of bacteria found in leaf or young stalk tissues at any growth stage. Using a chemical process, a unique segment of DNA from the disease bacterium is replicated and measured. The nucleic acid extraction step of the protocol was modified to reduce the time, effort, and expense needed to complete overall detection protocol. The real-time PCR protocol offers the flexibility to perform evaluations throughout the growing season and to evaluate greenhouse grown plants where it is not practical to grow them to maturity. The real-time PCR protocol was used in the spring of 2008 to determine the RSD status of seed cane of the newly released variety L 01-283 prior to distribution to sugarcane growers.

This accomplishment addresses National Program 303 Component III, Plant Disease Resistance; Problem Statement, Disease resistance in new germplasm and varieties.


Strains H, I, and M of Sorghum mosaic virus (SrMV) have been responsible for causing sugarcane mosaic disease in Louisiana since the 1960s. Leaf tissue samples were collected from sugarcane plants expressing mosaic symptoms during surveys conducted from 2004 to 2008. Using molecular techniques, SrMV strains I, H, and M were associated with 66%, 14%, and 6% of the samples, respectively. In 7% of the samples, the virus isolate was identified as SrMV from RT-PCR results, but the RFLP analysis indicated that the strain was different from strains H, I, or M, the strains previously described for SrMV. No RT-PCR product was produced by either the Sugarcane mosaic virus (SCMV) or the SrMV-specific RT-PCR primer set for 10% of the plants showing mosaic symptoms suggesting that another virus may cause sugarcane mosaic in Louisiana. Twenty-six of the Louisiana samples, including 20 that tested negative to the presence of SCMV or SrMV, and all the Florida samples were analyzed with RT-PCR for the presence of Sugarcane streak mosaic (SCSMV), a virus that has been reported to cause mosaic symptoms in sugarcane grown in several Asian countries. No sample tested positive for SCSMV. The discovery of the presence of new strains of SrMV indicates the virus has the potential to adapt to resistant sugarcane varieties and germplasm.

This accomplishment addresses National Program 303 Component I, Disease Diagnosis: Detection, Identification and Characterization of Plant Pathogens; Problem Statement, Detection, Identification, Characterization, and Classification of Pathogens.

6.Technology Transfer

Number of Non-Peer Reviewed Presentations and Proceedings3

Last Modified: 8/28/2016
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