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ARS Home » Southeast Area » Canal Point, Florida » Sugarcane Field Station » Research » Research Project #432517

Research Project: Identification of Resistant Germplasm and Markers Associated with Resistance to Major Diseases of Sugarcane

Location: Sugarcane Field Station

2019 Annual Report

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.

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
Economic losses caused by sugarcane diseases, especially sugarcane brown and orange rusts, mosaic, ratoon stunting disease (RSD), smut, and leaf scald, are substantial. Thus, the Canal Point (CP) cultivar development programs (CP programs) screen its germplasm for resistance to these diseases. Data are obtained in natural infection and inoculated trials ensuring that resistant or disease tolerant clones are advanced and released from the program. Because pathogenic changes occur over time, developing resistance is a continuous effort in the CP programs. Sugarcane orange rust appeared in the Western hemisphere in 2007 and impacted the Florida sugarcane industry as well as CP cultivar development program. Marker assisted selection along with phenotypic evaluation of disease resistance will benefit the CP program therefore quantitative trait loci associated with orange rust resistance as well as with brown rust resistance and yellow leaf virus (SCYLV) have been identified. Diagnostic markers for orange rust resistance have been developed. To find quantitative trait loci (QTLs) for other diseases, we have inoculated leaf scald, RSD and smut pathogen in the field for the diseases screen in the first ratoon crop of a population from a cross of CP 72-2086 and CP 01-2390. Currently we are analyzing the genotype data including marker filtering for mapping and QTL analysis. We were unable to make a reciprocal cross between CP 01-2390 and CP 72-2086 due to flowering issues. Since we have already identified and successfully validated the markers associated with orange rust, so we decided not to further validate the orange rust markers. We were unable to test the effectiveness of the SCYLV reported markers by original investigator using our historical population as corresponding author did not respond to our request to provide the marker sequence. However, we were able to analyze QTL associated with SCYLV resistance using another population derived from cross CP 95-1039 X CP 88-1762.

1. Improvement of disease resistance in the Canal Point (CP) sugarcane breeding programs. CP cultivar development programs have been releasing disease resistant high yielding cultivars for Florida sugarcane industry. Thus, all susceptible clones in the seedling, Stage I, and Stage II are eliminated if exhibiting disease symptoms based on natural infection. In two CP cultivar development programs (i.e., CP program for organic (muck) soils and CP program for mineral (sand) soils), clones in both the muck and sand programs were screened annually in inoculation tests at Stage III (135 clones), Stage III increase (40 clones) and Stage IV (13 clones) for their resistance to ratoon stunt, smut, brown rust, orange rust, leaf scald and mosaic. Clones in Stage I and II are screened for resistance to rusts, mosaic, leaf scald and smut by natural infection. All clones with acceptable resistance levels were advanced to later stages of the programs. High-yielding and disease resistant or tolerant clones in the Stage 4 increases are released for commercial cultivation. In 2019, one cultivar CP 12-1417 for muck soils and one CP 11-1640 for sand soils were released by the Florida Sugarcane Variety Committee. The two cultivars were developed by ARS researchers in Canal Point, Florida, with collaboration of University of Florida and Florida Sugar Cane League. The resistant CP cultivars have contributed greatly in a sustainable production of sugarcane in Florida. Also, these disease resistant high yielding sugarcane cultivars help Florida sugarcane growers to economically grow sugarcane and produce approximately 20% of the sugar consumed in the United States.

2. Development molecular markers for resistance to brown rust, orange rust, and other diseases. Quantitative trait loci (QTL) associated with orange rust resistance as well as with brown rust resistance have been identified by ARS researchers in Canal Point, Florida. Diagnostic markers have been developed for orange rust resistance. Analysis of the QTL associated with sugarcane yellowleaf virus (SCYLV) resistance using a population derived from cross CP 95-1039 X CP 88-1762 was performed. Genotyping of SCYLV and ratoon stunting disease (RSD) population from a cross between CP 72-2086 and CP 01-2390 has been completed using next generation sequencing based Exom capture sequence based technique. In addition, phenotype data (leaf scald, sugar and yield traits) from the plant cane have been collected for the same population. Additionally, two sugarcane populations derived from a cross between orange rust susceptible (brown rust resistant) and brown rust susceptible (orange rust resistant) cross and a reciprocal cross have been evaluated for its reaction to orange rust and brown rust for multiple years based on whorl inoculation. The phenotypic disease data obtained from this segregating population have been used for marker development. Brown rust and orange rust are monitored in increase plots.

Review Publications
Yang, X., Sood, S.G., Luo, Z., Todd, J.R., Wang, J. 2019. Genome-wide association studies identify resistance loci to orange rust and yellow leaf virus diseases in a diversity panel of polyploid sugarcane (Saccharum spp.). Phytopathology. 109(4):623-631.
Yang, X., Todd, J.R., Arunadale, R., Binder, J., Luo, Z., Islam, M.S., Sood, S.G., Wang, J. 2019. Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome wide association study. Industrial Crops and Products. 130:598-605.
Zhao, D., Comstock, J.C., Davidson, W.R., Gordon, V.S., McCord, P.H., Sandhu, H.S., Sood, S.G., Singh, M.P., Abbott, T., Islam, M.S., Baltazar, M., McCorkle, K.M. 2019. Registration of ‘CP 10-1208’ Sugarcane. Journal of Plant Registrations. 13(1):42-49.
McCord, P.H., Zhao, D., Abbott, T.E., Comstock, J.C., Singh, M.P., Davidson, R.W., Gordon, V.S., Sandhu, H.S., Sood, S.G., Baltazar, M., McCorkle, K.M. 2019. Registration of 'CP 09-2392' Sugarcane. Journal of Plant Registrations. 13:170-177.
Islam, M.S., Yang, X., Sood, S.G., Comstock, J.C., Zan, F., Wang, J. 2018. Molecular dissection of sugar related traits and it’s attributes in Saccharum spp. hybrid. Euphytica. 214:170.
Yang, X., Islam, M.S., Sood, S.G., Maya, S., Hanson, E.A., Comstock, J.C., Wang, J. 2018. Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane (Saccharum spp.). Frontiers in Plant Science. 9:350.
Davidson, W.R., Gordon, V.S., Sandhu, H.S., McCord, P.H., Zhao, D., Comstock, J.C., Singh, M.P., Sood, S.G., Baltazar, M., McCorkle, K.M. 2018. Registration of ‘CP 09-1952’ Sugarcane. Journal of Plant Registrations. 12:340-346.
Gordon, V.S., Sandhu, H., McCord, P.H., Zhao, D., Comstock, J.C., Singh, M.P., Davidson, R.W., Sood, S.G., Baltazar, M., McCorkle, K.M. 2018. Registration of ‘CP 09-1430’ Sugarcane. Journal of Plant Registrations. 12:314-323.
Sandhu, H., McCord, P.H., Zhao, D., Comstock, J.C., Singh, M.P., Davidson, W.R., Gordon, V.S., Sood, S.G., Baltazar, M., McCorkle, K.M. 2018. Registration of ‘CP 09-1822’ Sugarcane. Journal of Plant Registrations. 12:333-339.