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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Research Project #434376

Research Project: Genetic Improvement of Sugarcane for Adaptation to Temperate Climates

Location: Sugarcane Research

2019 Annual Report

1a. Objectives (from AD-416):
Objective 1: Develop and release sugarcane cultivars and germplasm with improved agronomic traits, adaptability, stress tolerance and genetic diversity. Sub-objective 1.A. Develop improved sugarcane cultivars utilizing parental germplasm derived from the SRU’s germplasm enhancement program (sub-objective 1.B.) that possess highly desirable traits. Sub-objective 1.B. Characterize and broaden the genetic base of Saccharum to support both sugarcane breeding for commercial cultivars, with specific emphasis on adaptation to temperate environments, disease resistance, and sugar content. Objective 2: Develop and deploy clone-and trait-specific genetic markers for sugarcane, and work with breeders to accelerate breeding and release improved sugarcane cultivars and germplasm.

1b. Approach (from AD-416):
The program’s breeding strategy is to increase the genetic diversity of parental clones through: (1) acquisition and maintenance of germplasm from wild species of Saccharum and related genera; (2) characterization of parents and progeny for traits (cold tolerance, stubbling ability, disease resistance, and sugarcane borer resistance) that will increase the adaptation of sugarcane to Louisiana’s temperate climate; (3) utilization of crossing and molecular marker techniques to produce interspecific and intergeneric hybrids containing new sources of disease and insect resistance and cold tolerance; and (4) recombination of progeny through backcrossing to develop parental material containing a concentration of desirable genes for the commercial breeding program. Screening procedures will be developed to determine relative cold tolerance among clonal material in the basic breeding program. Cultivar development will emphasize increased sugar yield, along with other import traits such as yield components (stalk number, height, and diameter), fiber concentration, rate of maturation, ratooning ability (stand longevity), harvestability (resistance to lodging, stalk erectness, and stalk brittleness), hardiness (winter survival, early spring vigor, and stalk and ratoon freeze tolerance), abiotic stress tolerance (droughts, floods, and heavy clay soils), and resistance to stalk boring insects (sugarcane borer and Mexican rice borer) and diseases (smut, rust, leaf scald, mosaic, yellow leaf virus, and ratoon stunting). Recurrent selection techniques will be utilized to accelerate the rate of genetic improvement for these important traits. In addition, trait-specific markers closely associated with traits such as sucrose accumulation, cold tolerance, and resistance to the sugarcane borer will be developed to assist breeders in eliminating undesirable plants early in the selection process.

3. Progress Report:
Commercial Program: The yearly cycle of crossing, field evaluations, and selections were made as part of the USDA-ARS commercial variety development program in Houma, Louisiana. Crosses were made at USDA-ARS facilities in both Canal Point, Florida and Houma, Louisiana, with the production of approximately 705,138 viable commercial seed. In fiscal year 2019, approximately 58,550 commercial seedlings (including those to be used in the unmanned aircraft system {UAS} study) were planted to the field. Of the approximately 59,983 seedlings planted in fiscal year 2018, a total of 6,378 were selected and advanced to the first-line trials. Selections planted in the fiscal year 2017 second-line trial were evaluated in the first ratoon. Of the 563 potential varieties in this trial, 76 received a permanent numerical assignment and were advanced for further testing (Milestones 1 and 2). In advanced stages of the program, 35 experimental varieties were advanced to off-station nurseries from the 2012 crossing series, and 23 were advanced to infield testing from crosses made in 2011 in fiscal year 2018. Stages in the commercial breeding program fall under the subordinate agreement, “Three-way (LSUAC, ASCL, ARS) Sugarcane Breeding and Variety Development” (Non-Funded Cooperative Agreement #58-6052-7-003N). Remote sensing images were taken of the seedling plots and 20 seedling families were planted in a replicated design for future imagery experiments (Milestone 1). Newly-named and selected varieties entering large-plot, off-station testing were transferred under the subordinate agreement entitled “Evaluating Sugarcane Varieties for the Rio Grande Valley Sugarcane Industry” (Trust Fund Cooperative Agreement #58-6052-9-0001) to Rio Farms, Inc., for testing in the Lower Rio Grande Valley of Texas. This program has proven to be valuable to the growers in Texas and has resulted in a sustained effort for variety improvement in the region. Germplasm Enhancement Program: All stages of breeding and selection were carried out in the Houma, Louisiana-based, basic breeding (germplasm enhancement) program. Approximately 370 crosses were made for this program at the crossing facilities in Houma, Louisiana, producing roughly 170,000 seed. Approximately 16,350 seedlings enhanced with traits of interest from wild relatives of sugarcane were planted to the field in April 2019. Newly-planted first-line trials contain 989 selections, and basic second-line trials contained 289 potential new varieties. Fifty-nine newly-selected parents enhanced with wild germplasm traits were planted as material for the 2019 crossing season (Milestone 1). In addition to using wet lab chemistry, fiber levels were assessed using a near infrared spectrometer (NIR) designed for efficient evaluation of cane quality. All varieties sampled from the second-line trials of the germplasm enhancement program were analyzed using an NIR, and enhanced calibration curves were established. Correlations with wet lab data were high. In addition to evaluation of fiber content using the NIR, a benchmark curve was created to evaluate the fiber components of hemicellulose, cellulose, lignin, and ash. This preliminary curve will be expanded as more samples are analyzed to increase the accuracy of the curve. Work on this objective was accomplished, in part, through an interagency agreement with the U.S. Department of Energy. Brown rust is a major concern in the Louisiana sugarcane industry and throughout the world. In the past, the disease has reduced crop yields in the industry by up to 30% and has resulted in the demise of previously high-yielding varieties. Because of a lack of durable resistance to the disease, thousands of varieties are dropped yearly. A genetic marker has been identified, Bru1, that is linked to brown rust resistance. In collaboration with researchers at Louisiana State University, all material to be used during the fiscal year 2020 crossing campaign in Houma, Louisiana, was screened for the presence of this deoxyribonucleic acid (DNA) marker. Information from the ongoing screening of new parental material was incorporated into the crossing program to increase the frequency of this marker and to enhance the likelihood of developing brown-rust resistant varieties. Based on this work, the frequency of the Bru1 allele has increased in parental clones developed for introgression (Milestone 1). In addition to screening for the Bru1 marker, USDA researchers, along with collaborators at the LSU AgCenter, have expended efforts to screen for resistance to Sugarcane Mosaic Virus and Sorghum Mosaic Virus. Mosaic viruses nearly bankrupted the industry in the 1920s, and have been historically controlled through the cultivation of resistant cultivars. Due to successful breeding efforts, the disease pressure is low, and difficult to detect. With low levels of inoculum, susceptible varieties are not detected early in the breeding cycle, and there is a concern that the frequency of susceptible varieties are increasing in the program. For this reason, all varieties used for breeding were screened for the virus prior to the beginning of the 2018 and 2019 crossing seasons. Based on results from inoculated tests, targeted crosses were made and selected for planting to avoid increasing susceptibility in the current breeding population. In addition, a study was begun to assess resistance levels in clones of wild species related to sugarcane (Milestone 1). To build on results of inoculated testing, samples were collected and DNA extracted for a study to identify genetic markers associated with mosaic resistance (Milestone 2). Work on mosaic resistance in the breeding population of sugarcane and related Saccharum was conducted, in part, by collaborative research. In 2018, 440 clones from commercial increase field plots, breeding nursery plots, and plants used in the crossing program were fingerprinted using DNA markers (SSRs). The new DNA-based fingerprint files were deposited into a local sugarcane molecular identity database and compared to previously established fingerprints. Verification of clones is a safeguard taken by the breeders to ensure that the proper varieties are increased for commercial production. This work identified two clones with mis-matched fingerprints in the commercial increase plots (Ho 05-961 and HoCP 16-685), which were subsequently replaced with the correct varieties. DNA was extracted from the sugarcane variety "LCP 85-384" and re-sequenced on a PacBio DNA sequencer through collaboration with the Fujian Agriculture and Forestry University. Additional SSR data was collected for identifying quantitative trait locus (QTL) markers that are associated with fiber, stalk diameter, and stalk number. Total nucleic acids (DNA and RNA) from both the nucleus and cytoplasm (maternally derived) was extracted from 80 clones of five Saccharum species, including 22 S. spontaneum clones. Information used from this study will be used to determine cytoplasmic diversity amongst the S. spontaneum accessions.

4. Accomplishments
1. Release of commercial sugarcane variety “Ho 12-615”. The Louisiana sugarcane industry is dependent on early-maturing varieties developed through the USDA breeding program and collaborators at the Louisiana State University Agricultural Center and the American Sugar Cane League of the U.S.A., Inc. There is no private breeding program for sugarcane in the United States, thus the industry is founded 100% on publicly developed varieties. USDA-ARS scientists from Houma, Louisiana, in collaboration with the American Sugarcane League of the U.S.A., Inc. and the Louisiana State University Agricultural Center, developed and released a new sugarcane variety in 2019. The new variety, Ho 12-615, appears to be resistant to sugarcane smut caused by Sporisorium scitamineum, susceptible, yet tolerant, to ratoon stunt caused by Leifsonia xyil subsp xylil, moderately susceptible to brown rust caused by Puccinia melanocephala, moderately susceptible to leaf scald caused by Xanthomonas albinlineans, and moderately resistant to sugarcane borer, Diatraea saccharalis. Sugarcane mosaic caused by the Sorghum mosaic virus has been detected in Ho 12-615 in several fields, but the effect of this disease on yields of cane of this variety is not yet known. The variety is a high-population, high-yielding and moderately maturing sugarcane. Its most significant attribute is its ability to yield well in ratoon harvests. The ability to harvest into late ratoons increases profits since planting costs are the biggest expense to a grower. The release of this variety offers growers a well-adapted variety that can increase industry profits and expand the genetic variability contained within the growing region.

Review Publications
Wu, Q., Pan, Y.-B., Zhou, D., Grisham, M.P., Gao, S., Su, Y., Guo, J., Que, Y., Xu, L. 2018. A comparative study of three detection techniques for Leifsonia xyli subsp. xyli, the causal pathogen of sugarcane ratoon stunting disease. BioMed Research International. 2018(2786458):1-11.
Ahmad, A., Wang, J., Pan, Y., Sharif, R., Gao, S. 2018. Development and use of simple sequence repeats (SSR) markers for sugarcane breeding and genetic studies. Agronomy. 8(11):260.
He, E.-Q., Pan, Y.-B., Fu, Y.-H., Lei, S.-F., Li, X.-Y., Lu, J.-J., Zhang, Z.-X. 2016. Genetic diversity analysis of nine chewing cane varieties (lines) and construction of their DNA fingerprints. Journal of Southern Agriculture. 47(11):1815-1821.
Todd, J.R., White, W.H., Dufrene Jr, E.O., Tew, T.L., Pan, Y.-B., Duet Jr, M.J., Verdun, D.L., Hale, A.L., Dalley, C.D., Grisham, M.P., Gravois, K.A., Jackson, W.R., Miller, J.D. 2018. Registration of ‘HoCP 04-838’ sugarcane. Journal of Plant Registrations. 12:324–332.
Ali, A., Pan, Y.-B. Wang, Q., Wang, J., Chen, J., Gao, S. 2019. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Scientific Reports. 9:1-10.
Wu, Q., Gao, S., Pan, Y.-B.., Su, Y., Grisham, M.P., Guo, J., Xi, L., Que, Y. 2018. Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria. PeerJ. 6:e5873.
Todd, J.R., Dufrene Jr, E.O., Pan, Y.-B., Tew, T.L., White, W.H., Hale, A.L., Duet Jr, M.J., Verdun, D.L., Grisham, M.P., Petrie, E.C., Gravois, K., Waguespack, H., Abbott, T.E. 2019. Registration of ‘HoCP 09-804’ sugarcane. Journal of Plant Registrations. 13:161–169.
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.
Muhammad, K., Ahmad, W., Ahmad, H., Ali, E., Iqbal, J., Pan, Y.-B. 2019. Recent developments in the biosystematics and molecular biology of sugarcane. In: Öztürk, M. et al. Crop Production Technologies for Sustainable Use and Conservation. Palm Bay, FL. Apple Academic Press Inc. p. 131-153.
Lee, D.K., Aberle, E., Anderson, E.K., Anderson, W.F., Baldwin, B.S., Baltensperger, D., Barrett, M., Blumenthal, J., Bonos, S., Bouton, J., Bransby, D.I., Brummer, C., Burks, P.S., Chen, C., Daly, C., Egenolf, J., Farris, R.L., Fike, J.H., Gaussoin, R., Gill, J.R., Gravois, K., Halbleib, M.D., Hale, A.L., Hanna, W., Harmoney, K., Heaton, E.A., Heiniger, R.W., Hoffman, L., Hong, C.O., Kakani, G., Kallenbach, R., Macoon, B., Medley, J.C., Missaoui, A., Mitchell, R., Moore, K.J., Morrison, J.I., Odvody, G.N., Ogoshi, R., Parrish, J.R., Quinn, L., Richard Jr, E.P., Rooney, W.I., Rushing, J., Schnell, R., Sousek, M., Staggenborg, S.A., Tew, T.L., Uehara, G., Viands, D.R., Voigt, T., Williams, D., Williams, L., Wilson, L.T., Wycislo, A., Yang, Y., Owens, V. 2018. Biomass production of herbaceous energy crops in the United States: Field trial results and yield potential maps from the multiyear regional feedstock partnership. Global Change Biology Bioenergy. 10:698-716.
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., Arundale, 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.
Fickett, N., Gutierrez, A., Verma, M., Pontif, M., Hale, A.L., Kimbeng, C., Baisakh, N. 2018. Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection. Genomics. Available: