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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

2020 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:
The yearly cycle of crossing, field evaluations, and selections were made by ARS researchers at Houma, Louisiana, as part of the USDA-ARS commercial variety development program. Crosses were made at USDA-ARS facilities in both Canal Point, Florida, and Houma, Louisiana, with the production of approximately 554,500 viable commercial seed. In fiscal year 2020, approximately 58,520 commercial seedlings were planted to the field by ARS researchers at Houma, Louisiana. These crosses will be utilized in the test for specific combining ability. Of the approximately 58,550 seedlings planted in fiscal year 2019, a total of 5,888 were selected and advanced to the first-line trials. Selections planted in the fiscal year 2018 second-line trial were evaluated by ARS researchers at Houma, Louisiana in the first ratoon. Of the 493 potential varieties in this trial, 66 received a permanent numerical assignment and then advanced for further testing (Milestones 1 and 2). In advanced stages of the program, 36 experimental varieties were advanced to off-station nurseries from the 2013 crossing series, and 11 were advanced to infield testing in fiscal year 2019 from crosses made in 2012. Stages in the commercial breeding program fall under the subordinate agreement, “Three-way (LSUAC, ASCL, ARS) Sugarcane Breeding and Variety Development”. Remote sensing images were taken of the seedling plot 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” 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. All stages of breeding and selection were carried out by ARS researchers at Houma, Louisiana, in the basic breeding (germplasm enhancement) program. Approximately 450 crosses were made for this program at the crossing facilities in Houma, Louisiana, producing roughly 72,000 seeds. Approximately 16,500 seedlings enhanced with traits of interest from wild relatives of sugarcane were planted to the field in May 2020. Newly-planted first-line trials contain 1324 selections, and basic second-line trials contained 280 potential new varieties. Fifty-three newly-selected parents enhanced with wild germplasm traits were planted by ARS researchers at Houma, Louisiana, as material for the 2020 crossing season (Milestone 1). Approximately 700 samples were fingerprinted by ARS researchers at Houma, Louisiana, from the sugarcane crossing cart parents, pathology greenhouse, historical nursery, seed increase plots, and a project established to explore the importance of sugarcane cytoplasm. In addition, samples were collected by ARS researchers from Canal Point, Florida, and the Lower Rio Grande Valley of Texas for variety validation. High-throughput fingerprinting was conducted in collaboration with researchers at USDA-ARS in Stoneville, Mississippi. Approximately, 15,000 fingerprint files were produced ultimately resulting in the construction of 717 molecular identities which were deposited into the USDA’s sugarcane molecular identity database. Of these molecular identities, 135 were for newly-named 2018-series USDA varieties, and 22 were new for the 2017-series Louisiana State University varieties. The molecular IDs were compared among themselves and with other IDs contained in the already established database. Fingerprinting from the 2019 analysis indicated all varieties contained in field increase plots were correctly labelled as was the Texas-grown Ho 13-710 and Florida-grown Ho 07-613. Five stalks of Ho13-710 with confirmed identity used as foundation material for micropropagation through tissue culture (Milestone 1). Artificial inoculations give a good indication of varietal response to both sorghum and sugarcane mosaic virus in sugarcane. All wild accessions and varieties (basic and commercial) used in the crossing program were screened for the virus prior to the beginning of the 2019 crossing season as well as all newly named varieties that will be used as parents in 2020 (Milestones 1 & 2). In addition, all 2018 varieties remaining active in the program were re-screened in 2019 to validate the previous results. To increase confidence in the test, leaf samples were collected and screened by ARS researchers at Houma, Louisiana, using PCR markers to validate the visual assessments. Adjustments were made based on polymerase chain reaction (PCR) results to achieve optimal timing of visual assessment. Results from greenhouse tests allowed breeders to make targeted crosses to avoid an increase in susceptibility in the current breeding population. Crosses were not generated between two susceptible varieties. This decision will ultimately save time in the future and increase the odds of developing new resistant varieties for the Louisiana program. In addition to inoculated testing, ARS researchers at Houma, Louisiana, continue to work on a modified genotyping by sequencing project with collaborators at Louisiana State University to identify genetic markers associated with mosaic resistance. Deoxyribonucleic acid (DNA) was extracted and sequencing is pending for genotyping by sequencing (GBS) studies (Milestone 3). One-hundred-thirty-two newly-named 2018 parents were screened by ARS researchers at Houma, Louisiana, for a molecular marker, BRU1, indicating resistance to brown rust as part of a collaborative project with colleagues at the LSU AgCenter. Four genotypes from the germplasm enhancement program and 30 from the commercial breeding program tested positive. An additional 121 varieties from 2019 were screened, and information on their BRU1 status was added to the database for the 2020 crossing season (Milestone 2). Crosses made during the 2019 crossing season were targeted to maximize the frequency of BRU1 in the progeny. Fiber components were analyzed by ARS researchers at Houma, Louisiana, from the second clonal trial of the germplasm enhancement program according to the forage fiber analysis method. Fiber quality was assessed by estimating cellulose, hemicelluloses, lignin, and ash concentrations. Fiber work was conducted as part of a subordinate agreement entitled “Center for Advanced Bioenergy and Bioproducts Innovation” (Interagency Reimbursable Agreement #60-6052-8-002). Putative amplified fragment length polymorphism (AFLP) markers for sequence characterized amplified region (SCAR) conversion were validated on a panel of 24 sugarcane genotypes from the LCP 85-384 self-progeny mapping population (Milestone 3). DNA samples were extracted by ARS researchers at Houma, Louisiana, from 87 clones of the World Collection of Sugarcane and Related Grasses and 90 clones of the SRU breeding nursery. The DNA samples were subject to PCR using universal primers to amplify the non-coding regions of the trnL and trnF fragments of the chloroplast genome. In addition, two additional primer pairs were used to amplify targeted chloroplast genomic regions. All amplicons were sequenced in both directions and the nucleotide sequence variability was analyzed (Milestone 3).


4. Accomplishments
1. Release of commercial sugarcane variety "Ho 13-739". There is no private breeding program for sugarcane in the United States, thus the industry is founded 100% on publicly developed varieties. 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 2020. The new variety, Ho 13-739, is resistant to sugarcane smut caused by Sporisorium scitamineum, moderately susceptible to ratoon stunt caused by Leifsonia xyil subsp xylil, moderately susceptible to brown rust caused by Puccinia melanocephala, resistant to leaf scald caused by Xanthomonas albinlineans, resistant to Sugarcane mosaic caused by the Sorghum mosaic virus, and moderately resistant to sugarcane borer, Diatraea saccharalis. Its most significant attributes are its early maturity and high sugar yields during early harvest. The ability to harvest early is important in Louisiana is critical because the harvest season is cut short due to late-season freezing temperatures. 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.

2. Release of commercial sugarcane variety ‘Ho 13-710’. There is no private breeding program for sugarcane in the United States, thus the industry is founded 100% on publicly developed varieties. ARS scientists from Houma, Louisiana, in collaboration with the American Sugarcane League of the U.S.A., Inc. Louisiana State University Agricultural Center, and Rio Farms Inc. developed and released a new sugarcane variety in 2020. The new variety, Ho 13-710, appears to be resistant to sugarcane smut caused by Sporisorium scitamineum, brown rust caused by Puccinia melanocephala, and leaf scald caused by Xanthomonas albinlineans, and susceptible to Mexican Rice borer, Eoreuma loftini. Ho 13-710 is susceptible to Sorghum mosaic virus, but this is not a problem in Texas. Its most significant attributes are disease resistance and cane yield, particularly in plant cane. The release of this variety offers Texas growers a well-adapted variety that can increase industry profits and expand the genetic variability contained within the growing region.

3. Release of commercial sugarcane variety ‘Ho 11-573’. There is no private breeding program for sugarcane in the United States, thus the Texas industry is founded 100% on publicly developed varieties. ARS scientists from Houma, Louisiana, in collaboration with the American Sugarcane League of the U.S.A., Inc. Louisiana State University Agricultural Center, and Rio Farms Inc. developed and released a new sugarcane variety in 2020. The new variety, Ho 11-573, appears to be resistant to leaf scald caused by Xanthomonas albinlineans, moderately susceptible to sugarcane smut caused by Sporisorium scitamineum, moderately susceptible to brown rust caused by Puccinia melanocephala, and susceptible to Mexican Rice borer, Eoreuma loftini. Sugarcane mosaic caused by the Sorghum mosaic virus has not been observed in Ho 11-573. Its most significant attribute is its cane yield, particularly in plant cane. 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.

4. Release of high-fiber sugarcane variety 'Ho 06-9002'. The U.S. has a growing interest in energy independence based on renewable fuels, and sugarcane is one of the most efficient producers of biomass of all plant species. ARS scientists from Houma, Louisiana, developed and released a new high-fiber sugarcane (energycane) variety. The new variety, Ho 06-9002, has a high fiber content, excellent ratooning ability, is cold tolerant, has a high stalk population, and produces excellent biomass yields. Ho 06-9002 showed no symptoms of brown rust (caused by Puccinia melanocephala H. and P. Sydow) or smut when exposed to high levels of natural inoculum. Mosaic (caused by either Sugarcane mosaic virus or Sorghum mosaic virus) was not observed in the variety under natural field conditions. Its most significant attribute is its cold tolerance and ability to yield high biomass in non-traditional cane growing regions.


5. Record of Any Impact of Maximized Teleworking Requirement:
The restriction of travel and the mandate of one-person-per-vehicle has made off-station test analysis difficult. It has reduced the number of individuals able to participate in evaluations and visual ratings of off-station tests. In addition, it has halted travel as part of technology transfer agreements with Texas and China. Trips where collaborative research was to be conducted were cancelled (both domestic and foreign). In addition, COVID restrictions have slowed the progress in the laboratory on fiber analysis and extramural funded projects as this work is not deemed "mission critical." Failure to meet milestones could impact competitiveness for future grant opportunities. While teleworking has been a challenge, it provided the opportunity and time to complete data entry on historical files in preparation for setting up a new database. Employees have been able to take online training through AgLearn to enhance their skill sets which may prove to enhance productivity in the future.


Review Publications
Wang, Z., Pan, Y.-B., Luo, J., You, Q., Xu, L., Zhang, H., Que, Y. 2020. SSR-based genetic identity of sugarcane clones and its potential application in breeding and variety extension. Sugar Tech. 22(3):367-378. https://doi.org/10.1007/s12355-019-00788-9.
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.
Todd, J.R., Pan, Y.-B., Boykin, D.L. 2020. Fidelity of sugarcane crosses assessed with SSR markers. Agronomy. 10(3):1-18. http://doi.org/10.3390/agronomy10030386.
Wu, J., Wang, Q., Xie, J., Pan, Y.-B., Zhou, F., Guo, Y., Chang, H., Xu, H., Zhang, W., Zhang, C., Qiu, Y. 2019. SSR marker-assisted management of parental germplasm in sugarcane (Saccharum spp. hybrids) breeding programs. Agronomy Journal. 9(8):449. https://doi.org/10.3390/agronomy9080449.
Fu, Y.-H., Wei, J.-J., Pan, Y.-B., Zhou, X., He, E.-Q., Liu, R., Huang, H., Lu, J.-J., Liu, F.-Z. 2019. Comparative analysis reveals changes in transcriptomes of sugarcane upon infection by Leifsoniaxyli subsp. xyli. Journal of Phytopathology. 167:633-644. https://doi.org/10.1111/jph.12856.
Xu, C., Liu, X., Burner, D.M., Abbas, Z., Pan, Y.-B., Elgamal, I.S., Lu, X., Su, H. 2020. Phenotypic and molecular characterization of a core collection of Saccharum spontaneum L. in China. Sugar Tech. 22(1):76–88. https://doi.org/10.1007/s12355-019-00761-6.