Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): 1. Breed new sugarcane cultivars and improved germplasm with superior agronomic traits, adaptation to variable weather conditions, and increased abiotic and biotic stress tolerance including cold tolerance(NP301, C1, PS1B). Anticipated products include new technologies and tools that will connect phenomic data collection, capture, and storage in databases with expanding breeding goals to include traits for sustainability of sugarcane production agroecosystems. Expected benefits include coordinated breeding and pre-breeding for sugarcane across all production regions with the goal to enhance new cultivar development for Florida and Louisiana production. Priority traits include cold-tolerance to expand the region for productive sugarcane production. 2. Broaden the genetic base of sugarcane and related genera to improve output-to-input ratios, yield stability, and specific adaptation to temperate environments. 3. Develop and deploy clone-and trait-specific genetic markers for marker- assisted selection of priority traits such as disease resistance to accelerate sugarcane breeding efforts. 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, ratooning 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. A newly available, but untested handheld NIR device will be tested and calibrated to hasten in-field analysis of sugar content. Cold tolerance screening and parental evaluation will be conducted with collaborators in Starkville, MS where yearly freezes occur. Diverse genotypes will be screened for phenolic content and antioxidant activity. Cultivar development will emphasize increased sugar yield, along with other important 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, disease resistance, fiber, and cold tolerance, will be developed to assist breeders in eliminating undesirable plants early in the selection process. Following disrupted years due to Hurricane Ida, the 2023 season started off with a promise. Unique and never-before-encountered research challenges continue, but the robust breeding program has adapted to keep up with the Unit�s mission. 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 600,000 viable commercial seed. In fiscal years 2023 and 2024, approximately 46,664 combined basic and commercial seedlings were planted, respectively to the field but not selected. Approximately 4,503 selections from commercial second ratoon seedling trials (planted in 2020) were advanced to first line trials. There were 576 sugarcane genotypes selected and planted in a second-line trial in FY24. Selections planted in FY2022 second-line trial were evaluated in the first ratoon. Of the 518 potential varieties in this trial, 50 received permanent numerical assignment and were advanced for further testing (Milestones 1 and 2). In advanced stages of the program, 32 experimental varieties were advanced to off-station nurseries from the 2017 crossing series, and 11 were advanced to infield testing in fiscal year 2024 from crosses made in 2016. 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 #58-6052-2-002N) (Milestone 1).Germplasm Enhancement Program: Following disrupted years due to Hurricane Ida, the 2023 season started off with a promise. The summer of 2023 in Louisiana was one of the hottest on record, with temperatures, on average, about four degrees warmer than records from the past 30 years. These high temperatures greatly affected sugarcane flower initiation. Despite the challenging weather conditions, the crossing team in Houma 184 crosses at the crossing facilities in Houma, LA producing roughly 61,550 seed. Eighty percent of the seedlings crossed in 2020 survived into the second ratoon in 2023, and 1028 individuals from this group were selected for advancement into the first clonal stage. Had hurricane Ida not occurred, these seedlings would have been selected in 2022, but selection was delayed, thereby offsetting the breeding program by a year. Of the 4,939 seedlings that were produced in 2021 and set to the field in 2022, 94 percent survived into the first ratoon. In May 2023, 10,210 seedlings derived from 79 basic crosses were set to the field. Two-hundred nineteen selections were made from the first-clonal trials and planted into the basic second clonal trials. There were no second clonal plant-cane evaluations conducted in 2023 because the seedling-stage of the program was not selected following the 2021 hurricane. The basic breeding program assigned 57 new parents in 2023. Parents in the USDA-ARS sugarcane breeding program were screened for a molecular marker indicating resistance to brown rust (BRU1 as part of a collaborative project with colleagues at the LSU AgCenter. The team screened 114 new parents used in the 2023 crossing season. Of these varieties, 23 tested positive for the BRU1 marker for rust resistance. Five of these varieties were from the basic breeding program and the remaining 18 were commercial. The varieties screened for the 2023 crossing season were recently named in the fall of 2022 (Milestone 2). The targeted effort to increase the frequency of BRU1 in the Louisiana breeding population has been successful and we continue to monitor the level of this marker in our breeding populations. USDA continues to work on a modified genotyping by sequencing project with collaborators from the Louisiana State University Agricultural Center to identify genetic markers associated with mosaic resistance. Greenhouse evaluations and DNA testing has been completed on a wide array of varieties used extensively in the breeding program. The markers were validated using a separate population. PCR-based primers were developed from the sequence information, and these will be tested against varieties with known resistance and susceptibility to the mosaic virus. If successful, these newly developed primers will provide a relatively inexpensive and fast, way to locally determine mosaic susceptibility of varieties in the laboratory. We anticipate this assay to be used similarly to the yearly BRU1 screen if successful. 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, a decision which will ultimately save us time in the future and increase our odds of developing new resistant varieties for the Louisiana program. In addition to inoculated testing, USDA continues to work on a modified genotyping by sequencing project with collaborators at the LSU AgCenter to identify genetic markers associated with mosaic resistance. Greenhouse evaluations and DNA testing has been completed on a wide array of varieties used extensively in the breeding program. The validation of potential markers using a separate population is has been completed. There has been a long-standing effort by USDA to breed for cold tolerant sugarcane varieties. Funding through the American Sugar Cane League (ASCL), the National Institute for Food and Agriculture, and the U.S. Department of Energy has allowed us to expand these efforts in recent years. In 2015, 26 varieties were selected in the third stubble in north Louisiana for having excellent yields despite yearly exposure to damaging freezes. These 26 varieties have been utilized in the crossing program in Houma to enhance cold tolerance. The varieties are being evaluated in replicated trials by the USDA in Houma by Mississippi State University in Starkville, MS, and by Alabama A&M University in Huntsville, AL. The third-ratoon trials were harvested in December 2023 in Houma, and the data is promising though different than the previous ratoons. All varieties survived the harsh winter following planting, and spring stalk counts were determined. There was a significant overlap between the best stalk population in Huntsville, AL and the top yielding varieties in Houma and Mississippi. The evaluation under yearly freezing conditions in Starkville highlights the differential impact that the environment can have on varieties and emphasizes the need to diversify the variety profile. While the top- yielding varieties differ by crop and location, some varieties outshine others in all three locations. Varieties which yield well in Mississippi and Louisiana, and appear to possess stubble cold tolerance were incorporated in to the crossing program to enhance this trait in our breeding populations. Additional varieties and seedlings have been sent to Mississippi and Alabama for selection and evaluation under yearly freezing conditions. This work was conducted as part of a subordinate agreement entitled �Center for Advanced Bioenergy and Bioproducts Innovation� (Interagency Reimbursable Agreement #60-6052-002).The sugarcane research community was invited to be part of the Breeding Insight On Ramp (B I OnRamp). The team has embraced the opportunity to partake of a newly available resource for breeders. In 2023, sugarcane was officially added as a crop to the Breeding Insight program after several years of work with OnRamp scientists. Over the past three years breeders in Houma in collaboration with a USDA database team and other sugarcane researchers, have developed a framework for a research database able to integrate traditional and molecular breeding. Many historical files and data have been incorporated into this database in a searchable format so that researchers can easily merge current and past data as well as DNA and field-based information. We are now exploring options to digitally upload information directly from the laboratory and field. The organization of the data will simplify analyses and make obtaining information more efficient. Sequencing of important varieties in the Louisiana breeding program is underway by our BIOnRamp partners in Stoneville, MS and genomic selection is being thoroughly explored in our breeding program. The basic breeding program has valuable traits that are being incorporated into the parental population of the commercial program. With emphasis being placed on disease resistance, cold tolerance, and ratooning ability, this program will continue to contribute to yield increases of disease resistant varieties. With recent additions to our laboratory, we have expanded the number of traits being characterized in the breeding population and continue to look for bio-markers for improved quality and yields. New technology and computer-based systems such as Breeding Insight have the potential to make the breeding process run more smoothly and eliminate time-consuming steps in the process. Embracing new technology to improve the program will enable us to continue to produce varieties adapted to the Louisiana industry. ACCOMPLISHMENTS 01 Release of Sugarcane Variety HoL 15-508.. There is no private breeding program for sugarcane in the U.S., thus the industry is founded 100% on publicly developed varieties. ARS scientists from Houma, Louisiana, in collaboration with the American Sugar Cane League of the U.S.A., Inc. and the Louisiana State University Agricultural Center, developed and released a new sugarcane variety in 2023. The new variety, �HoL 15- 508� has yields equal to the leading variety in the state, with higher sugar per ton of cane and lower fiber content. It is early maturing and is considered to have moderate cold tolerance. It is moderately susceptible to the sugarcane borer, smut, mosaic, and leaf scald. Early maturity is critical in a temperature growing region for economic production.
Impacts
(N/A)
Publications
- Cortes, J.D., Gutierrez, A.F., Hoy, J.W., Hale, A.L., Baisakh, N. 2023. Genetic mapping of quantitative trait loci controlling smut resistance in Louisiana sugarcane using bi-parental mapping population. Gene. 2352-4073. https://doi.org/10.1016/j.plgene.2023.100445.
- Pan, Y., Todd, J.R., Lomax, L.E., White Jr, P.M., Simpson, S.A., Scheffler, B.E. 2023. Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.. Agronomy Journal. https://doi.org/10.3390/agronomy13112728.
- Ellsworth, P.Z., White Jr, P.M., Todd, J.R. 2024. Gas exchange and time to reach maximum rate of photosynthetic rate and their relationship with whole-plant traits in sugarcane in water abundant Louisiana, USA. Photosynthetica. https://doi.org/10.32615/ps.2024.015.
- Mula-Michel, H.P., White Jr, P.M., Hale, A.L. 2023. Immediate impacts of soybean cover crop on bacterial community composition and diversity in soil under long-term sugarcane monoculture for applied soil ecology. PeerJ. 11.Article 15754. https://doi.org/10.7717/peerj.15754.
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