Project : USDA ARS

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

2022 Annual Report

Objectives
Objective 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. 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.

Approach
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.

Progress Report
Marked by the COVID-19 pandemic and the devastating Category 5 Hurricane Ida, the 2021 season was unique. Despite the encountered challenges, breeding and selection work continued, albeit not in the normal fashion. Adjustments were made to the breeding paradigm to mitigate the effects of the hurricane and to maximize the potential benefits of the changing approach. In the early stages of both the Commercial and Germplasm Enhancement Programs, the yearly cycle of crossing, field evaluations, and selections were made. Due to Hurricane Ida and the widespread devastation, power outages, and impassable roads during the early harvest season, the window to select seedlings for early sucrose was lost. Hurricane complications combined with the increasing importance of ratooning ability in the Louisiana sugarcane industry led scientists to postpone selection of first-ratoon seedlings into the 2022 second-ratoon crop. This change in the program will ultimately allow breeders to select for sucrose early in the next harvest season, while also selecting for enhanced yield stability. Because seedling selection is labor intensive and the number of seedlings currently awaiting selection in the field has now doubled, the shift in paradigm resulted in the decision to plant fewer seedings in Fiscal Year (FY) 2022. Since seedlings were not selected, no first line trials were planted in FY 2022 for either component of the program. All other stages of breeding and selection were carried out as planned. 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 693,925 viable commercial seed. In FY 2022, approximately 27,576 commercial seedlings were planted to the field. In 2020 and 2021, approximately 58,520 and 67,670 seedlings were planted, respectively, but not selected. Five-hundred-eighteen sugarcane genotypes planted in the FY 2021 first-line trials were selected and planted in a second-line trial in FY 2022. Selections planted in the fiscal year 2020 second-line trial were evaluated in the first ratoon. Of the 493 potential varieties in this trial, 60 received a permanent numerical assignment and were advanced for further testing (Milestones 1 and 2). In advanced stages of the program, 33 experimental varieties were advanced to off-station nurseries from the 2015 crossing series, and 15 were advanced to infield testing in fiscal year 2022 from crosses made in 2014. 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). Sixty 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: Despite the challenges presented by Hurricane Ida, breeding selection were carried out with some modification in the Houma, Louisiana-based, basic breeding (germplasm enhancement) program. Roughly one-third of the greenhouse complex housing parental varieties was destroyed during the storm, photoperiod treatments were interrupted, and there was a delayed re-opening of the station. Approximately 230 crosses were made for this program at the crossing facilities in Houma, Louisiana, producing roughly 100,000 seeds. Due to harvest delays, an early decision was made to postpone seedling selection to the second ratoon crop to maintain the ability to select for early sucrose and potentially enhance the selection for yield stability early in the program. With roughly 31,200 already planted seedlings enhanced with traits of interest from wild relatives already awaiting selection from plantings in 2020 and 2021, a small series of approximately 5,600 seedlings were planted to the field in May 2022. Newly planted basic second-line trials contain 222 potential new varieties, and 59 newly selected parents enhanced with wild germplasm traits were named in FY 2022 and planted as parents for the FY 2023 crossing season (Milestone 1). A total of 380 samples were fingerprinted from the sugarcane crossing cart parents, pathology greenhouse, and historical nursery along with primary station and outfield hot-water-treated seed increase plots. In addition, samples were collected from Canal Point, Florida, for variety validation. High-throughput fingerprinting was conducted in collaboration with the USDA-ARS, Genomics and Bioinformatics Research Unit in Stoneville, Mississippi. Approximately, 8,500 fingerprint files were produced and are being analyzed. One-hundred-twenty molecular identities will be assigned to the newly-named 2020-series USDA commercial clones and deposited into the USDA’s sugarcane molecular identity database. Fingerprints of the remaining 260 samples were compared either among themselves or with the fingerprints already present in the database. Fingerprinting from the 2021 analysis indicated the pedigree of HoCP 14-885 was in error, and it was corrected to reflect the proper parents (Milestone 1). Artificial inoculations give a good indication of varietal response to both sorghum and sugarcane mosaic virus in sugarcane. Efforts to screen material early in the crossing program were increased and inoculated tests have been conducted on all parents for the past several years. All varieties (basic and commercial) used in the crossing program were screened for the virus prior to the beginning of the 2021 crossing season. In addition, all 2019 varieties remaining active in the program were re-screened to validate the previous results. Due to Hurricane Ida, the varieties to be used in the 2022 crossing season were not screened because the greenhouse containing the plants for inoculation was lost in the storm (Milestones 1 & 2). 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, USDA continues to work on a modified genotyping by sequencing project with collaborators at Louisiana State University to identify genetic markers associated with mosaic. To capture markers having a strong association with mosaic resistance, sequencing was performed on 200 individuals from the current parental breeding population. Sequences were compared against the sugarcane reference genome to identify single nucleotide polymorphism markers. Putative markers for mosaic resistance were identified using a genome-wide association study (GWAS), including one representing 22% of the resistance variability and having a strong association with the trait (Milestone 3). One-hundred-twenty-seven newly-named 2020 parents (used in the 2021 crossing season) were screened for a molecular marker, BRU1, indicating resistance to brown rust as part of a collaborative project with colleagues at the LSU AgCenter. Of these varieties, 28 tested positive for the BRU1 marker for rust resistance. Ten of these varieties were from the germplasm enhancement program, and the remaining 18 were commercial. An additional 132 varieties from 2020 were screened, and information on their BRU1 status was added to the database for the 2021 crossing season (Milestone 2). Crosses made during the 2021 crossing season were targeted to maximize the frequency of BRU1 in the progeny. Older parents continue to be used in the breeding program, many of which contain the BRU1 marker, and there has been an increase in frequency of the marker after targeting selection for the past several years. While it used to be unusual to find a parent in the breeding program possessing BRU1, it is now much more common (Milestone 2). There has been a long-standing effort by USDA to breed for cold tolerant sugarcane varieties. Twenty-eight sugarcane lines previously selected for having excellent yields after exposure to damaging freezes were planted and evaluated in replicated trials by the USDA in Houma, Louisiana, and by Mississippi State University in Starkville, Mississippi. Cold tolerance has been validated in Mississippi with high yields despite a harsh winter following planting. The three most broadly adapted varieties were selected for breeding to enhance cold tolerance in future populations. The cane remains in the fields for testing of ratoon-harvest yields. This work was conducted as part of a subordinate agreement entitled “Center for Advanced Bioenergy and Bioproducts Innovation” (Interagency Reimbursable Agreement #60-6052-002). Fiber components were analyzed from the second clonal trial of the germplasm enhancement program according to the National Renewable Energy Laboratory’s Structural Carbohydrate Analysis protocol. Fiber quality was assessed using acid hydrolysis followed by quantification of soluble and insoluble lignin as well as structural carbohydrates (cellulobiose, arabinose, xylose, glucose, mannose, galactose, and acetic acid). Fiber work was conducted as part of a subordinate agreement entitled “Center for Advanced Bioenergy and Bioproducts Innovation” (Interagency Reimbursable Agreement #60-6052—002).

Accomplishments
1. Release of commercial sugarcane variety ‘HoL 15-508’. There is no private breeding program for sugarcane in the United States, thus the industry is founded 100% on publicly developed varieties. ARS researchers in 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 2022. The new variety, ‘HoL 15-508’ has large stalks and is extremely early maturing with good ratooning ability and low fiber. This gives growers and processors the desired ability to harvest early, process efficiently, provide a steady supply of cane, and remain profitable despite increasing input prices.

U.S. DEPARTMENT OF AGRICULTURE

Sugarcane Research: Houma, LA