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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Research Project #425242

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research

2017 Annual Report

Objective 1: Develop and release improved sugarcane cultivars and germplasm having a concentration of genes for specific, highly desirable traits, including resistance to yield-limiting insects and diseases. Objective 2: Broaden the genetic base of sugarcane and related genera to improve output-to-input ratios, yield stability, and specific adaption to temperate environments. Sub-objective 2.A. Characterize and broaden the genetic base of Saccharum to support sugarcane cultivar development. Sub-objective 2.B. Develop a predictive assay for cold tolerance in Saccharum. Objective 3: Develop and deploy clone- and trait-specific genetic markers for marker-assisted selection of priority traits to accelerate breeding efforts. Sub-objective 3.A. Develop genus-, species-, or clone-specific DNA markers. Sub-objective 3.B. Develop trait-specific DNA markers through genetic mapping and association studies.

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
Commercial Program: The yearly cycle of crossing, field evaluations, and selections were made as part of the Sugarcane Research Unit’s (SRU) Commercial Variety Development program. Crosses were made at USDA-ARS facilities in both Canal Point, Florida, and Houma, Louisiana, with the production of approximately 435,000 viable commercial seed. In fiscal year (FY) 2017, approximately 70,000 commercial seedlings were planted to the field. Of the 80,000 seedlings planted in FY 2015, a total of 7,576 were selected and advanced to the first-line trials. Selections planted in the FY 2015 second-line trial were evaluated in the first ratoon. Of the 739 potential varieties in this trial, 78 received an assignment and were advanced for further testing (Milestones 1 & 2). In advanced stages of the program in FY 2017, 56 experimental varieties were advanced to off-station nurseries from the 2010 crossing series, and 18 were advanced to infield testing from crosses made in 2009. Basic Program: The crossing team at the SRU continues to focus on optimizing flowering efficiency under artificial photoperiod treatments. In total, 2,713 flowers were produced at the Houma crossing facilities, which was an increase of 557 flowers over the FY 2016 season. A total of 773 biparental crosses were made at the facility in FY 2017, which is a slight increase (3.2%) over FY 2016. The new crossing and photoperiod facility at the USDA-ARS Ardoyne Research Farm has been in operation for seven years, and through optimization of treatments, the percent flowering stalks has risen from 37% in FY 2011 to 84% in FY 2017. All stages of breeding and selection were carried out in the SRU’s basic breeding program. Approximately 19,000 basic seedlings were planted to the field in April 2017. Newly-planted basic first-line trials contain 1,360 selections, and basic second-line trials contain 304 potential new varieties. Sixty-eight newly-selected basic parents were planted as parental material for the 2017 crossing season. 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, thousands of varieties are dropped yearly. A study was completed in FY 2017 on the distribution and frequency of a genetic marker linked to brown rust resistance, Bru1, in the Sugarcane World Collection housed at the USDA-ARS Sub-Tropical Research Center in Miami, Florida. Results from this study were published in Plant Breeding. In FY 2014, leaf tissue from all of the clones in the Sugarcane World Collection, housed at the USDA facility in Miami Florida, was collected and deoxyribonucleic acid (DNA) was extracted. In FY 2016, this material was screened for the presence of the Bru1 marker, which is linked to brown rust resistance. A manuscript was published on the distribution of this marker in the world collection in FY 2017. In addition, all material to be used during the FY 2018 crossing campaign in Houma was screened for the presence of this DNA marker. Information from the ongoing screening of new parental material was incorporated into the crossing database and crosses targeted at resistance to the disease were made. For the past several years, the Bru1-status of parental clones has been 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 is increasing in the breeding populations being developed for introgression. Further studies explored the underlying mechanisms of resistance to the disease, and results were published and presented. In FY 2015, the USDA-ARS-SRU purchased a Cane Presentation System (CPS) that uses Near Infrared Spectrometry (NIR) to efficiently assess cane quality. In FY 2017, 922 samples were run through the system, including both plant-cane and first-ratoon basic second line selections, and off-station tests for energy production. In addition, the system was used to analyze samples from commercial sugarcane mills on a weekly basis to continue a FY 2016 project on the evaluation of the system’s capabilities of quantifying mud and trash in commercial mill samples. Ongoing wet chemistry analysis is underway to enhance the existing calibration curves of the system (Milestone 3). In FY 2017, DNA fingerprints were constructed with 21 simple sequence repeat (SSR) primer pairs for duplicate samples of 26 candidate sugarcane varieties that received names in 2015, and 103 that were named in 2016 from the SRU’s breeding program in Houma, Louisiana. Plant genomic DNA was extracted from leaf samples, amplified using polymerase chain reaction (PCR), and visualized using capillary electrophoresis (CE)-based fragment analysis at the USDA-ARS-SEA Genomics and Bioinformatics Research Unit in Stoneville, Mississippi. Fingerprint data were manually scored and analyzed at the SRU to provide molecular identities for the 2015- and 2016-series varieties. The newly identified fingerprints were added to the Louisiana sugarcane molecular identity database. These molecular identities are used, when needed, for variety identification prior to the distribution of sugarcane seed for further evaluation and release (Milestone 4). The first-ratoon crop of population derived from self-pollinating sugarcane variety LCP 85-384 was grown in a field at the USDA-ARS Ardoyne Research Farm for seed increase and evaluation. Ninety-four clones, along with the LCP 85-384 parent were sampled and analyzed for cane quality traits (stalk weight, Brix, Pol, sucrose content and fiber content) at the SRU juice lab. Results from this analysis led to the selection of twenty clones with high- and twenty clones with low- sugar content. The sub-population of selections was planted and is being maintained in pots at the SRU in Houma, Louisiana, for a marker validation study (Milestone 5).

1. Release of six new varieties of energycane for the production of bioenergy from cellulose. USDA-ARS scientists in Houma, Louisiana, developed and released six new high-fiber sugarcane varieties in 2017. The new varieties, Ho 00-06, Ho 01-25, Ho 01-08, Ho 04-9076, Ho 07-9017, and Ho 07-9027 have yields of gross cane, soluble solids, fiber, and total dry biomass per acre that are equal to, or superior than the existing released commercial biomass varieties. The varieties have vigorous growth, high stalk population, and high fiber content. Sugarcane has one of the highest energy input-to-output ratios of any crop, and is expected to be a major player in the emerging biofuels industry. The release of these six genetically diverse varieties offers growers options that should enhance the genetic stability and longevity of the crop. Furthermore, the varieties have been yield tested outside of traditional cane growing areas of the U.S.

Review Publications
Khan, M., Pan, Y.-B., Iqbal, J. 2017. Development of an RAPD-based SCAR marker for smut disease resistance in commercial sugarcane cultivars of Pakistan. Crop Protection. 94:166-172.
Fu, Y.-H, Pan, Y.-B., Lei, C.-Y., Xie, H.-J., Lei, S.-F., Lu, J.-J. 2017. SSR-CE/FD assessment of Guizhou approved sugarcane cultivars and regional materials. Chinese Agricultural Science Bulletin. 33(8):5-12.
Anderson, W.F., Sarath, G., Edme, S.J., Casler, M.D., Mitchell, R., Tobias, C.M., Hale, A.L., Sattler, S.E., Knoll, J.E. 2016. Dedicated herbaceous biomass feedstock genetics and development. BioEnergy Research. 9:399-411.
Fu, Y., Pan, Y., Lei, C., Grisham, M.P., Yang, C.L., Meng, Q.Y. 2016. Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China. American Journal of Plant Sciences. 7:2209-2220. doi:10.4236/ajps.2016.715195.
Hale, A.L., Viator, R.P., Kimbeng, C., Veremis, J.C. 2017. Use of artificially-induced freezing temperatures to identify freeze tolerance in above-ground buds of Saccharum and Erianthus accessions. Euphytica. 213:46. doi:10.1007/s10681-016-1826-8.
Zhang, W., Zuo, S., Li, Z., Meng, Z., Han, J., Song, J., Pan, Y.-B., Wang, K. 2017. Isolation and characterization of centromeric repetitive DNA sequences in Saccharum spontaneum. Scientific Reports. 7:41659. doi:10.1038/srep41659(2017).
Todd, J.R., Sandhu, H., Hale, A.L., Glaz, B., Wang, J. 2017. Phenotypic evaluation of a diversity panel selected from the world collection of sugarcane (Saccharum spp.) and related grasses. Maydica. 62(2):M19.