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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

2018 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
This report marks the end of this project which has been replaced by project 6052-21000-015-00D, "Genetic Improvement of Sugarcane for Adaptation to Temperate Climates". During the course of this project, new sugarcane and energycane varieties were released and adopted by stakeholders. Selection and identification of potentially new varieties was conducted as part of the breeding and selection process. The effort to increase the frequency of deoxyribonucleic acid (DNA) markers associated with rust resistance were incorporated into the breeding program, and a new Near Infared Spectrometry (NIR) system for assessing cane quality was explored. The molecular identity database was expanded to include fingerprints of newly named material. DNA markers potentially linked to high sugar were identified, and collaborations with other breeding programs around the world were strengthened. Overall, all proposed milestones have been substantially met for the life of the project. 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 241,207 viable commercial seed. In fiscal year 2018, approximately 65,000 commercial seedlings were planted to the field. Of the approximately 70,000 seedlings planted in fiscal year 2016, a total of 6,334 were selected and advanced to the first-line trials. Selections planted in the fiscal year 2016 second-line trial were evaluated in the first ratoon. Of the 739 potential varieties in this trial, 65 received a permanent numerical assignment and were advanced for further testing (Milestones 1 and 2). In advanced stages of the program, in fiscal year 2018, 45 experimental varieties were advanced to off-station nurseries from the 2011 crossing series, and 29 were advanced to infield testing from crosses made in 2010. Basic Program: The crossing team at the SRU continues to focus on optimizing flowering efficiency under artificial photoperiod treatments. A three-year study was completed to determine the effects of soil type, fertilizer rate, and their interaction on flower induction. The results of this study were published in PLOS ONE, with evidence that we should change the historically-based nitrogen treatments applied during the crossing season. The study, with limited germplasm, indicates that the generally accepted practice of starving parental clones of nitrogen prior to the commencement of the photoperiod treatment yields less flowers at a later date in the season. Changing the fertilizer regime to a more steady application throughout the season may prove to be beneficial. All stages of breeding and selection were carried out in the SRU’s basic breeding program. Approximately 16,739 basic seedlings were planted to the field in April 2018. Newly-planted basic first-line trials contain 2070 selections, and basic second-line trials contain 321 potential new varieties. Sixty-nine newly-selected basic parents were planted as parental material for the 2018 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 genetic marker has been identified, Bru1, that is linked to brown rust resistance. All material to be used during the fiscal year 2019 crossing campaign in Houma, Louisiana, was screened for the presence of this 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 from six to 25 percent of parental clones developed for introgression. Cold tolerant selections from field-studies in northerly locations were incorporated into the basic breeding program to incorporate the cold tolerance trait into commercial varieties. Some of this material was also screened using artificial conditions in an attempt to develop an assay for selecting cold tolerant clones in the future. Preliminary results of the assay indicate that clones selected under freezing conditions in the field perform better in the assay than standard commercial varieties and that the use of growth chambers could be a viable alternative for selection. In fiscal year 2018, DNA fingerprints were constructed with 21 simple sequence repeat (SSR) primer pairs for 65 commercial sugarcane clones that were named in 2017 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-Southeast Area Genomics and Bioinformatics Research Unit in Stoneville, Mississippi. Fingerprint data were manually scored and analyzed at the SRU to provide molecular identities for the 2017-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.

1. Release of commercial sugarcane variety HoCP 11-537. ARS researchers at Houma, Louisiana, in collaboration with the American Sugarcane League of the U.S.A., Inc., and the Louisiana State University Agricultural Center developed and publically released a new sugarcane variety in 2018. The release of this variety is a result of a collaborative agreement between the USDA-ARS in Houma, Louisiana, and in Canal Point, Florida, and Rio Farms, Inc. (a non-profit research organization located in the lower Rio Grande Valley of Texas). HoCP 11-537 was released because it is adapted to the growing conditions of Texas, where there are few recently-released varieties available to the commercial industry. The high-yielding variety offers another option to the industry.

Review Publications
Ahmad, A., Wang, J., Pan, Y., Deng, Z., Chen, Z., Chen, R., Gao, S. 2017. Molecular identification and genetic diversity analysis of Chinese sugarcane (Saccharum spp. hybrids) varieties using SSR markers. Tropical Plant Biology. Available:
Todd, J.R., Pan, Y.-B, Kimbeng, C., Dufrene Jr, E.O., Waguespack, H., Pontif, M. 2017. Analysis of genotype by environment interaction in Louisiana sugarcane research plots by GGE biplots. Sugar Tech. 20(4):407-419. https://doi:10.1007/s12355-017-056-z.
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.
Niu, J., Huang, J., Phan, T., Pan, Y., Yang, L., Li, Y. 2018. Molecular cloning and expressional analysis of five sucrose transporter (SUT) genes in sugarcane. Sugar Tech.
Todd, J.R., Sandhu, H., Binder, J., Arundale, R., Gordon, V.S., Song, J., Glaz, B., Wang, J. 2017. Fiber composition of a diversity panel of the world collection of sugarcane (Saccharum sp.) and related grasses. Bragantia. 77(1):48-61.
Burner, D.M., Hale, A.L., Viator, R.P., Belesky, D.P., Houx III, J.H., Ashworth, A.J., Fritschi, F.B. 2017. Ratoon Cold Tolerance of Pennisetum, Erianthus and Saccharum Bioenergy Feedstocks. Industrial Crops and Products. 109C(2017)327-334.
Hale, A.L., White Jr, P.M., Webber III, C.L., Todd, J.R. 2017. Effect of growing media and fertilization on sugarcane flowering under artificial photoperiod. PLoS One. 12(8):1-10.