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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

2016 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
Another cycle of crossing, field evaluations, and selections were made. In collaboration with scientists and technicians at the Sugarcane Research Unit (SRU), Houma, Louisiana, the 2016 crossing season conducted at Canal Point, Florida, was another successful season. Estimated viable seed from crosses made at Canal Point was approximately 959,000. Of that seed, approximately 605,000 were made for the commercial breeding program at the SRU. The subsequent stages of the commercial breeding program were as equally successful. Approximately 70,000 seedlings were planted into the field and are scheduled to be selected during fiscal year (FY) 2016. Of the 72,333 seedlings in FY 2014, a total of 8,004 were selected for planting a first-line trial in FY 2016. In FY 2016, selections planted into the second-line trial in FY 2014 were evaluated. Of these canes, 116 received a permanent numerical assignment. (Milestones 1 and 2) The 2015 crossing season at the SRU in Houma, Louisiana, yielded a record number of seed for its new crossing and photoperiod facility. The new crossing and photoperiod facility has now been in operation for six years, and the SRU breeding team has been focused on optimizing flowering efficiency. Modifications made to the facility in FY 2015 to increase the number of isolation chambers were highly utilized during the 2015 season since the crossing season was short, with a flush of flowers in a short period. A total of 2,156 sugarcane tassels were produced under a photoperiod treatment, and these were used to make 723 bi-parental crosses (500 basic and 223 commercial). Approximately 473,761 viable seed were produced on site, for a 32% increase in 2014 and 45% increase in 2013 crossing season. The increase in production is attributed, in part, to an increase in germination rate per gram of seed. This germination rate has steadily increased over the past several years, from 50, to 66, to 73 seed per gram in the 2013, 2014, and 2015 crossing seasons, respectively. All stages of breeding and selection were carried out in the SRU’s basic breeding program. Approximately 21,000 basic seedlings were planted to the field in April 2016. Newly planted basic first-line trials contain 1,878 selections, and basic second-line trials contain 275 potential new varieties. Sixty-eight newly selected basic parents were planted as parental material for the 2016 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. 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. In addition, all newly selected parental material that will be included in the 2016 crossing campaign at the SRU was screened for the presence or absence of the Bru1 marker for brown rust resistance. 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. In FY 2015, the SRU purchased a Cane Presentation System (CPS) using funding from an established Cooperative Research and Development Agreement (CRADA). This self-contained sampling system shreds and analyzes sugarcane using Near Infrared Spectrometry (NIR). In 2015, a total of 1,238 samples were run through the CPS system. These samples included plant-cane and first-ratoon basic second line selections, samples from nine off-station tests for energycane production and ratooning ability, and one off-station commercial breeding test. In addition, the system was used to analyze samples from three different commercial sugarcane mills on a weekly basis and to begin to evaluate the system’s capabilities of quantifying mud and trash in commercial mill samples. Fiber samples were collected from many of the tests and are currently being evaluated in the laboratory in an attempt to calibrate the NIR for cellulose, hemicellulose, lignin, and ash. The results of this research generated a lot of interest from industry stakeholders in the NIR system and will continue to be explored as a possible method of calculating commercial cane payment. Most importantly, it has the potential to hasten the evaluation of quality components of upcoming cane varieties. In FY 2016, the deoxyribonucleic acid (DNA) fingerprints were identified for the 111 candidate sugarcane varieties that were named in 2015 from the SRU's breeding program. Genomic DNA was extracted from tissue samples of these varieties and quantified at the SRU. The Agricultural Research Service, Southeast Area, Genomics and Bioinformatics Research Unit in Stoneville, Mississippi provided high throughput polymerase chain reaction (PCR) and capillary electrophoresis (CE)-based fragment analysis. The molecular identities for the 2015-series varieties were constructed and added to the Louisiana Sugarcane Molecular Identity Database. Varietal molecular identities are valuable when identifying unknown sugarcane clones and when verifying the identity of candidate varieties prior to seed increase and distribution and large-scale evaluation in the variety development program. (Milestone 4) Progeny clones (175) of a genetic mapping population were transplanted to the field at the SRU's research farm for seed increase and evaluation. The seed will be used to plant randomized and replicated field plots in the fall of 2016 for subsequent phenotyping. (Milestone 5)

1. Release of a new variety of sugarcane. Sugarcane is the most profitable and economically important row crop grown in Louisiana. Sustainability of the sugarcane industry is dependent on varieties that are well adapted to Louisiana. ARS scientists in Houma, Louisiana, working cooperatively with scientists from Louisiana State University AgCenter and the American Sugar Cane League of the U.S.A., Inc., developed and released a new sugarcane variety for Louisiana in FY 2016. The new variety (HoCP 09-804) offers farmers another varietal choice with very good yields, early maturity, and very good ratooning ability.


Review Publications
Lu, X., Zhou, H., Pan, Y.-B., Chen, C.Y., Zhu, J., Chen, P., Cai, Q., Chen, R. 2015. Segregation analysis of microsatellite (SSR) markers in sugarcane polyploids. Genetics and Molecular Research. 14(4):18384-18395. DOI: 10.4238/2015.December.23.26.
Luo, J., Pan, Y.-B., Youxiong, Q., Zhang, H., Grisham, M.P., Liping, X. 2015. Biplot evaluation of test environments and identification of mega-environments for sugarcane cultivars in China. Scientific Reports. 5:15505. doi:10.1038/srep15505.
Luo, J., Pan, Y.-B., Xu, L., Grisham, M.P., Zhang, H., Que, Y. 2015. Rational regional distribution of sugarcane cultivars in China. Scientific Reports. 5:15701. DOI: 10.1038/srep15721.
Hale, A.L., Viator, R.P., Eggleston, G., Hodnett, G., Stelly, D., Boykin, D.L., Miller, D. 2016. Estimating broad sense heritability and investigating the mechanism of genetic transmission of cold tolerance using mannitol as a measure of post-freeze juice degradation in sugarcane and energycane (Saccharum spp.). Journal of Agricultural and Food Chemistry. 64(8):1657-1663. doi:10.1021/acs.jafc.5b03803.
Arro, J., Park, J.-W., Wai, C. M., Van Buren, R., Pan, Y.-B., Nagai, C., Da Silva, J., Ming, R. 2016. Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.). Euphytica. 209:477-493. DOI: 10.1007/s10681-016-1672-8
Song, J., Yang, X., Resende, M., Neves, L.G., Todd, J.R., Zhang, J., Comstock, J.C., Wang, J. 2016. Natural allelic variations in highly polyploidy Saccharum complex. Frontiers in Plant Science. 7:804. DOI: 10.3389/fpls.2016.00804.
Zhao, C.-H., Lin, Y.-H., Pan, Y.-B., Fu, H.-Y., Chen, R.-K., Grisham, M.P., Li, Y., Gao, S.-J. 2016. Population structure and selection pressure analysis among Sugarcane yellow leaf virus isolates based on P0 and P1 sequences. Tropical Plant Pathology. 41:237-245. DOI:10.1007/s40858-016-0096-2.