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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

2015 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
The fiscal year 2015 crossing season conducted at Canal Point, Florida, in collaboration with ARS scientists and technicians of the Sugarcane Research Unit (SRU), Houma, Louisiana, was another successful crossing season. Estimated viable seed from crosses made at Canal Point was approximately 1.5 million. Of that 1.5 million seed, approximately 1 million were made for the commercial breeding program at the SRU. The subsequent stages of the commercial breeding program were as equally successful. The number of seedlings sent to the field in fiscal year 2015 was the largest number since fiscal year 2005. Approximately 81,400 seedlings were planted into the field and are scheduled to be selected during fiscal year 2016. Of the 61,500 seedlings in fiscal year 2013, a total of 5,868 were selected for planting a first-line trial in fiscal year 2015. In fiscal year 2015, seven hundred twenty-two selections planted into the second-line trial in fiscal year 2013 were evaluated. Of these canes, 100 received a permanent numerical assignment. All of these numbers represent an increase from previous years, and are indications of a healthy commercial program. The 2014 crossing season at the Sugarcane Research Unit (SRU) in Houma, Louisiana, was successful. Since 2010, the SRU breeding team has been focused on optimizing the new crossing and photoperiod facility. Modifications were made to the new facility to increase the number of crossing isolation chambers and expanding the crossing capabilities. A total of 1,988 sugarcane tassels were produced under photoperiod treatment, and these were used to make 763 bi-parental crosses resulting in 322,436 viable seed. The number of seed produced increased by 20% over 2013, 27% over 2012, and 67% over the 2010 estimates. Of the seed produced, 69% were basic seed and 30% were commercial. The germination rate was increased from 50 seed per gram to 66 seed per gram over the 2013 crossing season. All stages of breeding and selection were carried out in the Sugarcane Research Unit’s basic breeding program in Houma, Louisiana. A total of 25,040 basic seedlings were planted to the field in April 2015. Newly planted basic first-line trials contain 1,888 potential varieties and 322 potential varieties were planted in the basic second-line trials. Seventy-nine newly selected basic parents were selected and planted as parental material for the 2015 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. 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) extracted. Screening of the collection for the Bru1 marker, which is linked to brown rust resistance, is underway. In addition, all newly selected parental material that will be included in the 2015 crossing campaign at the Sugarcane Research Unit in Houma, Louisiana, was screened for the presence or absence of the Bru1 marker for brown rust resistance. This information was incorporated into the crossing program to increase the frequency of this marker and to enhance the likelihood of developing brown rust resistant varieties. The use of the Bru1 marker in making targeted crosses for rust resistance was used for a second year in the crossing program, and will continue to be used in the future. The Sugarcane Research Unit purchased a Cane Presentation System (CPS) using funding from an established Cooperative Research and Development Agreement (CRADA). This is a self-contained sampling system, with a cane shredder connected to a conveyer. The cane is moved by conveyer, then “fluffed” using metal fingers, and subsequently passed through a window with a near-infrared (NIR) detector. The machine is calibrated based on light spectra, and can instantaneously determine sucrose, pol, fiber, moisture and other parameters. In the fall of 2014, a total of 396 clones from the basic second-line plant-cane trial were sampled and evaluated using the CPS. In addition, 43 samples from a replicated off-station energycane test were analyzed using the new system. Fiber samples were collected after juice processing and are currently being processed and evaluated in the laboratory to determine the levels of cellulose, hemicellulose, lignin, and ash. Results from this analysis will be used to calibrate the CPS for these compounds. In fiscal year 2015, the genomic fingerprints were identified for 91 candidate sugarcane varieties from the Sugarcane Research Unit’s (SRU) breeding program in Houma, Louisiana, that were advanced in 2014. Genomic deoxyribonucleic acid (DNA) was extracted from tissue samples of the varieties and quantified at the SRU. High-throughput polymerase chain reaction (PCR) and capillary electrophoresis (CE)-based fragment analysis were provided by the Agricultural Research Service, Southeast Area, Genomics and Bioinformatics Research Unit in Stoneville, Mississippi. The molecular identities for the 2014-series varieties were constructed and added to the Louisiana sugarcane molecular identity database. The variety fingerprints provide a valuable tool for identifying unknown sugarcane clones and verifying the identity of sugarcane varieties as they are increased and distributed in the variety development program.

1. Independent segregation of deoxyribonucleic acid (DNA) fingerprints among sugarcane pollen was demonstrated. Inheritance of sugarcane traits is difficult to understand because of the complexity of the plant’s genetic makeup that has multiple sets of chromosomes. Scientists and collaborators at the Sugarcane Research Unit, Houma, Louisiana, demonstrated independent segregation patterns of sugarcane DNA fingerprints among pollen of a sugarcane cultivar L 99-233 as well as progenies from a cross between HoCP 00-950 (female) and L 99-233 (male). Of the six parental DNA fingerprints, four were observed in approximately half of the pollen and in approximately half of the cross progenies, an indication of the independent segregation genetic principle discovered by a monk Gregor Mendel in 1800s. Unexpected segregation patterns were observed for two other DNA fingerprints, which might be associated with the genetic complexity of sugarcane and illustrated the needs of additional genetic studies in sugarcane. The results of this study will help sugarcane breeders and molecular biologists understand the inheritance of DNA fingerprints that are associated with desirable traits.

2. Unique deoxyribonucleic acid (DNA) fingerprints found among sugarcane varieties from different geographical origins. Genetic diversity among parents in a sugarcane breeding program is important in the development of more widely adapted and economically productive sugarcane varieties. The chemical composition of a sugarcane variety’s DNA is unique. This unique composition is often referred to as the variety’s “fingerprint.” Varieties that are closely related have similar chemical compositions or “fingerprints.” Among the fingerprints of 12 sugarcane varieties from India and 12 from the United States, some were unique to each group of varieties. Other fingerprints were common to the varieties from both countries. Using parents with diverse DNA fingerprints will assist sugarcane breeders in developing new varieties with a greater genetic diversity.

Review Publications
Pan, Y.-B., Liu, P., Que, Y. 2014. Independently segregating simple sequence repeats (SSR) alleles in polyploid sugarcane. Sugar Tech. 17(3):235-242. DOI: 10.1007/s12355-014-0330-5.
Chandra, A., Grisham, M.P., Pan, Y.-B. 2014. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane. Genome. 57:363–372. doi:10.1139/gen-2014-0072.
Wang, A., Ye, X., Huang, J., Niu, J., Liu, M., Pan, Y-B., Yang, L., Li, Y. 2015. Molecular cloning and functional analysis of an ethylene receptor gene from sugarcane (Saccharum spp.) by hormone and environmental stresses. Sugar Tech (Jan-Mar 2015) 17(1):22-30. DOI: 10.1007/s12355-014-0324-3.
Hameed, U., Pan, Y.-B., Iqbal, J. 2015. Genetic analysis of resistance gene analogues from a sugarcane cultivar resistant to red rot disease. Journal of Phytopathology. 163:755-763. DOI: 10.1111/jph.12372DOI:10.1111/jph.12372.
You, Q., Pan, Y.-B., Xu, L.-P., Gao, S.-W., Wang, Q.-N., Su, Y.-C., Yang, Y.-Q., Wu, Q.-B., Zhou, D.-G., Que, Y.-X. 2016. Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform. Sugar Tech. 18:380-390. DOI: 10.1007/s12355-015-0395-9.
Liu, P., Chandra, A., Que, Y., Chen, P.-H., Grisham, M.P., White, W.H., Dalley, C.D., Tew, T.L., Pan, Y.-B. 2016. Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane (Saccharum spp. hybrids) cultivar ‘LCP 85-384’. Euphytica. 207:527-549. doi:10.1007/s10681-015-1538-5.