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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC IMPROVEMENT OF SUGARCANE BY CONVENTIONAL AND MOLECULAR APPROACHES
2012 Annual Report


1a.Objectives (from AD-416):
The long-term goals of this project are to develop sugarcane cultivars that are better adapted and more economical to grow and harvest, to meet current and evolving needs of both a sugar and a biofuels industry, and to gain a greater understanding of sugarcane from genetic and physiological perspectives. The objectives are to utilize: (1) a basic breeding program to broaden the genetic base of parental germplasm and increase the adaptability of sugarcane to more temperate climates through the introgression of genes from wild species (Saccharum spontaneum) and related genera of sugarcane, and (2) parental clones from the basic program to develop sugarcane cultivars that are: higher yielding (gross cane and sugar), require fewer inputs, more tolerant to disease and insect pests, and adapted to a broader range of environments than current cultivars (commercial breeding program). To assist in the selection process, trait-specific molecular markers for early sucrose accumulation, sugarcane borer resistance, and cold tolerance will be developed.


1b.Approach (from AD-416):
Included in the basic program’s breeding strategy to increase the genetic diversity of parental clones are: (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. In the development of cultivars for sugar and bioenergy, emphasis will be placed on yield components (stalk number, height, and diameter), quality components (sucrose and fiber accumulation), longevity (stubbling ability), harvestability (root anchorage, stalk erectness, and stalk brittleness), hardiness (winter survival, early spring vigor, and stalk freeze tolerance), 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 disease). Recurrent selection techniques will be utilized to accelerate the rate of genetic improvement for important traits. In addition, trait-specific markers closely associated with desirable 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.


3.Progress Report:
In the fall of 2011, 6,007 candidate commercial clones and 446 clones from the recurrent selection for the sugarcane borer program (RSB) were advanced to first clonal stage, 615 candidate commercial clones and 63 candidate RSB clones were advanced to the second clonal stage, and 80 commercial sugar and 4 RSB clones were given permanent alphanumeric designations and advanced into multi-location nurseries for yield testing in 2011-2012 crop season. Currently, there are 25 clones developed at the Sugarcane Research Unit from the 2007 to 2010 assignment series that are being evaluated as commercial sugarcane varieties in advanced yield trials.

In 2012, 24,000 basic seedlings from the 2011 crossing season were planted to the field, 23,000 from the 2009 crossing season were advanced to the first clonal stage, 340 from the 2008 crossing season were advanced to the second clonal stage, and five from the 2007 crossing season were given permanent alphanumeric designations. Sixty-eight basic clones were selected for inclusion in the 2010 parental population on the breeding carts. Characterization of wild clones for traits of interest, in particular, cold tolerance and disease resistance, is continuing.

Sixty-four additional genetic markers were used to fingerprint the mapping population of 278 self progeny clones of LCP 85-384. ARS researchers at the Sugarcane Research Unit produced 17,856 fingerprinting files for the enrichment of the preliminary genetic linkage map of LCP 85-384. The enriched linkage map totaled 1,504 universal markers from 64 amplified fragment length polymorphism (AFLP), 12 targeted region amplification polymorphism (TRAP), and 83 SSR primer pairs. Of these polymorphic markers, 993 were placed onto 108 co-segregation groups (CGs). Sixty-three of the 108 CGs were successfully assigned into 11 homologous groups (HGs) based on the single sequence repeat (SSR) marker information. The number of CGs for each HGs ranged from as few as two to as many as 27. This enriched LCP 85-384 genetic linkage map is being used for mapping quantitative trait linkage (QTL) markers associated with sugar and fiber content in sugarcane.


4.Accomplishments
1. Release of new sugarcane variety. Varieties are the life-blood of the sugarcane industry in Louisiana and a continuous pipeline of new varieties are needed for the sustainability of that industry. Researchers at the Sugarcane Research Unit at Houma, LA, selected, evaluated, and released to the Louisiana sugarcane industry the variety Ho 05-961 for commercial sugarcane production. The new variety produces sustained yields through the third harvest, particularly in sugar per acre. It is resistant to the diseases rust, smut, and leaf scald. However, its reaction to mosaic is unclear and a vigorous clean seed program must be implemented as it is susceptible to ratoon stunting disease. The variety Ho 05-961 is resistant to both the sugarcane borer and Mexican rice borer and therefore an appropriate variety for planting in areas not suited to insecticide application. The positive performance of Ho 05-961 for many important traits suggests that it will be a variety that will contribute to the economic sustainability of the sugarcane industry.

2. Release of high-fiber sugarcane variety. High-fiber sugarcane varieties will be important for use as a biofuel feedstock to fill industry demands, as the technology develops to create bio-refineries capable of the economic conversion of fiber to fuel. Researchers at the Sugarcane Research Unit at Houma, LA, selected, evaluated, and released the high-fiber sugarcane vaviety Ho 02-113. Commercial entities in the U.S. are currently growing approximately 950 acres of Ho 02-113 and the production is expected to expand to a many as 10,000 by 2013. The variety is also currently being grown on 125 acres in Central America as well.

3. Sugarcane variety molecular identity database. Sugarcane varieties can easily be misidentified by both farmers and researchers. Although an intimate knowledge of the physical traits of an individual variety can frequently resolve questions of identify that arise, there are occasions when those traits are highly variable or subjective and therefore insufficient to assure correct identification. In these cases, clone specific markers are required for the ultimate resolution of identity. Researchers at the Sugarcane Research Unit at Houma, LA, updated their molecular identity database with new molecular identities of 200 clones of the 2009-series varieties and 20 active breeding lines or cultivars. Nearly 4,400 single sequence repeat (SSR) fingerprinting files were generated and processed with genotyping software for molecular identity construction. A special fingerprinting project was conducted on the cultivar L 01-283 showing undesirable off-types during the growing season. In 2008, 2010, and 2011, seventy-seven leaf samples were collected from both normal and off-type plants from multiple locations were fingerprinted with 21 SSR primer pairs. All samples produced the same fingerprints, indicating that the off-type of L 01-283 is not caused by genome (chromosome) instability.


Review Publications
Hameed, U., Pan, Y-B., Muhammad, K., Afghan, S., Iqbal, J. 2012. Use of simple sequence repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot. Genetics and Molecular Research. 11(2):1195-1204.

Gao, S., Lin, Y.-H., Pan, Y.-B., Damaj, M.B., Wang, Q., Mirkov, T., Chen, R. 2012. Molecular characterization and phylogenetic analysis of sugarcane yellow leaf virus isolates from China. Virus Genes. 45:340-349. DOI 10:1007/s11262-012-0774-1.

Last Modified: 10/24/2014
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