Research Project: Development of High-Yielding, Stress Tolerant Sugarcane Cultivars Using Agronomic, Genetic, and Molecular Approaches

Location: Sugarcane Field Station

2019 Annual Report

Objectives
1. Develop sugarcane breeding populations with high quality seed for use in Florida and Louisiana, and select and advance elite clones to produce and release improved sugarcane cultivars for sustainable production in Florida. 2. Characterize abiotic and biotic stress tolerance of sugarcane breeding populations to determine agronomic, physiological, and genetic relationships, and use the information in breeding programs to improve efficiency of selection methodologies. 2.A. Develop physiological and agronomic methodologies to screen yield components of sugarcane clones for tolerance to flowering characteristics. 2.B. Compare and determine methodologies that improve selection efficiency and maximize genetic gains in the Canal Point sugarcane breeding programs. 2.C. Develop and compare physiological testing and genetic x environmental interactions for sugarcane and its relatives, to determine abiotic tolerance and yield potentials that can be used for both sugarcane and biomass yield advancement. 3. Elucidate the molecular and genetic bases of disease resistance, low temperature stress, high sucrose content, and high biomass yield, develop molecular markers, and use molecular markers to screen germplasm and progenies for stress tolerance, yield, and quality. 3.A. Develop and test genomic prediction models for clonal and parental selection for disease resistance, biomass yield, and sucrose content. 3.B. Identify and screen sugarcane and its relative germplasm for freeze damage and cold tolerance. Utilize genotypic sequencing and phenotypic screening to ascertain putative associative markers linking abiotic tolerance and yield response with specific genetic loci. 3.C. Develop molecular markers for sugarcane disease resistance and high sucrose concentration. 3.D. Development and utilization of 100K single nucleotide polymorphism (SNP) array in Saccharum Spp.

Approach
The primary goal of this project is to improve yields and profits of Florida sugarcane growers by developing more productive and profitable cultivars with improved resistance and tolerance to biotic and abiotic stresses. Most research in genetics, agronomy, crop physiology, and molecular biology focuses on improving the breeding and selection of cultivars to yield more on muck and sand soils and have tolerance or durable resistance to diseases and abiotic stresses. This process will be enhanced through improved knowledge of classic and molecular genetics, identification of important traits for selection, and selection methodologies. A portion of the research aims to improve yields through modified agronomic practices. Specific efforts may focus on developing improved cultivars with disease resistance and high sucrose concentration using different approaches, especially our new sand-soil program and this may include the pursuit of links between traditional efforts to breed for increased sucrose yields and newer programs that use sugarcane and related species for cellulosic ethanol and enhanced evaluations of the genotypes. The scientists at Canal Point are expected to interact with each other and with colleagues at the University of Florida in Gainesville and its Everglades Research and Education Center in Belle Glade, and with other public and private industry scientists in Florida and Louisiana, Texas, and other areas. Over the next 5 years, we will focus on our specific objectives.

Progress Report
The challenges in the Florida sugarcane production are still the introduction of orange rust, brown rust, smut, leaf scald diseases and enhancement of cane sucrose content. Consistently developing disease tolerant and high sugar yield cultivars is important for sustainable sugarcane production. In addition to making efforts for improving the Canal Point (CP) sugarcane breeding and cultivar development programs (CP programs) for Florida, true seeds, developed from crosses at Canal Point, Florida, were sent to the ARS cultivar development program in Houma, Louisiana. It is estimated that in the 2018-2019 crossing season, approximately 658,123 seeds from 917 crosses were sent to Louisiana; 291,228 seeds from 707 crosses remained in Florida for the CP regular (muck-soil) breeding program; 60,609 seeds from 130 crosses made for the Florida CP sand-land breeding program; and 128,292 seeds from 242 crosses made for the Florida both soils or others. There were 95,455 seedlings from 302 crosses transplanted in the Seedling fields in 2019 at Canal Point and approximately 9,120 seedlings (from 71 crosses) transplanted in Clewiston for sand soils in Florida in May to early June 2019. Additionally, a total of 9,524 seedlings (from 175 crosses) were transplanted in the progeny tests at Canal Point. There were 7,637 genotypes planted in Stage I in late January – early February 2019 and 1,486 genotypes of CP-18 series planted in Stage II in late November 2018 at Canal Point, Florida. The CP cultivars developed by ARS occupied more than 94% of the sugarcane acreage in Florida in 2018. In 2019, for the nine consecutive years, all stages of the sand-land selection program were planted on sand soils, beginning with the seedling stage with some specific crosses made for sand soils. In addition, all stages of the selection for the muck-soil CP program were conducted on muck soils. There were two new varieties released, CP 12-1417 (for muck soils) and CP 11-1640 (for sand soils) in 2019. The two new released cultivars are expected to yield well and are resistant/tolerant to most diseases. In research to better understand molecular, physiological, and agronomic bases of biotic and abiotic stress resistance and yield improvement, to improve data accuracy and selection efficiency for high sucrose content and disease resistance, and to help growers meet Best Management Practices, several field and laboratory studies have been initiated by scientists in Canal Point, Florida. Data collection and analyses are in progress.

Accomplishments
1. Development of high-yielding and disease resistant sugarcane cultivars for commercial production. The biggest challenge sugarcane growers in Florida are facing is still orange rust and brown rust diseases. The rusts recently caused considerable yield losses and an increase in input costs of fungicide applications. Therefore, development of new cultivars with disease resistance, high yields, and high profits using different approaches, such as genetics, genomics, agronomy, physiology, and molecular biology, is the priority of the Canal Point (CP) sugarcane breeding and cultivar development programs. ARS researchers in Canal Point, Florida collaborated with other institutes and released two new high-yielding sugarcane cultivars (CP 12-1743 for muck soils and CP 11-1640 for sand soils) with disease resistance/tolerance on 28 May 2019 for growers to use in Florida. The new cultivars will mitigate negative effects of brown and orange rusts and other stresses on sugar yield and profits in Florida.

2. Development of molecular markers for sugarcane orange rust resistance. Sugarcane orange rust appeared in the Western hemisphere 12 years ago and negatively affected the Florida sugarcane industry as well as the Canal Point (CP) cultivar development programs. ARS researchers in Canal Point, Florida, and the University of Florida worked closely using a molecular approach to develop molecular markers for improving screening efficiency and enhancing the rust resistance. The phenotypic disease data obtained from the segregating population have been used for marker development. Quantitative trait loci associated with orange rust resistance has been identified. Diagnostic markers have been developed for orange rust resistance and will be further tested for potential use in the CP sugarcane cultivar development programs.

Review Publications
Davidson, W., Scott, A., Hernandez, E., Gordon, V.S., McCord, P.H., Sandhu, H., Zhao, D., Comstock, J.C., Sood, S.G., Singh, M., Islam, M.S., Baltazar, M., McCorkle, K.M. 2019. Registration of 'CP 08-1968' sugarcane. Journal of Plant Registrations. 13:178-186. https://doi.org/10.3198/jpr2018.05.0034crc.
Davidson, W.R., Gordon, V.S., Sandhu, H.S., McCord, P.H., Zhao, D., Comstock, J.C., Singh, M.P., Sood, S.G., Baltazar, M., McCorkle, K.M. 2018. Registration of ‘CP 09-1952’ Sugarcane. Journal of Plant Registrations. 12:340-346. https://doi.org/10.3198/jpr2018.02.0008crc.
Gordon, V.S., Sandhu, H., McCord, P.H., Zhao, D., Comstock, J.C., Singh, M.P., Davidson, R.W., Sood, S.G., Baltazar, M., McCorkle, K.M. 2018. Registration of ‘CP 09-1430’ Sugarcane. Journal of Plant Registrations. 12:314-323. https://doi.org/10.3198/jpr2017.09.0066crc.
Islam, M.S., Yang, X., Sood, S.G., Comstock, J.C., Zan, F., Wang, J. 2018. Molecular dissection of sugar related traits and it’s attributes in Saccharum spp. hybrid. Euphytica. 214:170. https://doi.org/10.1007/s10681-018-2252-x.
McCord, P.H., Zhao, D., Abbott, T.E., Comstock, J.C., Singh, M.P., Davidson, R.W., Gordon, V.S., Sandhu, H.S., Sood, S.G., Baltazar, M., McCorkle, K.M. 2019. Registration of 'CP 09-2392' Sugarcane. Journal of Plant Registrations. 13:170-177. https://doi.org/10.3198/jpr2017.09.0065crc.
Migneault, A., Sandhu, H., McCord, P.H., Zhao, D., Erickson, J. 2019. Albinism in sugarcane: significance, research gaps, and potential future research developments. Sugar Tech. 21(3):536-541. https://doi.org/10.1007/s12355-018-0668-1.
Yang, X., Sood, S.G., Luo, Z., Todd, J.R., Wang, J. 2019. Genome-wide association studies identify resistance loci to orange rust and yellow leaf virus diseases in a diversity panel of polyploid sugarcane (Saccharum spp.). Phytopathology. 109(4):623-631. https://doi.org/10.1094/Phyto-08-18-0282-R.
Yang, X., Todd, J.R., Arunadale, R., Binder, J., Luo, Z., Islam, M.S., Sood, S.G., Wang, J. 2019. Identifying loci controlling fiber composition in polyploid sugarcane (Saccharum spp.) through genome wide association study. Industrial Crops and Products. 130:598-605.
Zhao, D., Comstock, J.C., Davidson, W.R., Gordon, V.S., McCord, P.H., Sandhu, H.S., Sood, S.G., Singh, M.P., Abbott, T., Islam, M.S., Baltazar, M., McCorkle, K.M. 2019. Registration of ‘CP 10-1208’ Sugarcane. Journal of Plant Registrations. 13(1):42-49. https://doi.org/10.3198/jpr2018.07.0050crc.