Research Project: Genetic Improvement of Sugarcane for Adaptation to Temperate Climates

Location: Sugarcane Research

2023 Annual Report

Objectives
1. Breed new sugarcane cultivars and improved germplasm with superior agronomic traits, adaptation to variable weather conditions, and increased abiotic and biotic stress tolerance including cold-tolerance. 1.A. Develop improved sugarcane cultivars utilizing parental germplasm derived from the SRU’s germplasm enhancement program (sub-objective 1.B.) that possess highly desirable traits. 1.B. Characterize and broaden the genetic base of Saccharum to support both sugarcane breeding for commercial cultivars, with specific emphasis on adaptation to temperate environments, disease resistance, and sugar content. 2. Develop and deploy clone-and trait-specific genetic markers for sugarcane, and work with breeders to accelerate breeding and release improved sugarcane cultivars and germplasm.

Approach
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 is the final report for the project 6052-21000-016-000D which terminated in July 2023.The Louisiana sugarcane industry would not remain profitable without cultivars developed by public breeding programs in the state. The release of ready-for-market commercial cultivars has been the goal of the Louisiana breeding program since its inception. Researchers at the Sugarcane Research Unit at Houma, Louisiana, selected, evaluated, and released to the Louisiana sugarcane industry the cultivars Ho 11-573, HoCP 11-537, Ho 12-615, Ho 13-739, Ho 13-710, HoCP 14-885, and HoL 15-508 for commercial sugar production. With excellent ratooning ability and high stalk populations, Ho 12-615 was released in 2019. The varieties Ho 13-739, released in 2020, and HoL 15-508 (2022) have large stalks and are extremely early maturing with good ratooning ability and low fiber giving growers and processors the desired ability to harvest early, process efficiently, provide a steady supply of cane, and remain profitable despite increasing input prices. HoCP 14-885 was released in 2021 and created a level of enthusiasm amongst growers not seen in at least a decade. This variety is early maturing, and extremely sweet, and the ability to yield in late ratoons surpasses total yield across the crop cycle better than any variety historically released in Louisiana. The cultivars Ho 11-573, HoCP 11-537, and Ho 13-710 were released for the growers of the lower Rio Grande Valley of Texas to support an industry that had become increasingly less profitable. Through USDA-ARS breeding efforts, the industry is now thriving because of the release of higher-yielding and more disease resistant cultivars. During the course of this project, the breeding team made over 1600 basic crosses which produced very diverse progeny. Because sugar levels reached commercial standards, basic clones were advanced for use as parents in the commercial breeding program. Basic germplasm was planted in Starkville, Mississippi, in a replicated trial to assess cold tolerance. Two-hundred and ninety-one genotypes were named and used as parental material in the program between 2018 and 2023. These 291 genotypes along with 344 named accessions from the commercial breeding program were screened for the presence of the BRU1 gene and for durable rust resistance. In addition, all 635 of these genotypes were inoculated and screened for susceptibility to mosaic. Targeted crosses were made to increase the frequency of resistance to the two diseases in the breeding populations. When the screening work for the BRU1 marker was begun in 2012, only 4.4 percent of parental clones contained the marker among the Louisiana parental clones. By 2019, this frequency had increased to 29%. This project plan also focused on increasing mosaic resistance among parents. This is a long-term effort, where crosses were balanced between optimal sugar production and mosaic resistance. In the 2021 crossing season, no susceptible-by-susceptible crosses for mosaic were made in the basic breeding program which was made possible through increased screening efforts. A benchtop NIR machine was calibrated and optimized for the analysis of juice quality in both basic and commercial germplasm in the breeding program. Side-by-side wet lab and NIR analyses were conducted and calibration curves were established for sucrose and Brix in sampled sugarcane. The availability of new technology will allow for faster and less labor intensive analysis of cane in the breeding program in the future. The release of HoCP 14-885 and Ho 12-615 represents the ongoing efforts and output of the germplasm enhancement program at the SRU. These two varieties are products of the germplasm enhancement program and demonstrate the ongoing incorporation of new stress genes from wild germplasm. Both of these varieties contain multiple wild relatives in their pedigrees and show excellent yield stability. This is a trait of priority to the sugarcane stakeholders because it enhances the profitability of the industry. The sugarcane molecular identity database was updated annually with information from new cultivars. The information contained in this database is used to ensure the correct identification of varieties throughout the 13-year breeding cycle. Newly selected material was genotyped using SSR markers and fluorescence labeled capillary electrophoresis. The database has been used in the past to identify clones in multiple breeding and variety evaluation programs including those from U.S. Sugar Corp, Rio Farms, Inc., the American Sugar Cane League of the U.S.A., Inc., and agriculture consultants. In addition, international programs, including those in China, India, Pakistan, and the Philippines have adopted the program. Genome wide association studies (GWAS) were conducted by ARS scientists in Houma, Louisiana, to identify marker associated with mosaic resistance in the Louisiana sugarcane parental population. A population of over 200 individuals was inoculated and screened multiple times for susceptibility to sorghum mosaic virus. The individuals comprising the association panel were genotyped using sequencing-derived SNP markers, and 33 significant non-redundant SNPs were identified which were highly associated with mosaic resistance. The markers, many of which are associated with virus resistance or direct plant defense mechanisms demonstrated the potential use of GWAS to identify putative genes for resistance in sugarcane. A separate study identified putative markers associated with fiber and sucrose content using a mapping population of LCP 85-384. Ongoing work to validate the markers could lead to a reliable genetic marker to enhance breeding for increasing sugar yield and disease resistance in sugarcane.

Accomplishments
1. Release of commercial sugarcane variety ‘L 14-267’. There is no private breeding program for sugarcane in the United States, thus the industry is founded 100% on publicly developed varieties. ARS scientists from Houma, Louisiana, in collaboration with the American Sugar Cane League of the U.S.A., Inc. and the Louisiana State University Agricultural Center, developed and released a new sugarcane variety in 2021. The new variety, ‘L 14-267’ is resistant to mosaic, yellow leaf, smut, and ratoon stunt and moderately resistant to brown rust and leaf scald. ‘L 14-267’ is moderately susceptible to the sugarcane borer and the Mexican rice borer, both of which can be controlled through pesticide application. It has poor cold tolerance. The variety has mid-to-late season maturity but responds well to plant growth regulators. The variety’s most significant attributes are disease resistance, and high sugar yield and sucrose content in the plant-cane and first-ratoon crops. The release of this variety offers growers a well-adapted variety that exceeds the sugar yields of the currently leading variety in the plant-cane and first-ratoon crops.

2. Identification of selection preferences and predicting yield related traits in sugarcane seedling families using RGB spectral indices. The development of new sugarcane cultivars is important to the continued viability of the sugarcane industry. Breeding sugarcane is a long-term and labor-intensive investment, and researchers seek more cost-effective methods for variety development. Large numbers (>80,000) of genetically unique seedlings resulting from many parental cross combinations are planted and visually selected yearly in the USDA’s Louisiana Sugarcane Variety Development Program. Spectral imaging is one method that could reduce labor and time inputs by rapidly scanning large fields and identifying spectral indices that are linked to traits for selection. Replicated plots of sugarcane families were imaged using a drone equipped with a Red-Green-Blue camera. Some spectral wavelengths correlated with the seedling selection rates and yield traits such as height and Brix. These indices were captured in the plant-cane crop, and selections were made in first ratoon. The correlations demonstrated the potential of these indices to aid in in early decision making before harvest and reduce time and labor used to measure sugarcane plot manually.

Review Publications
Pontif, M., Kimbeng, C., Gravois, K., Taylor, Z., Sexton, D., Blanchard, B., Daigle, M., Fontenot, D., Hawkins, G., Hoy, J., Baisakh, N., Wilson, B., Orgeron, A., Todd, J.R., Hale, A.L., Waguespack, H. 2023. Registration of ‘L 14-267’ sugarcane. Journal of Plant Registrations. pp. 1-16. https://doi.org./10.1002/plr2.20267.
Wu, Q., Su, Y., Pan, Y.-B., Xu, F., Zou, W., Que, B., Lin, P., Sun, T., Grisham, M.P., Xu, L., Que, Y. 2022. Genetic identification of SNP markers and candidate genes associated with sugarcane smut resistance using BSR-Seq. Frontiers in Plant Science. 13:1035266. https://doi.org/10.3389/fpls.2022.1035266.
Lu, G., Wang, Z., Pan, Y.-B, Wu, Q., Cheng, W., Xu, F., Dai, S., Li, B., Que, Y., Xu, L. 2023. Identification of QTLs and critical genes related to sugarcane mosaic disease resistance. Frontiers in Plant Science. 14:1107314. https://doi.org/10.3389/fpls.2023.1107314.
Wu, Q., Chen, Y., Zou, W., Pan, Y.-B, Lin, P., Xu, L., Grisham, M.P., Ding, Q., Su, Y., Que, Y. 2023. Genome-wide characterization of sugarcane catalase gene family identifies a ScCAT1 gene associated disease resistance. International Journal of Biological Macromolecules. 232:123398. https://doi.org/10.1016/j.ijbiomac.2023.123398.
Xiong, H., Chen, Y.-B, Pan, Y., Shi, A. 2023. A genome-wide association study and genomic prediction for fiber and sucrose contents in a mapping population of LCP 85-384 sugarcane. Plants. 12(5):1041. https://doi.org/10.3390/plants12051041.
Xiong, H., Chen, Y., Pan, Y.-B., Shi, A., Wang, J. 2023. A genome-wide association study and genomic prediction for Phakopsora pachyrhizi resistance in soybean. Frontiers in Plant Science. 14(1179357):1-12. https://doi.org/10.3389/fpls.2023.1179357.
Todd, J.R., Johnson, R.M., Verdun, D.L., Richard, K.A. 2022. Identification of selection preferences and predicting tield related traits in sugarcane seedling families using RGB spectral indices. Agriculture. 12(9):1313. https://doi.org/10.3390/agriculture12091313.
Satpathy, S., Shahi, D., Blanchard, B., Pontif, M., Gravois, K., Kimbeng, C., Hale, A.L., Todd, J.R., Rao, A.R., Baisakh, N. 2022. Evaluation of models for utilization in genomic prediction in the Louisiana sugarcane breeding program. Agriculture. 12(9):1330. https://doi.org/10.3390/agriculture12091330.
Islam, M.S., McCord, P.H., Read, Q.D., Qin, L., Lipka, A.E., Sood, S.G., Todd, J.R., Olatoye, O.M. 2022. Accuracy of genomic prediction of yield and sugar traits in Saccharum spp. hybrids. Agriculture. 12:1436. https://doi.org/10.3390/agriculture12091436