Location: Plant Stress and Germplasm Development Research
2023 Annual Report
Objectives
Objective 1. Use national collections of germplasm to identify, characterize, and exploit superior physiological traits that enhance stress tolerance and increase yield in row crops, such as cotton, maize, peanut, and sorghum, to optimize crop production strategies in water-limited management systems.
• Sub-objective 1A: Evaluate a previously selected, diverse core-collection of cotton lines from the USDA germplasm collection and map developed populations for yield and fiber quality under mid- and late-season water-deficit stress and/or disease pressure.
• Sub-objective 1B: Identify cotton and peanut germplasm with physiological and morphological traits important to stress tolerance and stress acclimation.
• Sub-objective 1C: Characterize agro-morphological and physiological traits controlling water-deficit stress tolerance in diverse grain sorghum germplasm collections to broaden the genetic donor sources for sorghum breeding.
• Sub-objective 1D: Characterize genotypic plasticity and identify genetic components of heat tolerance in maize and sorghum.
• Sub-objective 1E: Isolation and genetic characterization of sorghum mutants with altered heat tolerance for major traits. Mapping and cloning the causal mutation in sorghum hs mutants and functional characterization of identified genes.
• Sub-objective 1F: Physiological characterization of maize core lines for their diversity in heat stress responses. Dissection of cellular and physiological mechanisms in heat stress response in maize. (Chen)
Objective 2. Develop and implement crop management systems that are most appropriate for exploiting the uniqueness or strengths of superior new varieties combined with diverse regional production practices.
• Sub-objective 2A: Implementation of crop simulation models to explore the GxExM interactions in rainfed cotton and sorghum production systems.
• Sub-objective 2B: Evaluation of new genetic sources of cold temperature tolerance in and development of new production schemes from planting date and in-season management to expand current season lengths and regional boundaries for sorghum production.
Objective 3. Determine variability in plant environmental stress responses, and exploit the diversity by designing and evaluating genotype-specific production schemes that include assessments of environmental limitations and management interactions.
• Sub-objective 3A: Advance new high-throughput, thermographic technologies for estimation of plant responses to abiotic stresses under relevant production conditions in the field.
• Sub-Objective 3B: Utilize existing gene mapping technologies/tools to identify and develop new single nucleotide polymorphism markers, biomarker-trait associations, and functional genes associated with tolerance and susceptibility to abiotic and biotic stress.
Approach
Unpredictable weather patterns and insect and disease pressures continually threaten yields and quality of virtually all cropping systems. These threats, coupled with accelerating global declines in water available for irrigation and increasing reliance on production from marginal lands present substantial obstacles to achieving the goal of the ARS Grand Challenge to deliver a 20% increase in quality production at 20% lower environmental impact by 2025. The long-term goals of this research are to improve understanding of plant resilience to biotic and abiotic stresses and to develop stress-tolerant cultivars that can be used in existing and future cropping systems.
The elucidation of how biological mechanisms control plant stress responses and how the environment, both natural and managed, defines and restricts crop productivity, provide the foundation for the ability to improve agricultural production in low-input systems. Significant changes in management strategies, improved selection methods, and improved germplasm will be required to meet future production demands. Genetic improvements will be derived from active, targeted selection of traits in diverse germplasm grown under relevant production scenarios. Investigations of the interactions among genetic resources, environments, and management systems provide a way to fit technologies from this research to various regional climatic zones.
The proposed research is relevant to the NP 301 Action Plan, Component 1 - Crop Genetic Improvement: Problem Statement 1A, Trait discovery, analysis, and superior breeding methods and 1B, New crops, new varieties, and enhanced germplasm with superior traits; Component 2 - Plant and microbial genetic resource and information management: Problem Statement 2A, Plant and microbial genetic resource and information management; Component 3 - Crop Biological and Molecular Processes: Problem Statement 3A: Fundamental knowledge of plant biological and molecular processes; and Component 4 - Information resources and tools for crop genetics, genomics, and genetic improvement: Problem Statement 4A, Information resources and tools for crop genetics, genomics, and genetic improvement.
Progress Report
This will serve as the final report for this project as it terminated in 2023 and was replaced with a new project (3096-21000-023-000D).
Objective 1, Objective 3. During the life of the project for the field evaluation of cotton germplasm lines for waterdeficit stress using two irrigation regimes (standard and limited 1/3 irrigation) in replicated trials, more than 4,000 research plots were evaluated consisting of over 800 germplasm lines. These evaluations also included 440 recombinant inbred lines derived from three cross-combinations between cultivars, Phytogen 72 and NM 67, Alcala NemX and Acala SJ-2, Upland okra leaf type-cultivars MD51ne and FiberMax 832. Cotton lines were planted at Lubbock, Texas, to confirm the yield, fiber quality, plant morphological advantages observed under water stress conditions. Seven Upland cotton germplasm lines growing under different irrigation regimes were developed, publicly released and registered possessing good lint yield, superior fiber strength, length, and uniformity when grown on the High Plains of Texas. These lines can be used as an alternative genetic source for improving fiber quality traits under reduced irrigation levels. For disease evaluation of Upland and Pima germplasm lines for Fusarium wilt race 4 (FOV4) resistance, more than 2,000 developed progeny and breeding lines derived from 6 diverse cross-combinations using 10 parental lines with different genetic background were evaluated for FOV4 infection-response or resistance to FOV4 in Texas and California naturally infested FOV4 fields in replicated trials. Seventeen Upland cotton germplasm lines growing under high concentration of the FOV4 fungus in the soil were developed and publicly released possessing improved resistance to FOV4 and superior fiber strength, length, and uniformity. This is the first set of Upland germplasm released to the public with FOV4 resistance. The germplasm lines will provide the needed source of FOV4 resistance, increase the genetic diversity in the Upland crop and reduce the vulnerability of the Upland industry to this fungal pathogen. In addition, three Pima cotton germplasm lines growing under high concentration of the FOV4 fungus in the soil were developed and publicly released possessing improved resistance to FOV4. Three Pima-like cotton germplasms lines with improved resistance to FOV4 were derived from crossing cotton Pima lines from the United States and Uzbekistan and will increase the genetic diversity and continuing to reduce the vulnerability of the Pima cotton to this fungal pathogen. Currently, additional cotton lines are being evaluated for growth, yield, fiber quality and Fusarium wilt race 4 (FOV4) resistance. Objective 1. Field evaluation of heat and water-deficit stress tolerance for sorghum was carried out at Lubbock, Texas. Trial-experiments were planted and are currently being evaluated for leaf and reproductive tissue response to naturally occurring heat wave events. Targeted sorghum mutant populations were sown as part of a phenotype and yield trial to evaluate for heat stress response, and mutant plants with altered heat tolerance traits in leaf and panicle tissues were identified. The seed-producing sorghum mutants were identified at the end of the growing season and verified for specific phenotypes in a greenhouse in fiscal year fiscal year 2021. In addition, development of new sorghum progeny was performed by backcrossing those mutants showing the altered heat tolerance traits with yielders sorghum cultivars. Phenotyping data using an unmanned aerial system (UAS) is being collected and will be analyzed with yield and biomass data at the conclusion of the growing season.
Objective 1, Objective 2. Post-flowering drought tolerance examination in sorghum was performed using high performance liquid chromatography (HPLC) to investigate the production of cell metabolites such as sucrose, glucose, fructose, and dhurrin in 56 diverse lines of grain sorghum. Dhurrin is a chemical product produced in the development of grain sorghum bicolor. Analyses showed that matured leaf dhurrin level is a reliable tool to screen for pre-and post-flowering drought tolerance in sorghum. In addition, a set of 42 diverse sorghum lines with Chinese and Ethiopian background for cold tolerance were evaluated for seed-to-seed yield penalty effect from early-season planting under field conditions in Lubbock, Texas. Performance with respect to less yield penalty was better in the Ethiopian sorghum lines compared to the Chinese sources for early-season cold tolerance sorghum.
Objective 2, Objective 3. An on-farm irrigation scheduling tool was used for canopy temperature, and soil probes, using UAS for evaluation of crop establishment and growth. A long-term rainfed planting date (8 sowing dates across 5 months) trial was sown for the 5th consecutive growing season. Additionally, an early season planting date experiment was sown to screen sorghum genotypes for cold temperature tolerance and early season seedling vigor. Crop establishment and growth data for both cotton and sorghum were collected with a UAS (drone) 3 times per week. As part of these experiments, we have developed and completed a software program to analyze the effect of gaps in plant stands that allows for tracking of individual plants from planting to harvest and provides a quantitative measure of plant growth compensation in varying plant population densities. A simulation model for cotton crop management (OZCOT) was modified and implemented for rainfed production systems. A user-friendly front end was developed in a Jupyter notebook framework. A UAS data analytics pipeline was developed in collaboration with Australian partners. The results of the initial simulations were compared to historic performance dataset of approximately 20 years of work for rainfed and irrigated cotton in Lubbock, Texas. In addition, a large regional on-farm trial in a 50,000-acre Luger-Altus Irrigation district was performed for two consecutive years. This research work involved USDA/ARS and Commonwealth Scientific an Industrial Research Organization from Australia (CSIRO), and included an infrared canopy temperature sensing technology, specifically through implementation of continuous field-level temperature sensing using Sentinel technology (SmartField, Inc.) and plant-level sensors (Goanna Ag. Australia). Data collected for the region has identified several areas for improved irrigation efficiency and the technology was employed by growers for the 2021 growing season. Cropping years 2020 and 2021 data were used in a meeting with the USDA Risk Management Agency in June 2021 and the Luger-Altus Irrigation District to determine water allocation for the 2021 season and to provide measured field data to crop insurers. This is a direct impact on production practice and production economics for this region and based, in part, on the data collected for this objective. Questions relating to the ability of producers to reduce yield and quality losses related to harvest and processing methodology are being addressed in terms of an “End-of-Season Value Capture Framework”. This work involves both USDA/ARS and scientists in the areas of crop physiology and fiber quality. The implementation of a canopy temperature based irrigation management system by an Australian agricultural management company (Goanna Ag) is underway on a 50,000-acre (13 growers) irrigation district in Oklahoma.
Accomplishments
1. Pima cotton germplasm with improved resistance to Fusarium wilt race 4. For almost two decades, a soilborne fungal pathogen named Fusarium oxysporum f. sp. vasinfectum, race 4 (FOV4) has impacted cotton production in California’s San Joaquin Valley, causing plant wilt and death and economic losses of millions of dollars. Recently, this pathogen was identified in New Mexico and Texas, near the Texas High Plains, the largest Upland cotton producing region in the United States. ARS scientists in Lubbock, Texas, developed three Pima-like cotton germplasm lines with improved resistance to FOV4 by crossing cotton lines from the United States and Uzbekistan. The lines will increase the genetic diversity and continue to reduce the vulnerability of the Pima industry to this fungal pathogen by avoiding future production disruption in affected cotton fields as previously observed in California, Texas, and New Mexico.
2. Deciphering cotton resistant to the southern Root-Knot Nematode. The southern Root-Knot Nematode (RKN) is a parasitic round-worm that causes significant damage to a large number of crops, including cotton, and is a constant threat to cotton production in the United States and world-wide. Although possible, chemical control of RKN is expensive and can be unreliable. Thus, developing resistant varieties through the identification of resistance mechanisms and conventional breeding is crucial and the most economically viable approach to create new varieties with RKN resistance. In this study, ARS scientists in Lubbock, Texas, with university cooperators investigated the mechanisms of RKN resistance in cotton varieties with different levels of resistance to RKN infection. The findings of this study identified several new candidate-genes and mechanisms for RKN resistance in cotton that may facilitate the introduction of RKN resistance genes into valuable commercial varieties of cotton.
3. First diverse set of Upland cotton germplasm with improved resistance to Fusarium wilt. The need to develop resistant Upland cotton commercial varieties has become urgent. Previous research by ARS scientists in Lubbock, Texas, identified high levels of resistance to Fusarium oxysporum f. sp. vasinfectum, race 4 (FOV4) in the cotton cultivar Pima S-6 and resulted in the public release of Pima germplasm with improved FOV4 resistance. However, the search for resistant Upland cotton has proved more challenging. ARS scientists developed and jointly released with university cooperators 17 Upland cotton germplasm lines with improved resistance to FOV4. These lines were derived from 6 diverse cross-combinations using 10 parental lines with different genetic backgrounds. Today, there is no known FOV4-resistant or highly resistant Upland commercial variety in the United States. This is the first set of Upland germplasm released to the public with FOV4 resistance. The lines will provide the needed source of FOV4 resistance, increase the genetic diversity in the Upland crop and reduce the vulnerability of the Upland industry to this fungal pathogen by avoiding future production disruption in affected cotton fields as previously observed in California, Texas, and New Mexico.
4. On-farm irrigation scheduling tool using canopy temperature and soil probes. This accomplishment is the culmination of approximately 20 years of work by ARS researchers in Lubbock, Texas, on using biologically derived crop optimal temperatures as a measure of plant water status and is now commercially available. ARS and a private company cooperator have tested the commercial system over a range of environments with grower cooperators to demonstrate its use for on-farm irrigation control and optimized efficiency. The system uses a combination of real-time crop, soil sensing, and climate forecasting models to optimize the timing and amount of irrigation applied to the of cotton crop to maximize irrigation use efficiencies and yield. This system has a direct impact on production practices relating to the ability of producers to reduce yield and quality losses related to harvest in terms of application of irrigation water.
5. High temperature stress of the sorghum male reproductive tissues. Sorghum is an important cereal crop for production in semi-arid and other marginal environments. High temperature stress that usually accompanies drought stress damages plant reproductive tissues and results in decreased yield. In sorghum, anthers and fertility are particularly sensitive to high temperatures. In this study, ARS scientists in Lubbock, Texas, and university collaborators examined the cellular changes of sorghum anthers and altered development under high temperature stress. The results showed 18 distinct stages of another development and significant alterations in several stages in response to high temperature stress that were correlated with decreased fertility. The findings of this study will serve as an important reference for future studies focusing on sorghum physiology, reproductive biology, genetics, and genomics and provide a baseline of anther development data for reference using new, heat tolerant sorghum lines. Improvements in anther heat tolerance will have a direct effect on sorghum yield.
6. Cold tolerance in Ethiopian sorghum germplasm lines. The ability for sorghum to germinate and grow under cooler conditions early in the growing season is a key trait of interest for sorghum production. Historically, sorghum lines from specific regions in China have been used as donor sources of cold tolerance. Problems with the use of Chinese cold tolerant lines include high tannin concentrations in the grain. Tannin is a complex chemical substance derived from phenolic acid. In addition, these lines are too tall for mechanized harvesting and are susceptible to many diseases. To resolve this problem, ARS scientists at Lubbock, Texas, identified 10 germplasm lines from the highlands of Ethiopia that have excellent cold tolerance, and do not contain the negative problems of sorghum production as compared to the Chinese germplasm lines. Furthermore, a seed-to-seed evaluation of early season cold resiliency showed that the Ethiopian lines had less yield penalty compared to their Chinese counterparts. These identified cold tolerant Ethiopian lines are currently being used by scientists to develop new and improved grain and forage sorghums.
Review Publications
Mendu, L., Jalathge, G., Dhillon, K., Singh, N., Balasubramanian, V., Fewou, R., Gitz, D.C., Chen, J., Xin, Z., Mendu, V. 2022. Mutation in Endo-ß-1,4-Glucanase (KORRIGAN) is responsible for thick leaf phenotype in sorghum. Plants. 11(24). https://doi.org/10.3390/plants11243531.
Chen, J., Laza, H., Burow, G.B., Hayes, C.M., Burke, J.J., Emendack, Y., Xin, Z. 2022. Registration of two novel grain sorghum nuclear male sterile mutants: BTx623ms9-1 and BTx623ms9-3. Journal of Plant Registrations. https://doi.org/10.1002/plr2.20251.
Khan, A., Khan, N., Bean, S.R., Chen, J., Xin, Z., Jiao, Y. 2023. Variations in total protein and amino acids in the sequenced sorghum mutant library. Plants. 12(8). https://doi.org/10.3390/plants12081662.
Emendack, Y., Sawadogo, N., Ramadjita, T., Laza, H. 2023. Assessment of photoperiod sensitivity and the effect of sowing date on dry-season sorghum cultivars in Southern Chad. Agronomy Journal. 13(932). https://doi.org/10.3390/agronomy13030932.
Chaudhuri, S., Roy, M., McDonald, L., Emendack, Y. 2023. Land degradation–desertification in relation to farming practices in India: An overview of current practices and agro-policy perspectives. Sustainability. 15(8). https://doi.org/10.3390/su15086383.
Laza, H., Acosta Martinez, V., Cano, A., Baker, J.T., Mahan, J.R., Gitz, D.C., Emendack, Y., Slaughter, L., Lascano, R.J., Tissue, D., Payton, P.R. 2023. Elevated [CO2] enhanced soil respiration and AMF abundance in a semiarid peanut agroecosystem. Agriculture, Ecosystems and Environment. 355. https://doi.org/10.1016/j.agee.2023.108592.
Chavez-Montes, R., Ulloa, M., Biniashvili, T., Zackay, A., Kfir, N., Lopez-Arrendondo, D., Herrera-Estrella, L. 2023. Assembly and annotation of the Gossypium barbadense L. 'Pima-S6' genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes. BMC Genomics. 24. Article 11. https://doi.org/10.1186/s12864-022-09102-6.
Mendu, L., Ulloa, M., Payton, P.R., Monclova-Santana, C., Chagoya, J., Venugopal, M. 2022. Lignin and cellulose content differences in roots of different cotton cultivars associated with different levels of Fusarium wilt race 4 (FOV4) resistance-response. Journal of Agriculture and Food Sciences. 10. Article 100420. https://doi.org/10.1016/j.jafr.2022.100420.
Ulloa, M., Hutmacher, R.B., Zhang, J., Schramm, T., Roberts, P.A., Ellis, M.L., Dever, J.K., Wheeler, T.A., Witt, T.W., Sanogo, S., Hague, S., Keely, M.P., Arce, J., Angeles, J., Hake, K., Payton, P.R. 2022. Registration of 17 upland cotton germplasm lines with improved resistance to Fusarium wilt race 4 and good fiber quality. Journal of Plant Registrations. 1-12. https://doi.org/10.1002/plr2.20258.
