Location: Plant Stress and Germplasm Development Research
2021 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
Objective 1, Sub-objective 1A, Objective 3, Sub-objective 3C. A replicated deficit irrigation trial (2 irrigation levels) with 190 recombinant inbred lines (RILs) derived from a cross between Upland okra leaf type-cultivars MD51ne and FiberMax 832 was planted at Lubbock, Texas, in May 2021 and is currently being evaluated for growth, phenology, and fiber quality.
For disease evaluations, replicated trials with 110 RILs derived from a cross between cultivars Alcala NemX and Acala SJ-2 were planted in infested Fusarium wilt race 4 (FOV4) fields in California and Texas. These entries are currently being evaluated for FOV4 tolerance/resistance. Around 100 additional selections and breeding lines are being evaluated at the same infested FOV4 field locations in California and Texas.
Objective 1, Sub-objective 1B. Field trials for selected genotypes are on-going and in-field root screening data was published in fiscal year (FY) 21. Previous efforts for detailed root growth experiments in controlled environments were delayed due to storm damage to the polyhouses and limited access to growth chambers. Repairs to the polyhouses are completed and experiments are planned for Fall 2021 as growth chamber access becomes available.
Objective 1, Sub-objective 1C. Chemical analyses of secondary metabolites (sucrose, glucose, fructose, and dhurrin) in 56 diverse lines of grain sorghum showed matured leaf dhurrin level as a reliable tool to screen for pre- and post-flowering drought tolerance in sorghum.
Objective 1, Sub-objective 1D. Field trials are underway for FY 21 and data evaluating heat stress responses of accessions to the naturally occurring heat waves events in leaf and reproductive tissues are being collected manually and by aerial photogrammetry.
Objective 2, Sub-objective 2A and C. A large, regional on-farm trial in a 50,000-acre irrigation district is currently in its second year. Data collected for the region has identified a number of areas for improved irrigation efficiency and the technology is currently being 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 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.
Objective 2, Sub-objective 2B. 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 yield penalty was better in the Ethiopian compared to the Chinese sources of early-season cold tolerance sorghum.
Accomplishments
1. Release of Upland cotton germplasm with improved tolerance to Fusarium wilt. Fusarium oxysporum f. sp. Vasinfectum, race 4 (FOV4) causes Fusarium wilt disease in cotton. This disease is devastating to cotton production and to date, there is no source of resistance in Upland cotton. Recently, this disease was identified in West Texas and poses a threat to the cotton industry. ARS scientists at Lubbock, Texas, released 17 Upland cotton germplasm lines with improved resistance to FOV4. This is the first set of Upland germplasm released to the public with FOV4 resistance.
2. Identification of cold tolerance in sorghum germplasm. The ability for sorghum to germinate and grow under cool, early season conditions key trait of interest for the sorghum community. Historically, germplasm from specific regions in China have been used as genetic sources of cold tolerance but are known to have grain quality and harvestability issues. 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 agronomic traits associated with Chinese germplasm. A seed-to-seed evaluation of early season cold tolerance showed the Ethiopian lines having less yield penalty compared to their Chinese counterparts. ARS scientists at Lubbock, Texas are now actively using these new sources in the development of new grain and forage sorghums to develop cold-tolerant sorghum varieties for U.S. production. This improvement will expand sorghum growing region and add flexibility to planting dates.
3. Identification of alternative sources of stay-green in sorghum. Though considered drought tolerant, the ability of sorghum to be productive under drought condition depends on the level of pre- and post-flowering drought tolerance. There are limited sources of the post-flowering drought tolerance trait, known as stay-green and many have poor agronomic traits for grain yield and quality. ARS scientists at Lubbock, Texas, have identified alternative sources of the stay-green trait with better agronomics from Ethiopian germplasm and are incorporating this material into new sorghum varieties for improved drought tolerance.
Review Publications
Emendack, Y., Sanchez, J., Hayes, C.M., Nesbitt, M.E., Laza, H., Burke, J.J. 2021. Seed-to-seed early-season cold resiliency in sorghum. Nature Scientific Reports. 11. Article 7801. https://doi.org/10.1038/s41598-021-87450-1.
Wang, C., Ulloa, M., Nichols, R., Roberts, P.A. 2020. Sequence composition of BAC clones in a transgressive root-knot nematode resistance chromosome region in tetraploid cotton. Frontiers in Plant Science. 11:574486. https://doi.org/10.3389/fpls.2020.574486.
Ulloa, M., Hutmacher, R.B., Schramm, T.L., Ellis, M.L., Nichols, R., Roberts, P.A., Wright, S.D. 2020. Sources, selection and breeding of Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 (FOV4) resistance in Upland (Gossypium hirsutum L.) cotton. Euphytica. 216:109. https://doi.org/10.1007/s10681-020-02643-5.
Bangshing, W., Haoxi, C., Yingli, Z., Yun, S., Wannian, Y., Chen, J., Xin, Z., Huazhong, S. 2019. The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing. Journal of Experimental Botany. 71(4):1598–1613. https://doi.org/10.1093/jxb/erz523.
Wang, L., Lu, Z., Regulski, M., Jiao, Y., Chen, J., Ware, D., Xin, Z. 2021. BSAseq: An interactive and integrated web-based workflow for identification of causal mutations in bulked f2 populations. Bioinformatics. 37(3):382-387. https://doi.org/10.1093/bioinformatics/btaa709.
Witt, T.W., Ulloa, M., Schwartz, R.C., Ritchie, G.L. 2020. Response to deficit irrigation of morphological, yield and fiber quality traits of upland (Gossypium hirsutum L.) and Pima (G. barbadense L.) cotton in the Texas High Plains. Field Crops Research. 249:107759. https://doi.org/10.1016/j.fcr.2020.107759.
Zou, G., Zhai, G., Chen, H., Yan, S., Zhou, L., Ding, Y., Lu, P., Liu, H., Chen, J., Xin, Z., Zhen, X., Liu, X. 2020. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. Journal of Experimental Botany. https://doi.org/10.1093/jxb/eraa277.
Zhang, J., Abdelraheem, A., Zhu, Y., Wheeler, T.A., Dever, J., Frelichowski, J.E., Love, J., Ulloa, M., Jenkins, J.N., McCarty Jr, J.C., Nichols, R., Wedegaertner, T. 2020. Assessing genetic variation for Fusarium wilt race 4 resistance in tetraploid cotton by screening over three thousand germplasm lines under greenhouse or controlled conditions. Euphytica. 216:108. https://doi.org/10.1007/s10681-020-02646-2.
Gapili, N., Emendack, Y., Baloua, N., Vom Brocke, K., Hassan, M., Sawadogo, N., Amos, D., Reoungal, D., Giles, T., Laza, H. 2020. Characterization of semi-arid Chadian sweet sorghum accessions as potential sources for sugar and ethanol production. Nature Scientific Reports. 10, Article 14947.
Li, X., Shi, W., Broughton, K., Sharwood, R., Payton, P.R., Bange, M., Tissue, D. 2020. Impacts of growth temperature, water deficit and heatwaves on carbon assimilation and growth of cotton plants (Gossypium hirsutum L.). Environmental and Experimental Botany. 179:104204. https://doi.org/10.1016/j.envexpbot.2020.104204.
Mauget, S.A., Kothari, K., Leiker, G.R., Emendack, Y., Xin, Z., Hayes, C.M., Ale, S., Baumhardt, R.L. 2020. Optimizing dryland crop management to regional climate. Part II: U.S. Southern High Plains sorghum production. Frontiers in Sustainable Food Systems. 3:119. https://doi.org/10.3389/fsufs.2019.00119.
