Location: Plant Physiology and Genetics Research
2024 Annual Report
Objectives
Objective 1: Characterize the molecular and physiological mechanisms governing crop response to heat and drought, including interactions, to use the information to identify and verify new genes and molecular markers useful for plant breeding.
Sub-objective 1A: Characterize the physiological and genetic mechanisms governing
wax content and composition and heat shock proteins in cotton, under heat and
drought conditions.
Sub-objective 1B: Characterize the physiological and genetic mechanisms governing
wax content and composition and aquaporins in oilseeds, under heat and drought
conditions.
Objective 2: Develop and validate field-based, high-throughput phenotyping strategies for rapid assessment of crop responses to heat and drought, including evaluation and validation of sensors, proximal sensing vehicles, and methods of data capture, storage, analysis, and interpretations.
Sub-objective 2A: Develop and deploy novel sensing platforms, sensor calibration
devices, and sensor validation protocols for field-based high-throughput
phenotyping.
Sub-objective 2B: Develop a database that can be queried, and a geospatial data processing pipeline for proximal sensing and imaging data collected from terrestrial platforms for field-based high-throughput phenotyping.
Objective 3: Characterize the molecular mechanisms of oil accumulation in agriculturally important plants under various inclement conditions, including heat and drought conditions, to identify and verify new genes and molecular markers to increase oil yields in both food and bioenergy crop plants.
Sub-objective 3A: Characterize the molecular and physiological mechanisms governing
seed number, size, and weight for oilseeds and biofuel crops in response to heat and
drought stress conditions.
Sub-objective 3B: Characterize the function of lipid droplet-associated proteins (LDAPs) and identify new genes involved in abiotic stress responses and oil production pathways in plants.
Sub-objective 3C: Use transgenic and gene-editing approaches to increase oil content and abiotic stress tolerance in crop plants.
Approach
A variety of experimental approaches including phenomics and associated “big data” management, field studies of cotton and camelina, genomics, and the molecular and biochemical studies of the model plant Arabidopsis, as well as camelina, Brassica napus, and cotton are involved.
Objective 1: To characterize the physiological and genetic mechanisms governing crop response to heat and drought, cotton and Brassica napus plants will be examined for genetic variability of these traits using conventional and high-throughput phenotyping approaches to determine canopy temperature, cuticular wax content and composition, and leaf chlorophyll content. A transcriptomics approach will be used to determine if known genes involved in wax or chlorophyll biosynthesis are underpinning the observed phenotypes, and ribonucleic acid (RNA) sequencing will be conducted with either PacBio or Illumina HiSeq technology.
Objective 2: To develop and validate field-based high-throughput phenotyping (FBHTP) strategies for assessment of crop responses to heat and drought, novel platforms and sensor arrays, including carts, small robots and imagery, will be tested in cotton fields grown under high heat or drought stress. The FB-HTP collected traits will be assessed for accuracy and consistency using in-field calibration targets and ground truthing measurements. Semi-automated pipelines and databases will be developed to process and manage the data for statistical analysis of crop response to the environmental conditions.
Objective 3: To characterize the molecular and physiological mechanisms governing seed development and lipid-droplet-associated proteins (LDAPs) in biofuel crops, candidate gene-based and transgenic approaches will be used to examine the model system Arabidopsis and camelina. Gene function will be characterized using a combination of forward and reverse genetic approaches, coupled with cellular and biochemical studies of protein activity. Oil production in response to abiotic stress tolerance will be studied by examining the function of LDAPs and other lipidrelated proteins in leaves and seeds of plants. Transgenic approaches will be used to increase oil content and abiotic stress tolerance in camelina.
Progress Report
The project, 2020-21000-013-00D, entitled "Molecular Genetic and Proximal Sensing Analyses of Abiotic Stress Response and Oil Production Pathways in Cotton, Oilseeds, and Other Industrial and Biofuel Crops”, expired in March 2023. That project was replaced by the bridging project 2020-21000-014-000D with no change in the project title, objectives, or milestones. A new project is currently being written and expected to go through OSQR Ad Hoc Review in December 2025. Research continues on the existing Objectives and Sub-objectives and the following provides an update on the progress that has been made in FY 2024.
In support of Objective 1, a field experiment has been initiated by ARS researchers in Maricopa, Arizona, to characterize the response of crop varieties to reduced soil moisture in a high temperature environment. Several reproductive stages (flowering and grain filling) have been identified to be sensitive to reduced soil moisture. However, the extent of information on how increased temperature impacts the sensitivity with limited soil moisture on crop reproductive growth and development is limited. Ten varieties of soybean and cotton were planted on April and May 2024, respectively. The varieties will be exposed to three and four irrigation treatments for soybean and cotton, respectively. Every two weeks the reproductive structures present at each mainstem node are counted. Reproductive structures are then dried and weighed to record total dry weight for both soybean and cotton yield characteristics, which will be recorded from harvested seed and cotton lint quality will be determined.
In additional support of Objective 1, work has been initiated to develop artificial intelligence to predict seed traits from hyperspectral images of crop seeds by ARS researchers in Maricopa, Arizona, in collaboration with ARS researchers from Mississippi and Missouri, University of Arizona, Tucson, Arizona, and Bridgestone in Eloy, Arizona. Important seeds traits impacting agriculture are seedling establishment, nutritional composition, and germination. Development of a non-destructive imaging-based method to predict these traits would allow researchers to extend experiment data collection and search for additional avenues of crop seed research. The initial dataset to determine the feasibility of using artificial intelligence to predict seed traits used data from 100 soybean genotypes.
Also in support of Objective 1, research continued on the analysis of plant pigments. ARS researchers in Maricopa, Arizona, migrated a High-Performance Liquid Chromatography method to ultra-High Performance Liquid Chromatography. This new method is faster and will use half of the solvent as the previous method for analyzing plant pigments. Tissue from a panel of diverse soybean genotypes were grown in a higher temperature environment by ARS research in Maricopa, Arizona, and in a control temperature environment by researchers at the University of Missouri in Columbia, Missouri. These samples will provide insight on how high temperature impacts plant pigment quantities. Plant pigments influence physiological processes like radiation use-efficiency, photosynthesis, and nitrogen use-efficiency. Genotypes that showed improved plant pigment quantities in response to high temperature will be identified to improve plant breeding.
Additionally, in support of Objective 1, work has continued on a field study to better understand how reduced soil moisture impacts guayule dormancy. Guayule is a naturally producing rubber crop that is being developed to provide an additional source of rubber for industrial products. Due to the lack of knowledge on guayule production, best irrigation management practices are lacking crucial information. When to stop irrigation for the dormancy period of guayule is still widely unknown. To better manage guayule production and determine best practices for irrigation, a study was initiated in 2023 between ARS researchers in Maricopa, Arizona, and researchers with Bridgestone at the Bridgestone Agro Operations Research Farm in Eloy, Arizona, where guayule was irrigated every three weeks and once from April to October. To determine how the reduced irrigation impacted guayule growth, development, and dormancy, data is collected bi-weekly to measure canopy growth and development. To determine the impacts on dormancy photosynthesis and transpiration, measurements are conducted bi-weekly to identify when the dormancy of both irrigation treatments occur. To determine if the reduced irrigation treatment impacts rubber yield biomass is collected after dormancy, dry weights are determined, and rubber is extracted.
Accomplishments