Location: Plant Physiology and Genetics Research
2022 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 (FB-HTP) 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 lipid-related proteins in leaves and seeds of plants. Transgenic approaches will be used to increase oil content and abiotic stress tolerance in camelina.
Progress Report
This report documents progress for project 2020-11000-013-000D, titled “Analysis and Quantification of G x E x M Interactions for Sustainable Crop Production” which was certified in September 2018 and continues research from project 2020-11000-012-000D titled, “Strengthening the Analysis Framework of G x E x M under Climate Uncertainty.” The following documents the research progress made in fiscal year (FY) 2022.
Several field experiments are ongoing in support of Sub-objective 1. A cotton trial planted in 2020, 2021, and again in 2022 is being conducted to identify rate limiting steps in upland cotton radiation use-efficiency. Radiation use-efficiency is a determination of how well plants utilize energy adsorbed from the sun to generate biomass. Most C3 plants, like cotton, are very inefficient, utilizing approximately only 3% of the adsorbed energy. The trial has 8 cotton genotypes known to have variation in radiation use-efficiency, replicated 3 times, and grown under well-watered conditions. The plots are sampled bi-weekly for chlorophyll fluorescence, light interception, biomass, and leaf area as well as traits captured using a high-throughput phenotyping cart. The trial will be completed this year and statistical analysis on all three years will be conducted. Another cotton field experiment began in 2022 to better understand the impacts of reduced soil moisture on cotton growth and development. This experiment includes four irrigation treatments, determined by an irrigation scheduling tool, and soil moisture measurements are recorded weekly using a neutron moisture meter. Monthly measurements of plant node number and height, and collections of reproductive tissue are planned. A multi-location soybean trial, planted in Maricopa, Arizona, and Columbia, Missouri, in 2022 is being conducted to assess the extent of epigenetic changes on seed development caused by high temperatures. The trial has two sub-populations of 50 soybean varieties from a larger diversity population. One of the sub-populations was produced from seed obtained from plants grown in Missouri and the second sub-population was produced from seed obtained from plants grown in Arizona. Tissue will be collected from the sub-populations, both in Maricopa and Missouri for DNA extractions.
In support of Sub-objective 1B, two Brassica napus genotypes were planted in a replicated growth chamber experiment to study the effects of drought and high temperatures, and their interactions on gene expression. Our data indicated that annotated expressed genes, in response to these abiotic stressors, are involved in stress tolerance mechanisms such as fatty acid metabolism and elongation, cutin and wax biosynthesis, starch and sucrose metabolism and flavonoid biosynthesis. Our results demonstrated that the ribonucleic acid sequencing (RNAseq) analysis can detect gene expression differences on a genome-wide level. In agreement with other RNAseq studies, using three biological replicates could be a robust approach to validate gene expression data.
Several projects are ongoing in support of Sub-objective 2A. A cotton trial including the regional breeders testing network cotton panel was planted. Plots were measured with a semi-autonomous high-throughput phenotyping cart equipped with infrared thermometers (IRT) and five red|green|blue cameras as seedlings emerged. After seedling emergence, stand counts were taken for each plot. Pending analysis will determine the accuracy of IRTs and imagery to determine the effectiveness of this method to measure cotton stand establishment. Field trials in cotton and soybean were planted in 2020, 2021 and again in 2022 for the development and validation of a high-throughput phenotyping method to deploy a light induced fluorescence transient system on a proximal sensing cart. The light induced fluorescence transient system measures chlorophyll fluorescence which is a non-destructive indicator of photosynthetic efficiency in plants. This year will conclude the validation process for use in sorghum, soybeans, and cotton. Finally, analysis has been completed on the high-throughput phenotyping method to measure leaf chlorophyll content in field-grown plants. Chlorophyll are the primary light harvesting pigments and are responsible for driving photosynthesis for production of photosynthates. Our previous work indicated that leaf chlorophyll content in high heat and water deficit conditions was an important factor for maintaining cotton fiber yield. However, measuring leaf chlorophyll content is very time consuming so a high-throughput method has been in development since 2020. Later this year or early 2023 we anticipate the publication of this method.
Sub-objective 2B was completed ahead of the milestones. Last year we had intended to make changes to the database to be more compatible with the new USDA information technology structure changes, access to Internet 2. However, those changes have not yet been fully implemented so no further work has been done on the database or supporting pipelines.
In support of Sub-objective 3A, two Camelina genotypes differing in seed size were planted in a growth chamber experiment under drought, high temperatures, and combinations of both abiotic stresses to study the alteration in gene expression of fatty acid accumulation pathways. Leaf tissue for RNA extractions were harvested from developing seeds at two, four, and six weeks after flowering. Preliminary transcriptomic analyses of data showed differential gene expression levels in response to the abiotic stresses. The expressed genes were shown to be associated with stress tolerance and fatty acid biosynthesis.
Accomplishments
1. Novel cotton imaging method provides collaborative cotton seed research. Increasing cotton fiber yield has caused cotton seed size to decrease. Smaller cotton seed has generated processing problems at gins and oil mills. The National Cotton Council requested cotton breeders focus on seed size, but this trait is time consuming to measure. ARS researchers at Maricopa, Arizona, created a low-cost, open-source cotton seed imaging method to measure seed size. The imaging method has generated collaborations to quantify and genetically map seed size traits from cotton diversity populations and identify seed from the national cotton germplasm collection that will be useful to breeders.
Review Publications
Thompson, A.L., Conley, M.M., Herritt, M.T., Thorp, K.R. 2022. Response of upland cotton (Gossypium hirsutum L.) leaf chlorophyll content to high heat and low-soil water in the Arizona low desert. Photosynthetica. 60(2):280-292.
Herritt, M.T., Thompson, A.L., Thorp, K.R. 2022. Irrigation management impacts on cotton reproductive development and boll distribution. Crop Science. 62(4):1559-1572. https://doi.org/10.1002/csc2.20749.
Elshikha, D.M., Hunsaker, D.J., Waller, P.M., Thorp, K.R., Dierig, D., Wang, G., Cruz, V.M., Katterman, M.E., Bronson, K., Wall, G.W., Thompson, A.L. 2022. Estimation of direct-seeded guayule cover, crop coefficient, and yield using UAS-based multispectral and RGB data. Agricultural Water Management. 265. Article 107540. https://doi.org/10.1016/j.agwat.2022.107540.
Thorp, K.R., Calleja, S., Pauli, D., Thompson, A.L., Elshikha, D. 2022. Agronomic outcomes of precision irrigation management technologies with varying complexity. Transactions of the ASABE. 65(1):135-150. https://doi.org/10.13031/ja.14950.
Schutze, I., Yamamoto, P., Malaquias, J., Herritt, M.T., Merten, P., Thompson, A.L., Naranjo, S.E. 2022. Correlation-based network analysis of the influence of Bemisia tabaci feeding on photosynthesis and foliar sugar and starch composition in soybean. Insects. 13(1). Article 56. https://doi.org/10.3390/insects13010056.
Melandri, G., Thorp, K.R., Broeckling, C., Thompson, A.L., Hinze, L.L., Pauli, D. 2021. Assessing drought and heat stress-induced changes in the cotton leaf metabolome and their relationship with hyperspectral reflectance. Frontiers in Plant Science. 12. Article 751868. https://doi.org/10.3389/fpls.2021.751868.
