Location: Plant Physiology and Genetics Research
2025 Annual Report
Objectives
With increasing global climate change challenges, there is an increasing demand for new clean bioenergy resources such as developing new crops, and genetically improving current crops to increase their tolerance to environmental changes and to sustain the agricultural sectors in semi-arid regions. The overall goal of this research project is to investigate genetic variations in bioenergy and industrial crops such as camelina, guayule, sorghum, and soybean to identify candidate genes controlling abiotic stress tolerance traits and identify new germplasm that can be used to develop superior cultivars with high yield and stable productivity to meet those challenges. The specific objectives of the project are:
Objective 1: Conduct research to identify alleles, candidate genes, and molecular markers for drought and/or heat tolerance of oilseed and biomass crops in semi-arid field conditions and determine association of abiotic stress tolerance with agronomic performance and biofuel traits such as biomass yield and conversion.
Sub-objective 1.A: Identify alleles/genes and associated molecular markers controlling oil content and composition, and related abiotic stress tolerance traits in camelina.
Sub-objective 1.B: Identify alleles/genes and associated molecular markers conditioning seed quality and composition and related stress tolerance traits in soybean.
Sub-objective 1.C: Identify alleles/genes and associated molecular markers conditioning biofuel production, biomass yield, and traits related to abiotic stress tolerance in bioenergy sorghum.
Sub-objective 1.D: Screen USDA guayule germplasm collection to discover biofuel-related traits, determine their variation in pyrolysis production, and associations with abiotic stress tolerance.
Objective 2: Conduct research to determine and effectively utilize bioinformatics and other genomic processing pipelines, such as transcriptomics and metabolomics, to enhance genetic improvement and trait enhancement of food, industrial, and biofuel crops.
Sub-objective 2.A: Characterize the genetic mechanisms governing wax content and composition in soybean growing under abiotic stress conditions.
Sub-objective 2.B: Explore guayule resin pathway(s) and related candidate genes using multi-omics approaches.
Approach
This project establishes a sustainable agricultural system for semi-arid regions using new and established crops for biofuel and industrial purposes. The approaches will explore genetic variation in bioenergy and industrial crops to discover abiotic stress tolerance traits and identify genes/alleles controlling those traits.
Objective 1 will focus on identifying candidate genes for abiotic stress tolerance using developed populations (camelina) and diversity panels (soybean and sorghum) planted under stress/non-stress conditions. Oil content and composition, biofuel and related abiotic stress tolerance traits will be collected using traditional and high throughput phenotyping platforms and analyzed using MIXED model. G×E interaction analyses will be conducted across irrigation levels for recorded traits. In Camelina, Quantitative Trait Loci (QTL) associated with recorded traits and stability parameters will be conducted. Candidate genes under QTL interval will be identified using SNP position on the camelina reference genome. GWAS analyses will be conducted for soybean and sorghum diversity panels. Candidate genes from multiple GWAS analyses will be identified from genomic intervals in the soybean and sorghum reference genome assemblies. Guayule will be planted under stress/non-stress conditions and traits related to abiotic stress tolerance will be collected. Rubber and resin, pyrolysis and biofuel related traits will be determined.
Objective 2 will focus on identifying candidate genes using multi-omics approaches, such as transcriptomics and metabolomics, to characterize genetic mechanisms governing wax content in soybean and resin in guayule. For transcriptome analyses, RNA will be harvested from soybean and guayule plants planted under stress/non-stress conditions and cDNA libraries will be sequenced. Following the structured pipeline, the paired-end clean reads will be aligned and mapped. Genes, with an adjusted p value, will be declared as differentially expressed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) will be used to annotate genes to biological/metabolic pathway.
For metabolomic approach, tissues from guayule will be harvested and resins will be extracted, purified and analyzed using liquid chromatography–mass spectrometry. Raw data will be processed to identify unknow compounds, search chemical databases for putative candidates, and annotate spectra with predicted fragmentation. Principal component analysis will be used to identify abundant metabolites and putative biomarkers responsible for differences among resin content in guayule genotypes and irrigation treatments. To interpret the metabolite’s function, pathway enrichments for detected metabolites will be calculated using KEGG database.
Progress Report
This report documents the FY 2025 progress of project 2020-21410-008-000D, titled, “Developing Biofuels and New Industrial Crops for Sustainable Semi-arid Agricultural Systems”, which began in June 2023.
Objective 1 is to study the mechanisms involved in abiotic stress tolerance in oilseed and industrial crops growing under semi-arid field conditions. Sub-objective 1A, focuses on camelina, an oilseed crop that shows great potential as a non-food source of biofuel, but the yields of the crop can be greatly diminished when planted under water-limited environments. A Recombinant Inbred Lines (RIL) population was developed and advanced to an F5 generation. The population and checks were planted under well-watered and water-limited conditions in Maricopa, Arizona. Field based high throughput phenotyping (HTP) data were collected using established protocols for measuring canopy temperature and vegetation indices. At physiological maturity, plots were harvested to estimate seed related traits, oil and protein contents and fatty acid composition. Statistical analyses over environments indicated that genotypes responded differently to drought stress conditions. Both genotype and irrigation treatment significantly influenced normalized difference vegetation index (NDVI) estimates. Seed characteristics, fatty acid profiles, and oil and protein contents were significantly affected by genotypes, environments, but no Genotype x Environment (GxE) interactions were observed for the studied traits.
In support of Sub-objective 1B, a diversity panel consisting of 350 soybean accessions plus check varieties were planted in Maricopa, Arizona, under well-irrigated and reduced-irrigation conditions. High-throughput phenotyping and canopy temperature data were collected throughout the growing season. At physiological maturity, plots were harvested and seed related traits including oil and protein contents as well as amino acids and fatty acid profiles, were determined. Analyses of variance over environments indicated significant effects of accessions, drought stress levels, and Genotype x Environment (GxE) interactions for the studied traits. The observed significant effects for accessions indicate the wide genetic variation of the soybeans in the panel. Several soybean accessions showed stability in growth and productivity when planted under drought stress conditions compared to nonstress conditions, placing them as new parental candidates to increase soybean drought stress tolerance.
For Sub-objective 1C, 360 bioenergy sorghum accessions were planted for seed increase to study the effect of drought stress on bioenergy related traits in sorghum. At the vegetative stage, plant tissue samples were scanned for variations in biofuel related traits such as lignin, hemicellulose, and cellulose using Near-Infrared Spectroscopy (NIRS). Preliminary data showed wide phenotypic variation among the sorghum bioenergy accessions for biofuel related traits when grown at Maricopa, Arizona.
Sub-objective 1D focuses on exploring biofuel related traits and characteristics in guayule. Field trials, including USDA guayule accessions and a wild relative, mariola, were grown at Maricopa, Arizona, under two irrigation regimes (well-irrigated vs. reduced irrigation). Mariola, the closest relative to guayule, has been used to transfer cold tolerance traits to guayule to potentially expand its production zones up to northern regions. Biofuel related traits such as lignin, hemicellulose, and cellulose were estimated and analyzed. Significant genotypic and environmental effects were observed for lignin, cellulose and hemicellulose concentrations and yields, indicating the wide genetic variability among guayule accessions for bio-energy-related traits. Moderate to high heritability values for lignin, cellulose, and hemicellulose suggested that selection is feasible to enhance genetic gain. Significant positive correlations were found among cellulose and hemicellulose concentrations and yields, indicating the possibility to select multiple traits together during breeding cycles. High positive correlations between rubber and resin and lignin, cellulose and hemicellulose yields highlight the opportunity to develop guayule germplasm with enhanced multiuse traits for industrial applications. Wide phenotypic variations in drought stress indices (stress tolerance index, yield index and yield stability index) underscore the environmental impact on the lignocellulosic traits. Several genotypes were identified with high stress index scores and could be parental candidates for improving guayule for arid and semi-arid sustainable agricultural systems.
Objective 2 focuses on using omics approaches to identify the molecular mechanisms controlling abiotic stress tolerance in food, industrial, and biofuel crops. Sub-objective 2B focuses on exploring the molecular mechanisms enhancing abiotic stress tolerance in guayule. A study was designed to investigate guayule’s transcriptional response to drought stress in two USDA-developed cultivars, AZ-4 and CAL-2, selected for their contrasting responses to drought stress. RNA sequencing and bioinformatics analyses revealed key transcription factors governing metabolic and stress-response pathways, highlighting distinct regulatory strategies in those cultivars. For example, 6167 transcripts were significantly differentially expressed (4210 down, 1957 up) in AZ-4 plants grown under drought stress and irrigated conditions. While, CAL-2 had expressed 5396 transcripts (3063 down, 2333 up). Data indicated 5350 transcripts were significantly expressed (3474 up, 1876 down) under drought conditions of both cultivars. Results revealed that under drought stress conditions, AZ-4 exhibited a more dynamic regulatory approach with more transcripts differentially regulated, emphasizing resource management and adaptive stress-response mechanisms. In contrast, CAL-2 maintained stability through precise regulatory adjustments and external defense strategies, as indicated by gene ontology (GO) term enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses. The two cultivars demonstrated core stress-response mechanisms, particularly regulating AP2/ERF, MYB, and NAC transcription factor families for downstream regulations. Additionally, aquaporin expression patterns suggested selective upregulation of PIP1-2, PIP1-4, and NIP5-1, as a compensatory mechanism for maintaining physiological functions under drought stress. These findings enhance our understanding of guayule’s drought tolerance and rubber production potential.
Accomplishments
1. Biofuel traits increase guayule’s potential as a semi-arid crop. Guayule, a desert industrial crop, is primarily grown for rubber and resin production. The crop residual after chemical extraction, called bagasse, could be used as a bioenergy feedstock to meet the growing bioenergy and biofuel demands but is not well characterized. ARS researchers in Maricopa, Arizona, have found considerable diversity in lignocellulosic compositional components and yield within the USDA guayule collection and identified several genotypes capable of high yield under restricted irrigation. These genotypes could be candidate parental materials to improve bioenergy-related traits and enhance guayule breeding efforts to grow guayule for multiple profitable products in semi-arid regions.
Review Publications
King-Smith, N.P., Fontana, T.R., Cornish, K. 2025. Evaluation of hydroponic systems for Taraxacum kok-saghyz and comparisons with greenhouse and field production methods. Journal of Agriculture and Food Research. 21. Article 101977. https://doi.org/10.1016/j.jafr.2025.101977.
Veatch-Blohm, M.E., Teetor, V.H., Ray, D.T., Saba, B., Cornish, K. 2025. Suppression of guayulin content in transgenic guayule (Parthenium argentatum Gray). Discover Plants. 2(75). https://doi.org/10.1007/s44372-025-00136-0.
Blakeslee, J.J., Han, E., Lin, Y., Lin, J., Nath, S., Zhang, L., Li, Z., Cornish, K. 2024. Proteomic and targeted lipidomic analyses of fluid and rigid rubber particle membrane domains in guayule. Plants. 13(21). Article 2970. https://doi.org/10.3390/plants13212970.
Herkins, A., Davis, S., Cornish, K. 2025. Development of a circumallergenic guayule latex endotracheal tube cuff. Biomedical Materials & Devices. https://doi.org/10.1007/s44174-024-00274-1.
Junkong,, J., Ohashi,, T., Phakkeeree,, T., Miyaji,, K., Iwasaki,, S., Cornish, K., Ikeda,, Y. 2025. Two-cycle strain-induced crystallization behavior of peroxide cross-linked solid guayule natural rubber. Macromolecular Materials and Engineering. 310(6). Article 2400349. https://doi.org/10.1002/mame.202400439.
King-Smith, N.P., Anderson, V.M., Pillai, A.S., Puskas, J.E., Cornish, K. 2025. Optimal planting density of Taraxacum kok-saghyz bred for large root size: Seed, latex, and rubber yields. HortScience. 60(4):457-466. https://doi.org/10.21273/HORTSCI18374-24.
Abdel-Haleem, H.A., Masterson, S.D., Sedivy, A.M., Mitchell, R. 2025. Phenotypic diversity in cell wall lignocellulosic constituents and ethanol yield of USDA guayule and mariola germplasm. Plants. 14(8). Article 1239. https://doi.org/10.3390/plants14081239.
Saba, B., Scott, D., McMahan, C.M., Shintani, D., Cornish, K. 2025. Rubber accumulation and rubber transferase activity during root development of Taraxacum kok-saghyz dandelion. Discover Plants. 2. Article 2. https://doi.org/10.1007/s44372-024-00075-2.
Devney, E.P., Polyak, P., Kaszas, G., Amstutz, N., Puskas, J.E., Cornish, K., Molnar, K. 2025. Microcompounding of small samples of natural rubber. Rubber Chemistry and Technology. 98(1):78-89. https://doi.org/10.5254/rct.24.00033.
King-Smith, N.P., Davis, S.A., Cornish, K. 2025. Rubber Dandelion (Taraxacum kok-saghyz) latex films: Implications for medical and latex product development. Rubber Chemistry and Technology. 98(1):90–108. https://doi.org/10.5254/rct.24.00035.
Herkins, A., Dey, S., Conroy, D., Cornish, K. 2024. Nitrile glove composition and performance—substandard properties and inaccurate packaging information. PLOS ONE. 19(1). Article e0312891. https://doi.org/10.1371/journal.pone.0312891.
Akinola, S., Saba, B., Christy, A., Cornish, K., Ezeji, T.C. 2025. Biohydrogen and biobutanol production from spent coffee and tea waste using Clostridium beijerinckii. Fermentation. 11(4). Article 177. https://doi.org/10.3390/fermentation11040177.