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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Research Project #434578

Research Project: Development of Genetic, Genomic and Molecular Resources to Improve Performance, Adaptability and Utility of Cool Season Grasses and Cover Crops

Location: Forage Seed and Cereal Research Unit

2019 Annual Report

The long-term objective of this project is to improve the performance of grasses and cover crops. Specifically, during the next five years we will focus on the following objectives. Objective 1: Develop cover crops with increased performance and adaptability in end use environments. • Sub-objective 1A: Develop tools to select for acidic soil syndrome tolerant plants and breed tolerant annual ryegrass germplasm. (Hayes) • Sub-objective 1B: Improve annual ryegrass winter cover crop germplasm for reliable spring termination. (Hayes, Martin) Objective 2: Identify disease resistant germplasm in cool season grass species. • Sub-objective 2A: Evaluate grass cultivars (cvs) for susceptibility to Barley Yellow Dwarf Viruses. (Dombrowski, Martin) • Sub-objective 2B: Identify and evaluate choke resistant germplasm in orchardgrass. (Dombrowski, Martin) • Sub-objective 2C: Develop stem rust resistant germplasm and breeding tools in perennial ryegrass and determine the potential durability of resistance. (Hayes) Objective 3: Isolate endophytes from grasses found in arid regions to identify novel endophytes that improve persistence and performance of forage and turf related grasses in environments with limited water resources. Objective 4: Develop genetic and molecular resources that can be applied to reduce the impact of abiotic stresses on the adaptability and performance of grasses in diverse environments. • Sub-objective 4A: Sequence and annotate Lolium sp. genome for development of a public genome database. (Dombrowski, Martin) • Sub-objective 4B: Identify genes or pathways common to stress responses in multiple types of abiotic stress. (Dombrowski, Martin) • Sub-objective 4C: Evaluate Brachypodium overexpressing transcription factors for improved abiotic stress tolerance. (Dombrowski, Martin)

Forage, turf, and cover crop species are critical components of sustainable landscapes and agroecosystems. Most of the cool season grass seed in the United States is grown in the Pacific Northwest due to the mild winters and dry summers that are ideal for grass seed production. Development of adaptable, high-yielding, animal-compatible, low-input grass and cover crop cultivars are needed to enhance the utility of these crops in environments different from those of the Pacific Northwest, to expand their market potential, and meet the goals of improved food security. The challenges to the grass industry require a multifaceted research approach to develop genetic resources for improved adaptability and stress tolerance in grasses and cover crops to accelerate the pace of cultivar development. The research in this project will develop new selection techniques and breed germplasm of annual ryegrass with enhanced tolerance to acid soil syndrome and reliable spring termination when used as a cover crop (Objective 1). New grass germplasm, quantitative trait loci (QTL), and molecular markers linked to resistance QTL will be identified in order to reduce the impact of the diseases stem rust, choke and barley yellow dwarf virus on crop performance (Objective 2). The project will identify novel endophytes from grasses found in arid regions and test their ability to improve persistence and performance of forage and turf related grasses in environments with limited water resources (Objective 3). Transcriptome and whole genome sequencing along with gene function studies will develop the genetic and molecular resources needed to accelerate the breeding of new grass cultivars with improved performance. The development of biological, genetic, genomic and molecular resources from this project will lead to improved performance, adaptability and utility of cool season grasses and cover crops in diverse end use environments.

Progress Report
This report documents progress for new project 2072-21000-054-00D, which began in February 2019, and continues research from projects 2072-21000-050-00D, "Improvement of Biotic and Abiotic Stress Tolerance in Cool Season Grasses" and 2072-22000-042-00D, "Disease Modeling and Genetic Approaches to Enhance Wheat and Grass Seed Crop Biosecurity." Abiotic and biotic stresses are the major causes of reduced crop yields worldwide. Identification of viable strategies to improve stress tolerance in crops will become increasingly important for the goal of global food security. Crop production practices may result in soil acidification; i.e., soils with a pH under 5.5 are considered acidic soil syndrome soils. These soils reduce growth of forage, turf, and cover crops by limiting essential plant nutrients and increasing plant toxic cations, particularly aluminum (Al3+). Chemical compounds that chelate Al3+ are found in plant root exudates and are known to condition tolerance to Al3+ toxicity. A scientist in Corvallis, Oregon, developed a high throughput method to measure root exudate chelation capacity of individual grass seedlings as part of research to address Sub-objective 1A. A preliminary selection experiment in annual ryegrass using this assay showed the data value from the colorimetric assay is a heritable trait that can be selected for in breeding populations. Research addressing Sub-objective 1B was conducted to develop annual ryegrass with increased susceptibility to the herbicide glyphosate. This is needed to improve the ease of spring termination when annual ryegrass is grown as winter cover crop. Initial greenhouse experiments were conducted with annual ryegrass to create dose response curves to the herbicide glyphosate. The experiments will be repeated to determine the herbicide rate needed to select herbicide susceptible annual ryegrass. Field plots were established to advance Barley yellow dwarf viruses (BYDVs) and Cereal yellow dwarf virus (CYDV) research that addresses Sub-objective 2A. The experiment contains 25 varieties each of tall fescue, fine fescue, perennial ryegrass and orchardgrass with resistance or tolerance to BYDVs and CYDV, and are currently being maintained and tested for virus infection. The identification of disease resistant germplasm can be utilized by researchers studying grass disease genetics and by grass breeders for use in their breeding programs to improve yield and stand persistence in forage and turf grass related systems. The disease choke in orchardgrass (Dactylis glomerata L.) is caused by the fungus Epichloë typhina. About 95 percent of U.S. orchardgrass seed is produced in Willamette Valley Oregon. The pathogen is now present in almost every orchardgrass seed production field, which can lead to yield losses as great as 30 percent. At present there are no known control methods for choke. The best long-term solution to disease management is host resistance. Research to address this problem is part of Sub-objective 2B. Previously, potential choke resistant germplasm was identified in field trials conducted by the ARS and industry partners. Progeny from 24 different potentially choke resistant maternal lines and susceptible control cvs Baraula and Potomac were grown in the greenhouse and transplanted in replicated trials at two locations. Entries included five early-, thirteen mid-, and six late- flowering germplasm. During this project, 27 different germplasms, including potential choke resistant and known susceptible lines, were infected with Epichloë typhina. These infected plants were also included in the replicated field trials. Research was conducted on stem rust of perennial ryegrass grown for seed as part of Sub-objective 2C. Resistant germplasm has been developed by ARS researchers in Corvallis, Oregon, and this resistance will be more useful if the resistance is consistently expressed in diverse environments, but nothing is known about the stability of resistance in this germplasm. Multi-location field experiments were conducted with ARS developed germplasm and preliminary analysis indicates that resistance is consistently expressed across the nine tested environments. More evaluations will be conducted to confirm this result. The diversity of the stem rust fungal pathogen, Puccinia graminis f. sp. lolii (Pgl), is unknown. Simple sequence repeat (SSR) markers are being used to assess the diversity in isolates collected from seed producing areas. Eighty-five SSR markers previously used to study stem rust on wheat (Puccinia graminis f. sp. tritici) were tested for amplification in Pgl using polymerase chain reaction (PCR). It was found these SSRs produced PCR products in Pgl and are therefore useful to study Pgl diversity. Drought is another abiotic stress impacting agricultural systems. With diminishing water resources, development of drought-tolerant grass varieties with reduced inputs is essential. Research that advances Sub-objectives 4A and 4B seeks to better understand the genetics of drought tolerance in grasses. Four Lolium perenne grass lines (the cultivar Manhattan, and two drought-sensitive and one drought-tolerant line) were grown and will be utilized for gene expression studies under drought conditions. The plants were treated with fungicide to remove any endophytes, which are symbiotic fungal organisms that may improve a plant's drought tolerance. We are currently conducting drought studies and will generate transcriptomes for control and drought stressed plants for each genotype. We are also in the process of selecting an individual from the endophyte-free Lolium perenne cv Manhattan plants for genome sequencing as part of the National Turf Grass Genome Sequencing Initiative. Another major stress that many grasses are subjected to is mechanical wounding. Transcriptomes from wounded Lolium plants generated from a process known as RNA Sequencing (RNA-Seq) are currently being analyzed. The identification of genes and molecular pathways used by the plant in response to wounding may provide insight and approaches to improve recovery or growth of grasses before or after cutting or grazing. This research addresses Sub-objective 4B. Most stresses have an oxidative stress component; identification and utilization of oxidative stress response factors may provide useful strategies for increasing tolerance to multiple stresses in grasses. Therefore, we are focusing our research on finding regulatory components or factors that modulate the oxidative stress response to increase stress tolerance. In the previous project, we identified four transcription factors (TF) that may be involved in the regulation of oxidative stress in plants and overexpressed them in the model grass species, Brachypodium (Bd). Research on the effect of TF on stress tolerance is part of Sub-objective 4C. Transcription factors are genes that regulate the expression of other genes. Salt stress eventually leads to oxidative stress in many plants; therefore, long-term and short-term salt stress transcriptomes were generated for wild type and previously generated Bd transgenic lines transformed with different TF constructs. A transcriptome is a catalogue of all genes expressed by plant tissues, in this case while under stress conditions. We are currently analyzing plants for their tolerance to salt stress and are conducting a detailed analysis of salt stress induced transcriptomes for Bd overexpressing a transcription factor that was previously shown to be induced upon exposure to multiple stresses.


Review Publications
Dombrowski, J.E., Kronmiller, B.A., Hollenbeck, V.G., Rhodes, A., Henning, J.A., Martin, R.C. 2019. Transcriptome analysis of the model grass Lolium temulentum exposed to green leaf volatiles. Biomed Central (BMC) Plant Biology. 19:222.
Kesoju, S., Greene, S.L., Martin, R.C., Kramer, M.H., Walsh, D., Boydston, R.A. 2019. Isolation distances for transgenic alfalfa seed production in the Pacific Northwest. Crop Science. 59(4):1701-1708.
Hernandez, J., Steffenson, B.J., Filichkin, T., Fisk, S.P., Helgerson, L., Meints, B., Vining, K.J., Marshall, D.S., Del Blanco, A., Chen, X., Hayes, P.M. 2019. Introgression of rpg4/Rpg5 into barley germplasm provides insights into the genetics of resistance to stem rust race TTKSK. Phytopathology. 109:1018-1028.
Doug, J.K., Scott, J.C., Cheng, Q., Alderman, S.C., Kaur, N., Walenta, D.L., Kenneth, F.E., Hamm, P.B. 2018. Detection and quantification of airborne Claviceps purpurea sensu lato ascospores from hirst-type spore traps using real-time quantitative PCR. Plant Disease. 102:2487-2493.
Dung, J.K., Kaur, N., Walenta, D.L., Alderman, S.C., Frost, K.E., Hamm, P.B. 2018. Reducing Claviceps purpurea Sclerotia germination using soil-applied fungicides. Crop Protection. 106:146-149.