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United States Department of Agriculture

Agricultural Research Service


Location: Plant Science Research

2013 Annual Report

1a. Objectives (from AD-416):
Objective 1: Develop germplasm and determine genetic and biological processes that regulate forage use for bioenergy and livestock production. Sub-objective 1.1. Identify genes and breeding strategies to be used for alfalfa improvement. Sub-objective 1.2. Improve energy availability from forages by modifying genetic, metabolic, and developmental processes that control cell wall synthesis and breakdown. Sub-objective 1.3. Identify and utilize mechanisms to improve nutrient uptake in Medicago spp. Objective 2: Develop and evaluate crop management strategies to increase use of perennial forages for livestock and bioenergy, and to protect the environment. Sub-objective 2.1. Develop management practices and systems to optimize alfalfa composition and biomass yield for the efficient production of liquid fuels and syngas. Sub-objective 2.2. Evaluate strategies to reduce root and foliar disease in alfalfa. Sub-objective 2.3. Develop and test management strategies to expand the role of alfalfa and other perennial forages in protecting water quality.

1b. Approach (from AD-416):
Alfalfa is the backbone of sustainable practices for producing crops and animals while protecting water and soil resources. However, use of alfalfa is not always maximized due to several limitations, and new germplasm and management systems are needed for biofuel production. The objectives of this project are to: (1) develop germplasm and determine genetic and biological processes that regulate forage use for bioenergy and livestock production, and (2) develop and evaluate crop management strategies to increase use of perennial forages for livestock and bioenergy, and to protect the environment. Alfalfa germplasm with greater stem in vitro neutral detergent fiber digestibility (IVNDFD) will be developed through selection and breeding utilizing near-infrared reflectance spectroscopy. Populations will be assessed for changes in cell wall chemistry and biofuel conversion under conventional and biomass management systems. Breeding strategies will be evaluated to increase yield potential. Yield will be evaluated in replicated field trials in multiple locations. Populations with highest yield will be evaluated for total forage yield under conventional and biomass management systems. Management methods for reducing diseases that impact yield and persistence will be assessed. The effect of glyphosate on foliar diseases (rust, powdery mildew, anthracnose, spring black stem) will be evaluated in Roundup Ready alfalfa. Alfalfa cultivars will be screened for resistance to brown root rot and the role of crop debris in pathogen survival and increase will be measured. The potential for green manures and traffic tolerance to reduce crown rot will be evaluated. Genes for disease resistance, cell wall biosynthesis, and nutrient uptake will be isolated to provide new knowledge on the genetic underpinnings of these traits and markers for plant improvement. Transcript profiling will be done to identify candidate genes involved in these traits. The function of specific genes will be investigated through detailed transcript expression studies, investigating promoter activity, biochemical assays, over-expression, and gene knock down. Alfalfa germplasm with greater capacity to remove soil nitrate will be developed by recurrent selection using bromide as a nitrate analog. Populations will be evaluated in multiple field locations for bromide and nitrate uptake. Removal of nitrogen from soil by alfalfa will be tested at the field scale in replicated plots in multiple locations. Forage samples will be analyzed for dry matter and N yield; topsoil will be measured for total N and C. Removal of nitrate from irrigation water via phytofiltration will be tested on a field scale. Replicated plots will be irrigated at normal, high, and intermediate rates and the total nitrate leached determined. Biocurtain strips along tile drainage sites will be managed using conventional and biomass systems along side a corn-soybean rotation. Inorganic N will be measured throughout the growing season in tile drainage water. Fulfilling the objectives will help meet the emerging needs of the nation in livestock and bioenergy production and environmental protection.

3. Progress Report:
This project terminated in 2013. This project developed improved alfalfa for livestock production with greater potential resilience in a changing climate; tools for alfalfa improvement; and crop management strategies to increase alfalfa persistence and yield, reduce inputs, and reduce nutrient losses to the environment. Alfalfa with increased energy available to ruminants was developed by selecting plants with increased stem fiber digestibility. A high throughput assay (near infrared spectroscopy, NIRS) was developed to accelerate the selection of more digestible stems. Evaluations are in progress for digestibility at different stages of forage maturity to enable farmers to have greater flexibility in harvest timing. Increased digestibility reduces feed costs and manure production. A novel selection method was developed and used to produce alfalfa lines that were either much better at removing nitrate from the soil to help prevent nitrate losses directly, or less capable of nitrate uptake so neighboring plants such as grasses can thrive while removing the nitrate. Nitrogen is an essential element for crop production, but nitrate, the most important form of nitrogen available to plants, tends to 'get away', polluting water supplies and increasing global warming. This new plant selection procedure provides plant breeders a reliable way to change nitrate uptake capacity in alfalfa and other plants, which should lead to better crop production and less environmental damage. Alfalfa lines were selected for highly branched root systems that are more beneficial under low nutrient supply and highly tap-rooted types that are better at finding water deep in the subsoil during drought. The root system architecture was expressed consistently across environments and also appeared to affect nutrient uptake. The first alfalfa gene index was generated using unique alfalfas selected for cellulosic biofuel production having either increased or reduced cellulose and lignin in stem cell walls. Genes regulating cell wall composition and DNA markers distinct in each line were identified. A NIRS assay was developed to rapidly predict the cell wall composition and potential ethanol production. Diseases reduce forage yields and plant persistence. Alfalfa cultivars were identified with greater persistence under brown root rot pressure. Specific rotation crops were identified that reduce the pathogen density in soil and enable fields to be brought back into high productivity. The herbicide glyphosate was found to protect glyphosate tolerant cultivars from damage by rust disease and reduce damage from other foliar diseases. Incorporating buckwheat or sorghum-sudangrass green manures increased pathogen suppression in soil and treatment increased forage yield under wheel traffic stress. An extensive set of on-farm trials showed no nitrogen fertilizer is required on most farms by the first corn crop after the alfalfa stand is terminated and incorporated, even when corn yields exceed 230 bushels/acre. This represents a fertilizer savings of more than $80/acre compared to corn grown after corn and will reduce potential nitrate water contamination and greenhouse gas emissions.

4. Accomplishments

Review Publications
Tesfaye, M., Silverstein, K.T., Nallu, S., Wang, L., Botanga, C.J., Gomez, S., Harrison, M., Samac, D.A., Glazebrook, J., Katagiri, F., Gutierrez-Marcos, J.F., VandenBosch, K.A. 2013. Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes. PLoS One. 8(3):e58992.

Nallu, S., Silverstein, K.A., Samac, D.A., Bucciarelli, B., Vance, C.P., VandenBosch, K.A. 2013. Regulatory patterns of a large family of defensin-like genes expressed in nodules of Medicago truncatula. PLoS One. 8(4):e60355.

Castell-Miller, C.V., Samac, D.A. 2012. Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris). Plant Pathology. 61(5):903-914.

Gronwald, J.W., Bucciarelli, B. 2013. Comparison of stem morphology and anatomy of two alfalfa clonal lines exhibiting divergent cell wall composition. Journal of the Science of Food and Agriculture. 93:2858-2863.

Lamb, J.F., Jung, H.G., Riday, H. 2012. Harvest impacts on alfalfa stem neutral detergent fiber concentration and digestibility and cell wall concentration and composition. Crop Science. 52(5):2402-2412.

Yost, M.A., Coulter, J.A., Russelle, M.P. 2013. First-year corn after alfalfa showed no response to fertilizer nitrogen under no-tillage. Agronomy Journal. 105(1):208-214.

O'Rourke, J.A., Yang, S.H., Miller, S.S., Bucciarelli, B., Liu, J., Rydeen, A., Uhde-Stone, C., Tu, Z., Allan, D., Gronwald, J.W., Vance, C.P. 2012. An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiology. 161(1):705-724.

Yost, M.A., Russelle, M.P., Coulter, J.A. 2013. Nitrogen requirements of first-year corn following alfalfa were not altered by fall-applied manure. Agronomy Journal. 105(4):1061-1069.

Last Modified: 10/17/2017
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