Location: Plant Science Research
Project Number: 5062-21500-001-000-D
Project Type: In-House Appropriated
Start Date: Feb 27, 2024
End Date: Feb 26, 2029
Objective:
Objective 1: Develop genomic tools for alfalfa to accelerate breeding and facilitate identification and validation of genes for important agronomic traits.
Sub-objective 1.A: Compare alfalfa genomes to improve understanding of genome architecture and complexity.
Sub-objective 1B: Identify DNA markers associated with biotic stresses to facilitate germplasm development.
Subobjective 1C: Improve transformation and gene editing in elite genotypes to accelerate field testing of novel edited plants.
Objective 2: Develop breeding methods and understanding of genetic control of important agronomic traits in alfalfa for plant improvement.
Sub-objective 2.A: Improve environmental resiliency and abiotic stress tolerance in alfalfa using genomic selection and machine learning.
Sub-objective 2.B: Develop alfalfa germplasm with enhanced forage quality and digestibility.
Sub-objective 2.C: Develop germplasm with novel root traits that enhance herbage biomass and utilization of alfalfa in agroecosystems.
Sub-objective 2.D: Develop novel germplasm with protein and nutritional profiles desired in human food products.
Objective 3: Establish innovative methods and new standards for assessing and evaluating alfalfa quality for multiple uses.
Sub-objective 3.A: Quantify and characterize variability of non-structural carbohydrates in alfalfa for improved nutritive value.
Sub-objective 3.B: Increase alfalfa fiber digestion by the investigation of cell wall lignification and digestion in alfalfa with reduced lignin concentrations.
Objective 4: Increase understanding of the interactions among forage crops, soils, and microbiomes to reduce risk, improve agronomic outcomes, and build resilience.
Sub-objective 4.A: Evaluate the impacts of alfalfa cultivar, cutting frequency, and fall dormancy on root production, root turnover, root litter quality, C inputs to soil, and interactions with microbial communities.
Sub-objective 4.B: Develop methods to isolate, identify, and characterize emerging plant pathogens.
Sub-objective 4.C: Evaluate alfalfa establishment and termination strategies, diverse crop rotations, and winter annual cover crops for improving soil C balances and reducing greenhouse gas emissions.
Sub-objective 4.D: Measure total root biomass, root:shoot ratios, root responses to management, and C fractions in forage systems to improve C accounting and model parametrizations of alfalfa and other forage crops.
Approach:
Alfalfa is the engine that drives dairy and beef production and is unparalleled for providing environmental services. However, the slow progress in increasing forage yield and re-establishment costs after winter injury have discouraged greater utilization of alfalfa. Modern breeding methods and -omics technologies provide the opportunity to break the yield bottleneck, improve plant persistence and forage nutritive value, and develop novel products and environmental services. In support of these goals, we will assemble, annotate, and carry out an in-depth characterization of the alfalfa genome for structural and repeat number variants using bioinformatic tools. DaRTag SNP markers will be used to identify superior germplasm with improved winter survival, greater forage nutritive value, and root architecture to increase yield potential, and to identify markers associated with resistance to major yield-limiting diseases. Methods will be developed to improve alfalfa gene editing in diverse germplasm. Compositional analyses of alfalfa herbage using biochemical and chromatographic methods will lay the groundwork for utilization of alfalfa in human food products. In-depth analyses of stem cell wall development and ruminal degradation will be done to gain a better understanding of developmental and structural changes that improve forage quality. High throughput sequencing and metagenomic analyses will help fill knowledge gaps in the composition and function of key microbial communities associated with alfalfa in diverse soils and with biotic and abiotic stress. Conventional and novel crop rotations utilizing forages will be evaluated for their effect on greenhouse gas emissions and carbon sequestration using field-scale eddy covariance flux measurements and measurements of total root biomass, root:shoot ratios, root responses to management, and C fractions in forage systems to improve C accounting and model parametrizations of alfalfa and other forage crops.
