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Harnessing Natural Variation in the Crop Model Grass Brachypodium Distachyon to Elucidate Microbial Associations that Improve Plant Growth

Principal Investigator/Project Leader: 
Ana L.
Co-Principal Investigator/Co-Project Leader: 
Department of Project: 
Biology Dept.
Project Description: 

Current agricultural practices on available arable land will not meet the nutritional needs of a population that will reach nine billion people by the middle of this century (Ray et al. 2013). In parallel, climate change will increase extreme weather events, including drought (Dai, 2011, Trenberth et al., 2014), and continued urbanization of farmland is eliminating arable land (Song et al. 2015). There is a clear need for sustainable agricultural innovations that can increase yields and provide food security without incurring environmental degradation. Soil microbes are known to form associations with plants and affect plant health, and in recent years, interest has grown in exploiting the beneficial associations that plants establish with microbes. The plant microbiome abounds with plant growth-promoting rhizobacteria (PGPR) that can help plants acquire more nutrients from the soil and tolerate stressors like drought (Barnawal et al. 2013, Bresson et al. 2014). PGPR can also control plant pathogens (Chowdhury et al. 2013), promote beneficial mycorrhizal colonization (Labbe et al. 2014), and produce potentially valuable secondary metabolites (Raaijmakers et al. 2012). Finding ways to harness these beneficial microbes to improve crop growth and yield has the potential to ameliorate the challenges imposed by the world's growing population and environmental degradation.                                                                                                                                                                                                                                                                                                We recently partnered with the startup company, Endobiome (, to explore the effects of potentially beneficial PGPR on plant growth. Endobiome uses a systems biology approach to discover microbes that enhance agricultural productivity and sustainability, and has created an efficient rhizobacterial isolation system. However, they have a need for efficient testing of these isolates in plant systems to discover which are the most likely to be useful for agricultural applications. With a pilot study, we demonstrated that the grass model species, Brachypodium distachyon, can serve as an ideal plant system for screening and evaluation of PGPR. As a genetically tractable species that is easily grown in a laboratorysetting, and is closely related to wheat, rye, oats, barley, and several forage grasses, B. distachyonoffers a tractable screening system that is likely to ensure translation of findings to relevant crops.  Building on the potential revealed by our pilot project and our expertise in functional and evolutionary genomics of B. distachyon, here we propose to develop this model species as an efficient and high-throughput plant system in which to investigate PGPR with agricultural applications and the molecular mechanisms governing PGPR interactions. With the research proposed, we will develop robust protocols that will permit identification of microbial strains that provide improved growth across different plant genotypes and identify the growth phenotypes most impacted by microbial strains. We will further establish a set of PGPR that will permit assessment of the genetic basis of successful microbe-genotype interactions by harnessing the power of genome-wide association studies (GWAS) and the diversity of genotypes available for B. distachyon.  Our project will have very clear industrial and societal benefits. Commercialized biologicals for agriculture are a rapidly growing biotechnology sector, predicted to have a compound annual growth rate of 14% by 2022. BASF, EndoBiome, Ginko Bioworks, Indigo, and Monsanto are heavily or exclusively involved in the arena of biologicals for agriculture, all with facilities in Massachusetts. Genoverde Biosciences, GreenLight Biosciences, Inari Agriculture, and Yield10 Biosciences are Massachusetts Ag Biotech companies, two of which license UMass intellectual property. Successful product development by these companies has the potential to revolutionize agriculture by providing environmentally sound ways to increase crop yields. Endobiome, for example, targets wheat, corn and soybean growers, with outputs worth about $1 trillion globally each year. Our proposal will expand on corporate areas of expertise and will provide unique workforce training and research collaborations to facilitate continued growth in the plant microbe industry. Developing an efficient system in which to evaluate the output of these companies benefits Massachusetts biotechnology investments as well as national goals toward more sustainable and productive agriculture.  Scientific knowledge will also be advanced through our efforts. Our team has been at the forefront of assembling a diverse germplasm collection of the grass model B. distachyon and at generating genomic resources for use in gene identification via genome-wide association studies (GWAS). Many of these activities were carried out with previous Hatch funding and put us in a unique position to leverage said resources for investigating the genetic basis of genotype-specific microbial interactions. By characterizing phenotypic diversity for microbial interaction and identifying underlying loci in a model species, we are also accelerating the discovery of similar genes in energy, cereal, and forage crops and ensuring translation of our findings to agriculture.


Agriculture topics: 
Crop and Cropping System
Field Crops
Energy topics: 
Biomass/ Biofuels