RESEARCH-PGR: Functional Genomics of Beneficial Legume-microbe Interactions

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Legume crops are a primary source of food for humans, feed for livestock, and raw materials for industry. Legumes are integral to sustainable agricultural systems by virtue of symbiotic nitrogen fixation with bacteria called rhizobia, which injects 50 million tons of fixed-nitrogen into such systems annually. Legumes also form beneficial arbuscular mycorrhizal symbioses with soil fungi, which enhance the acquisition of soil phosphorous and other nutrients. These two symbioses enable productive plant cultivation with less fertilizer, which reduces the environmental impact of agriculture. Focusing on the legume species, Medicago truncatula this project will identify key plant genes required for symbiosis with bacteria and/or fungi and advance our understanding of what are arguably the two most important plant-microbe symbioses in agriculture. This project brings together seven research groups from six research and teaching institutions in five states to form a world-class, virtual center for legume symbiosis research that will generate great synergy and provide outstanding trans-disciplinary training opportunities in genomics, bioinformatics and other disciplines. Training will be provided at career levels ranging from postdoctoral researchers, graduate students, to undergraduate students with the aim of developing skillsets necessary for successful scientific careers. Outreach components of this project will engage high & middle school students, adults in the general public and children in educational and fun scientific experiences. The proposed activities will benefit society by helping to train the next generation of scientists and by helping to make agriculture more sustainable and environmentally-friendly.Legumes are integral to sustainable agricultural systems by virtue of symbiotic nitrogen fixation (SNF) with bacteria called rhizobia, and beneficial arbuscular mycorrhizal (AM) symbioses with soil fungi that enhance the acquisition of soil phosphorous and other nutrients. Although thousands of plant genes have been associated with these symbioses via transcriptome studies, the symbiotic role and importance of most of these genes remain unclear. Focusing on the legume, Medicago truncatula this project will take advantage of a very large existing Tnt1 transposon-insertion mutant population for functional genomics of SNF and AM symbiosis. One hundred and ninety Tnt1 insertion mutants with novel Nod+Fix- or regulatory phenotypes have already been identified in a genome-wide non-biased forward genetic screen. New sequence-capture technologies will accelerate the identification of the causal mutations enabling the identification of new genes involved in nitrogen fixation and autoregulation of nodulation. Functional genomics activities, enabled by a large Tnt1 mutant population and indexed flanking sequence tag resource will focus on transporter proteins involved in nutrient transport during rhizobial and AM symbioses. A combination of Tnt1 mutants and mutants generated through CRISPR-Cas9 genome editing will be used to investigate a set of 138 genes conserved for AM symbiosis identified previously through a comparative phylogenomics approach. Together, these activities will identify key symbiotic genes and advance our understanding of two plant-microbe symbioses that are crucial for sustainable agriculture.