RESEARCH-PGR: Deciphering the molecular basis of elite red alder lines and their Frankia alni symbionts

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Red alder is a hardwood tree of economic importance in the Pacific Northwest, exceeding the annual value of the dominant softwood species Douglas-fir. Red alder is used for quality cabinetry, utensils and handles, and as a biomass/biofuels crop. It grows in inhospitable environments and on unproductive land, meaning that it does not compete with food production. Demand for saplings suitable for planting currently greatly exceeds supply. With better understanding of its genetics, scientists would be able to breed trees that grow faster and in more inhospitable environments. This would expand the area available for growing, and increase the annual yield for timber and biomass fuel. Additionally, red alder does not require nitrogen fertilizers. It achieves this by harnessing Frankia, a microbe, to provide the nitrogen for it. The relationship between the tree and the microbe requires scientific study. Some Frankia strains are better than others, and some combinations of tree and microbial strains are well suited to certain environments. This project seeks to understand how the red alder genetics, soil type, Frankia strain, and other bacteria in the soil interact to promote tree growth. The result will be the ability to develop new tree strains suited to certain environments, to expand planting to meet growing demand. The project includes training opportunities for students (high school through graduate level) and supports a high school summer innovation academy that targets underserved students. It promotes access to research by native and Hispanic underrepresented groups.Red alder (Alnus rubra Bong.), has significant economic importance, yet is an orphan in terms of scientific understanding of its genetic variability and its relationship with its nitrogen-fixing symbiont Frankia alni. This project will create an omics-based resource upon which to base a breeding and improvement program, aimed at improving tolerance to abiotic stresses and growth in marginal land area. Objectives are to create the following: (1) a de novo genome reference assembly of an elite high-performing red alder clone, using PacBio sequencing and BioNano physical mapping, (2) reference genome sequences and epigenomic signatures of the five Frankia strains that result in the best tree performance and symbiosis, using PacBio sequencing with epigenetic modifications determined using the SMRTanalysis suite,(3) a dense set of molecular markers to enable accelerated predictive breeding and improvement, through genotyping of 350 tree lines using the TASSEL-GBS pipeline, and (4) measurements of interactions among tree genotype, rhizosphere microbiome, root transcriptome, symbiont (and other endophyte) transcriptomes, and their impacts on juvenile tree growth on good and marginal soils, through 16s rRNA surveys of rhizosphere microbial communities. The project includes a summer science outreach program for underserved high school students.