Red alder - Frankia symbiosis

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. We are developing an omics-based research foundation upon which
 to base a breeding and improvement program, aimed at further improving tolerance to abiotic stresses and increasing marginal land area devoted to its growth. We aim to
 develop insights into interactions among tree genotype, rhizosphere microbiome, root transcriptome, symbiont (and other endophyte) transcriptomes, and soil characteristics during
 a seasonal cycle on good and marginal soil types. Objectives: 1. Create a de novo genome reference assembly of an elite red alder clone that outperforms all other known clones.
 2. Create reference genome sequences and epigenomic signatures of the five Frankia strains that result in the best tree performance and symbiosis.
3. Develop a dense set of molecular markers to enable accelerated predictive breeding and improvement. 4. Develop insights into 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. Methods: 1. PacBio sequencing. De novo assembly and physical map integration. 2. PacBio sequencing with epigenetic modifications determined using the SMRTanalysis suite. 3. Genotyping by sequencing of 350 tree lines using the TASSEL-GBS pipeline. 4. 16s rRNA survey of rhizosphere microbial communities in the field and under experimental conditions. Root and nodule RNA
seq (tree roots and and their associated endophytes).

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