Whole Genome Resequencing-Enabled Discovery and Functional Validation of Allelic Variants Associated with Cell Wall Chemistry and Mycorrhizal Symbiosis in Populus

A whole genome re-sequencing effort targeting the model tree and biofuels feedstock Populus was implemented under the auspices of the US-Department of Energy (DOE) to facilitate the elucidation of molecular processes leading to sustainable improvement of lignocellulosic biofuels production. We have successfully leveraged this whole-genome re-sequencing resource in combination with QTL and LD-based association mapping to clone loci affecting divergent phenotypes including cell wall recalcitrance and Populus-laccaria mycorrhizal symbiosis. QTL intervals ranging from 0.5 to 1.4 Mb identified in a pseudo-backcross pedigree were resolved to intervals less than 10 kb harboring single candidate genes. Based on protoplast transient expression assays, allelic differences were observed in pathway activation of marker genes associated with the lignin, cellulose and hemicellulose pathways for 2 transcription factors and a protein kinase. The same resource was brought to bear in cloning a major QTL contributing up to 60% of the phenotypic variance explained in colonization by the fungal symbiont Laccaria bicolor of F₁ progeny from a P. trichocarpa x P. deltoides pedigree. We identified a species-specific whole-gene deletion in P. deltoides which co-segregated with colonization efficiency. This gene was absent in 60 P. deltoides genotypes from diverse geographical origins but was highly conserved in 673 P. trichocarpa genotypes evaluated. Variants resulting in up to 3X more ethanol yield and 2X more colonization by the fungal symbiont have been identified in Populus. Deployment of favorable alleles of these genes using traditional breeding and transgenic approaches will contribute towards the economic viability of Populus-based biofuels.