Harnessing the potential of natural loss-of-function allelic variants in wild poplar germplasm for accelerated forest tree domestication

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While medical research has had great success recently in correlating phenotypes (disease, e.g.) with rare defective alleles (premature or abolished stop codons, altered start codons, alternative splice sites in genes), there has been no systematic exploration of such connection in forest trees, yet, few already detected natural loss-of-function alleles could be connected with advantageous wood phenotypes (substantially less lignin, e.g.) and have therefore high potential for accelerating wood improvement in the context of tree breeding. The access to such rare mutations in tree genomes and their carriers is now facilitated by next-generation sequencing. The proposed research under the NSERC DG program aims at linking wood components' valorization and in-forest genomic selection tools and in this respect demonstrate the feasibility and provision of a roadmap towards the future use of gene function discovery and exploitation approach in tree breeding. This integrative approach will generally be proof-of-concept for rapid improvement of undomesticated outbred plants. Here, the proposed aim is the generation of substantially improved Populus (poplars) for industrially relevant traits such as improved fibre characteristics from a natural base population. In the pilot study presented here, the gene space (exome) from whole genome sequence data of a large number of natural poplar accessions (c.900) will be investigated for rare functionally defective variants within bio-pathway genes to obtain a pre-selection of candidates. Those variants that will be highlighted in complex trait rare variant association genetics will be further tested; but not in the conventional way through cumbersome rounds of breeding. Carrier of these rare recessive alleles and their offspring are more likely to be heterozygous. Therefore, precise site-specific genome modification technology will be used to introduce biallelic modifications and bypass backcross breeding efforts to obtain homozygous individuals carrying the desired mutation. The proposed genome editing technology (CRISPR/Cas9) can tackle less tractable genotypes and is therefore well suited to perform targeted mutagenesis (via homology-directed repair mediated knock-in) on the best elite varieties originating from a local base population, as proposed here. The new germplasms' performance in terms of a stable, controlled overall phenotype will be further evaluated. Inheritance of the introduced modification in pedigreed families, the desired change in wood fibre properties, stress responses, and adaptation (phenology) will be followed. The project will address many research questions in the context of evolution that relates to selection acting on quantitative traits, and plant breeding, while directly aiming at delivering more productive options for the forest growing and forest product sectors.