Anthropogenic activities have substantially modified natural forested ecosystems around the world through species exploitation, land-use changes, soil degradation, pollution and introduction of exotic species. The impacts of these activities are being exacerbated today by climate change that is expected to become more severe over the coming decades. Modern landscape genomics has made advances in identifying genes that are associated with phenotypic expression, but they have been unable to prove that the associations are more than correlative. The threats to biological diversity raised by climate change, underscore the need to have an improved understanding of the genetic basis of phenotypic traits. In sedentary, long-lived tree species this becomes of utmost importance, as the success of populations is likely to depend, in large part, on existing standing genetic variation. The most recent technologies of gene editing (CRISPR/Cas9) promise to be an elegant approach that will move forest tree genomics to the next level, by allowing the rigorous testing of gene function and its role in the adaptation of trees to their environment. This perspectives paper looks at how genome editing technologies can be used to advance our understanding of the role genes play in adaptation to climate change in woody plants. We discuss the different CRISPR modes than can be used in studies of adaptive traits in perennial species.

It has recently been described that the Japanese plum "Santa Rosa" bud sport series contains variations in ripening pattern: climacteric, suppressed-climacteric and non-climacteric types. This provides an interesting model to study the role of ethylene and other key mechanisms governing fruit ripening, softening and senescence. The aim of the current study was to investigate such differences at the genomic level, using this series of plum bud sports, with special reference to genes involved in ethylene biosynthesis, signal transduction, and sugar metabolism. Genomic DNA, isolated from leaf samples of six Japanese plum cultivars ("Santa Rosa", "July Santa Rosa", "Late Santa Rosa", "Sweet Miriam", "Roysum", and "Casselman"), was used to construct paired-end standard Illumina libraries. Sequences were aligned to the Prunus persica genome, and genomic variations (SNPs, INDELS, and CNV's) were investigated. Results determined 12 potential candidate genes with significant copy number variation (CNV), being associated with ethylene perception and signal transduction components. Additionally, the Maximum Likelihood (ML) phylogenetic tree showed two sorbitol dehydrogenase genes grouping into a distinct clade, indicating that this natural group is well-defined and presents high sequence identity among its members. In contrast, the ethylene group, which includes ACO1, ACS1, ACS4, ACS5, CTR1, ERF1, ERF3, and ethylene-receptor genes, was widely distributed and clustered into 10 different groups. Thus, ACS, ERF, and sorbitol dehydrogenase proteins potentially share a common ancestor for different plant genomes, while the expansion rate may be related to ancestral expansion rather than species-specific events. Based on the distribution of the clades, we suggest that gene function diversification for the ripening pathway occurred prior to family extension. We herein report all the frameshift mutations in genes involved in sugar transport and ethylene biosynthesis detected as well as the gene CNV implicated in ripening differences.