Transcriptome Dynamics of the Dormancy - Growth Transition in Douglas-Fir Needles

In temperate zone trees, the onset of spring growth requires the integration of environmental cues from many organs. We examined transcriptome variation in Douglas-fir needles over a 99-day interval spanning the transition from dormancy to growth. Our study uses common-garden grown trees that derive from different climate zones, and show differences in the timing of spring growth. Illumina-based RNA-seq was conducted on 12 trees over four time points, and analysis by negative-binomial GLM was used to partition expression variation to date, geographic source, and family. Approximately 85,000 transcripts were detected in needles, and 33,608 transcripts met our minimum threshold (median > 5). From this reduced pool of transcripts, 53% fit a “date variation” model, 12% fit a “source-within-date” model, 3% fit a “family-within-source-and-date” model, and 32% were not variable by date. Cluster analysis of all date transcripts shows that 34% are down-regulated, 26% are up-regulated, and 20% show transient changes that coincide with the onset of spring growth. Enriched terms for down-regulated transcripts include genes associated with organelle repair, function and transport, while up-regulated transcripts include genes associated with cellular organization, secretory functions, heat stress responses and secondary metabolism. Finally, we contrast seasonal variation with diurnal variation to highlight the genes that are most sensitive to sampling time. These analyses provide a resource for dissecting daily and seasonal transcriptome variation in conifer needles, and a reference for identifying environmentally responsive genes in conifers that lack obvious homologs in angiosperms.