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

In temperate zone trees, spring growth represents the outcome of a complex interplay between competing physiological processes of stasis and growth, and the integration of environmental signals from diverse sensory organs. To understand needle-mediated inputs to annual growth, we are examining transcriptome changes in Douglas-fir (Pinaceae) needles during the transition from winter dormancy to spring growth. Our study uses common-garden grown families from three sources with different climate (warm/dry; mesic/wet; cold/wet) and that show different timing for spring growth. This allows us to partition gene expression variation to geographic source, family, and individuals. Using high-throughput RNA-seq, we generated 489 M strand-specific single-end reads and used de novo assembly methods to assemble a “needle-specific” transcriptome reference for Douglas-fir. This reference includes 90,730 gene models totaling 78.2 Mbp. RNA-seq mapping at 4 time points over 99 days (dormancy to growth) detects 85,708 gene models; for our analysis, we focused on 30,395 gene models showing a median > 5 mapped reads. Using this reduced gene set, analysis by negative binomial GLM shows that “sample date” accounts for 16,382 differentially expressed transcripts, and that “seed source within date” accounts for 3,440 differentially expressed transcripts. Hierarchical clustering of differentially expressed genes reveals that a decrease in transcript abundance is the most frequent pattern, exhibited by nearly 70% of genes. Our results suggest that the resumption of spring growth is accompanied by a massive re-patterning of the needle transcriptome (and possibly the proteome) that resets the conditions for a new season of growth.