Extensive Transcriptome Changes during Natural Onset and Release of Vegetative Bud Dormancy in Populus

Endodormancy is a state of suspended plant growth maintained in harsh environments or even during favorable growing periods.  To explore genetic basis of vegetative bud endodormancy, we collected paradormant, endodormant, and ecodormant axillary buds from Populus trichocarpa trees growing under field conditions in western Oregon.  Of 44,441 gene models analyzed by NimbleGen microarrays, 4% were differentially expressed among at least two dormancy states (false discovery rate p-value < 0.05).  Of all differentially expressed genes, 69% were down-regulated from paradormancy to endodormancy, suggesting an overall reduced metabolic activity during endodormancy.  Multiple chromatin-associated genes showed different expression levels in three states, and two of them (similar to SPT, SUPPRESSOR OF TY) were strongly up-regulated during endodormancy.  Transcription factor genes that showed atypically increased expression during endodormancy include a gene that seems to encode a trihelix transcription factor, and genes associated with proteins involved in responses to ethylene, cold, and other abiotic stresses.  Analyses of phytohormone-associated genes suggest important changes in responses to ethylene, auxin, and brassinosteroids occur during endodormancy.  Weaker or little changes were found in genes associated with salicylic acid, jasmonic acid, gibberellins, abscisic acid, and cytokinin.  We identified 315 upstream sequence motifs associated with eight patterns of gene expression, including novel motifs and motifs previously associated with the circadian clock and responses to photoperiod, cold, dehydration, and ABA.  Analogies between the regulation of flowering and endodormancy suggest important roles for genes similar to SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL), DORMANCY ASSOCIATED MADS-BOX (DAM), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1).