Gene expression and alternative splicing responses to abiotic stress in sunflower and canola

Understanding the genetics and physiology of plant responses to abiotic stresses may offer insights into how crops might be modified to better avoid or tolerate such stresses. For my dissertation, I studied transcriptional (gene expression) and post-transcriptional (alternative splicing - AS) responses of canola and sunflower to several different abiotic stresses. First, I generated transcriptome data for canola, Brassica napus L., under heat, cold, and drought stress conditions. Brassica napus is an allotetraploid crop plant derived from B. rapa (AT) and B. oleracea (CT). Therefore, I focused on changes in gene expression and AS between homoeologous pairs of genes. I identified overall AT subgenome biases in gene expression and CT subgenome biases in the extent of alternative splicing under all three stress treatments. My results suggest that divergence in gene expression and AS patterns between duplicated genes may increase the flexibility of polyploid crops when responding to abiotic stressors. Second, I investigated drought responsive non-additive expression and AS events in parental and hybrid sunflower (Helianthus annuus L.) cultivars. Sunflower is a hybrid crop, and I employed well-characterized maternal and paternal lines and their F1 hybrid for this experiment. I showed that the expression of genes that were missing one or the other parental lines was complemented in the hybrid in both the control and drought treatment, offering a straightforward explanation for hybrid vigor or heterosis. Heterosis under drought stress was further associated with down-regulation of unnecessary metabolic pathways, via both a reduction in gene expression levels and an increase in non-functional splice forms. Lastly, using mixed model and gene co-expression network approaches, I found that up-regulation of ethylene-responsive transcription factors and down-regulation of metabolic, energy production, and photosynthesis-related pathways occurred in both the resistant and susceptible sunflower cultivated lines, and thus represent general responses to flooding stress. Greater flooding tolerance of the resistant line was associated with earlier and stronger up-regulation of the alcohol fermentation pathway and more rapid recovery of pre-flooding gene expression levels. Thus, adjustments to the timing of gene expression responses appear critical for establishing flooding stress tolerance in sunflowers.Science, Faculty ofBotany, Department ofGraduat