Genome-Wide Expression and Alternative Splicing in Domesticated Sunflowers (Helianthus annuus L.) under Flooding Stress

Approximately 10% of agricultural land is subject to periodic flooding, which reduces the growth, survivorship, and yield most crops, reinforcing need understand enhance flooding resistance in our crops. Here, we generated RNA-Seq data from leaf root tissue domesticated sunflower explore differences gene expression alternative splicing (AS) between a resistant susceptible cultivar under both control conditions at three time points. Using combination mixed model co-expression analyses, were able separate general responses stress those that contribute greater tolerance line. Both cultivars responded by upregulating levels known submergence responsive genes, such as alcohol dehydrogenases, slowing metabolism-related activities. Differential AS reinforced differences, with reduced frequencies typically observed for genes upregulated expression. Significant found genotypes, including earlier stronger upregulation fermentation pathway more rapid return pre-flooding genotype. Our results show how changes timing following induction release increased tolerance.