Transcriptomic Changes Due to Water Deficit Define a General Soybean Response and Lineage-Specific Pathways of Drought Avoidance

Among abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI416937 is somewhat robust to water deficit and has been used previously to map the trait in a biparental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean. Contrasting data from PI416937 and a sensitive cultivar, we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit. These responses involve not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI416937's unique drought avoidance strategy. Interestingly, genes that showed genotypic differences in expression were more likely to show an environmental response compared with genes that did not. This finding suggests that genes that differ in expression between genotypes generally function in stress response, as would be expected for transcriptional regimes that have been selected under unique local conditions.