Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean

Authors: O`Rourke, Jamie; McCabe, Chantal; Graham, Michelle

Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2019
Publication Date: 10/26/2019
Citation: O'Rourke, J.A., Mccabe, C.E., Graham, M.A. 2020. Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean. Functional and Integrative Genomics. 20:321-341. https://doi.org/10.1007/s10142-019-00709-9.
DOI: https://doi.org/10.1007/s10142-019-00709-9

Interpretive Summary: Plants require 17 nutrients for proper growth and development. Iron (Fe) deficiency is a widespread problem throughout the major soybean growing regions of the United States. Similarly, phosphate (Pi) is often provided to plants as costly fertilizer. This experiment looked at all the genes expressed in soybean leaves and roots in response to either iron or phosphate deficiency stress, after one and two rounds of nutrient stress. In the case of iron, soybean gene expression responds to deficiency, returning to little gene activity when iron in resupplied. In contrast, soybean fails to responds to phosphate deficiency, instead responding when phosphate is resupplied. Interestingly, the same biological pathways were affected by both nutrients. Finally, we identified so called “memory” genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress exposure. Together, these genes likely play important roles in regulating plant stress responses. While similar experiments have been done in model species, it is important to remember that crop species have been selected for improved yield for thousands of years, often in unique environments. Conducting these experiments in crops, will identify novel adaptations to nutrient stress that can be leveraged for crop improvement.

Technical Abstract: Preserving crop yield is critical for United States soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the U.S., and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole genome expression responses of leaves and roots to iron (Fe) and phosphate (Pi) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 hours. While soybean responds largely to -Fe deficiency, it responds strongly to Pi resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3,375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.