Examining short-term responses to a long-term problem: RNA-seq analyses of iron deficiency chlorosis tolerant soybean

Authors: Moran Lauter, Adrienne; RUTTER, LINDSAY - Iowa State University; COOK, DIANNE - Monash University; O`Rourke, Jamie; Graham, Michelle

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/14/2020
Publication Date: 5/19/2020
Citation: Moran Lauter, A., Rutter, L., Cook, D., O'Rourke, J.A., Graham, M.A. 2020. Examining short-term responses to a long-term problem: RNA-seq analyses of iron deficiency chlorosis tolerant soybean. International Journal of Molecular Sciences. 21:3591. https://doi.org/10.3390/ijms21103591.
DOI: https://doi.org/10.3390/ijms21103591

Interpretive Summary: Iron Deficiency Chlorosis (IDC) is a global crop production problem, significantly impacting yield. Since IDC-prone fields are not uniform and IDC tolerant lines tend to have low yield on non-IDC prone soil, farmers prefer to run the risk of using high yielding, IDC susceptible lines. However, in the North central United States IDC yield loss estimates exceed $150 million per year. While various genetic approaches have been used to identify genes involved in iron stress tolerance from model species, these studies ignore the impact of thousands of years of crop improvement. Therefore, this study explores the speed and diversity of the soybean iron stress response to find new avenues for crop improvement. We identified over 10,000 genes whose activity was changed in response to iron stress in an iron stress resistant line. Our analyses revealed that genes involved in iron uptake, defense and regulation of cell replication are hallmarks of the soybean iron stress response. Our findings suggest soybean uses a novel root to shoot signal to initiate the iron stress response. These findings suggest a novel approach for soybean improvement and highlight the need for conducting additional IDC studies in diverse, agronomically important crop species.

Technical Abstract: Iron Deficiency Chlorosis (IDC) is a global crop production problem, significantly impacting yield. To understand the speed and diversity of the soybean iron stress response, we conducted RNA-seq of leaf and root tissue from the iron efficient soybean (Glycine max) cultivar Clark, at 30, 60 and 120 minutes after transfer to iron stress conditions. We identified over 10,000 differentially expressed genes (DEGs), with the number of DEGs increasing over time in leaves, but decreasing over time in roots. While DEGs were largely specific to a single time point and tissue, we observed the same biological pathways as identified in previous late term iron stress exposure studies. To investigate these responses, we clustered our expression data across time to identify suites of genes, their biological functions, and the transcription factors that regulate their expression. These analyses allowed us to link the regulation of DNA replication/methylation to defense, and iron uptake/homeostasis, the hallmarks of the soybean iron stress response. In addition, these analyses suggest root to shoot signaling initiates the soybean iron stress response. These findings suggest a novel paradigm for crop stress adaptations and highlight the need for conducting additional IDC studies in diverse, agronomically important crop species.