Characterizing short and long term iron stress responses in iron deficiency tolerant and susceptible soybean (Glycine max L. Merr.)

Nutrient deficiencies limit growth and yield in many different crop species. The calcareous soils in the upper Midwestern United States favor the development of iron deficiency chlorosis (IDC) in soybean (Glycine max L. Merr.). Even minor symptoms result in end of season yield loss. To identify molecular pathways and networks underlying tolerance to iron deficiency stress in soybean, we leveraged two near isogenic lines (Clark and Isoclark) that differ in their tolerance to iron stress. Clark and Isoclark were grown in hydroponics in one of three treatments: iron sufficient media for ten days, iron deficient media for ten days, or iron sufficient media for eight days followed by transfer to iron deficient media for two days. Following phenotyping, plant tissues were harvested for RNA-seq analysis. To facilitate analyses, we clustered differentially expressed genes across genotypes and timepoints in both roots and leaves. With this experimental design, we could identify iron stress response differences between Clark and Isoclark, evaluate the impact of iron stress duration, and link expression clusters with discrete biological functions and the transcription factor families that regulate them. We identified thousands of differentially expressed genes associated with soybean stress tolerant responses including the cell cycle, gene silencing, iron acquisition, and defense. In Clark, the number of differentially expressed genes and magnitude of expression increased with increasing iron stress duration. In contrast, Isoclark decreased the number and magnitude of differentially expressed genes across time. Differences in gene expression corresponded to phenotypic differences. The shifting expression patterns between timepoints and tissues suggests novel mechanisms for iron stress signaling between source and sink tissues.