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

Abstract

Preserving crop yield is critical for US 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 USA 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 (P i) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to-Fe deficiency, it responds strongly to P i 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 3375 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.

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean

“…We also compared our results between tissues, identifying 896 DEGs common to -Fe-P i leaves and roots with 110 of these specific to the -Fe-P i treatment ( Figure 5 , Supplemental File 1: Table S4 ). This is interesting because previous studies have shown very little overlap in DEGs between these two tissues [ 29 , 33 ]. Gene annotation analysis identified 27 statistically significant GO terms associated with the 896 DEGs common to -Fe-P i leaves and roots, all of which are associated with growth and/or defense.…”

“…Nine expression profiles could be found in both leaves and roots, three were specific to roots, and three were not expressed. As previously demonstrated, genes with similar expression patterns are often associated with the same biological processes [ 33 , 34 ]. Thus, we looked at the annotations of the genes for each of the 15 expression profiles.…”

“…Modifying the transcriptional profiles of growth and DNA replication/methylation processes is a hallmark of the Clark iron deficiency response [ 26 , 30 ]. This is particularly interesting as genes associated with DNA replication and methylation are largely repressed after single stress exposure, regardless of stress duration [ 26 , 29 , 33 , 34 ]. The identification of 12 GO terms (343 genes) associated with photosynthesis reflects the importance of iron and phosphorus in photosynthetic process and the importance of photosynthates in the roots as an energy source.…”

“…This study found that sequential stress exposures shifted the timing of the expected changes in gene expression patterns. We know from previous studies that the number of DEGs in leaves increases through time (30, 60 and 120 min) after -Fe stress exposure [ 33 ] and root differential gene expression precedes leaf responses. Thus, it is logical that a short term initial -Fe stress exposure could reduce the time required to induce changes in the transcriptional response upon a second (-P i ) stress, resulting in an increase in DEGs in -Fe-P i stressed leaves compared to -Fe-Fe or -P i -P i stressed leaves.…”

“…Previous soybean studies provide an excellent foundation for understanding the genetic and molecular underpinnings of soybeans’ nutrient deficiency stress response and highlight the need to conduct these studies within crop species [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. However, there is a shortage of studies examining the transcriptomic responses of soybean to sequential abiotic stresses, conditions faced regularly by crops.…”