Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

Saurabh Gupta, Brijesh S. Yadav, Utkarsh Raj, Shiri Freilich, Pritish K. Varadwaj

Deficiency of necessary macronutrients, i.e., Potassium (K), Magnesium (Mg), Nitrogen (N), Phosphorus (P), and Sulfate (S) in the soil leads to a reduction in plant growth and yield, which is a result of changes in expression level of various genes. This study was performed to identify the differentially expressed genes and its associated metabolic pathways occurred in soil grown wheat root samples excavated from the control and treated fields. To identify the difference in gene expression levels due to deficiency of the said nutrients, a transcriptomic, meta-analysis was performed on array expression profile data. A set of 435 statistically significant probes encoding 398 Nutrient Deficiency Response Genes (NRGs) responding at-least one nutrients deficiency (ND) were identified. Out of them 55 NRGs were found to response to minimum two ND. Singular Enrichment Analysis (SEA) predicts ontological based classifications and functional analysis of NRGs in different cellular/molecular pathways involved in root development and growth. Functional annotation and reaction mechanism of differentially expressed genes, proteins/enzymes in the different metabolic pathway through MapMan analysis were explored. Further the meta-analysis was performed to revels the active involvement each NRGs in distinct tissues and their comparative potential expression analysis in different stress conditions. The study results in exploring the role of major acting candidate genes such as Non-specific serine/threonine protein kinase, Xyloglucan endotransglucosylase/hydrolase, Peroxides, Glycerophosphoryl diester phosphodiesterase, S-adenosylmethionine decarboxylase proenzyme, Dehydrin family proteins, Transcription factors, Membrane Proteins, Metal binding proteins, Photosystem proteins, Transporter and Transferase associated in different metabolic pathways. Finally, the differences of transcriptional responses in the soil-grown root of T. aestivum cv. and in-vitro grown model plants under nutrients deficiency were summarized.