Research Overview

The primary goal of this analysis is to examine gene expression in soybean roots treated with phytohormones. Differential gene expression was assessed on RNA extracted from soybean roots treated with salicylic acid, jasmonic acid, and indole-3-acetic acid. A total of 9 root samples were collected and sequenced using Illumina technology. The experimental design included three biological replicates for each treatment, with RNA samples collected 8 hours after exposure to the phytohormones, while control samples were collected without hormone exposure. In RNA sequencing (RNA-Seq), gene expression is quantified by counting the number of reads mapped to each gene. However, raw counts must be normalized to account for variables such as gene length and sequencing depth. RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalizes both gene length and total read count within a sample , which is useful for comparing gene expression within a single sample. TPM (Transcripts Per Million) also accounts for gene length but performs normalization after adjusting for it, making it more suitable for comparing gene expression across different samples. For comparisons between samples, statistical methods such as DESeq2 was used, as these models correct for biases like sequencing depth, providing more accurate results in differential gene expression analysis.

Differential Gene Expression (DGE) analysis identifies genes whose expression levels change significantly between different biological conditions. In our study, we aim to compare gene expression in Glycine max prior to and after exposure of phytohormones and identified Glycine max genes that are upregulated or downregulated in response to how the soybean plants responds to phytohormones highlighting the plants defense mechanisms and other signaling pathways.