Differential Gene Expression in Wheat under Salt Stress

Quality-controlled reads were mapped to the wheat genome sequence (https://www.ncbi.nlm.nih.gov/assembly/GCA_900519105.1wgsc_refseqv1.0) by Hisat2 (Kim et al., 2015 (link)). Gene expression was quantified as fragments per kilobase of transcript per million (FPKM). Differential expression analysis between the control and salt stress groups was performed using DESeq2, which used a model based on a negative binomial distribution to identify DEGs from the whole gene set (Love et al., 2014 (link)). The p-values were adjusted using the Benjamini–Hochberg method, and the corresponding false discovery rate (FDR) was determined (Anders and Huber, 2010 (link)). Genes with FDR<0.01 and fold-change>2 were assigned as DEGs (Fu et al., 2019 (link)). GO and KEGG enrichment analyses were carried out using clusterProfiler (version 3.10.1) (Yu et al., 2012 (link)) in R software. Venn graphs of the overlaps of DEGs at different time points were generated using BMKCloud (www.biocloud.net).