RNA-seq based expression of DEGs in roots and leaves of bread wheat

RNA from roots and leaves of twenty eight bread wheat genotypes was
extracted, purified, quantified and sent to Beijing Genomics Institute
(BGI) for sequencing. Briefly, mRNAs were isolated and fragmented from
total RNA using the oligo (dT) method for cDNA synthesis. The 75-bp
single-end sequencing libraries were constructed, and sequencing was
performed on HiSeq X Ten (Illumina, San Diego, USA) using standard
protocols. Adapters with unknown bases (N’s > 5%) and low quality
were removed from raw reads to produce ‘clean data’ as FastQ data files
using a quality control software, SOAPnuke version 2.1.6. High quality
single-end reads were mapped to the bread wheat reference genome (IWGSC,
INSDC Assembly GCA_900519105.1) using HISAT2 (Hierarchical
Indexing for Spliced Alignment of Transcripts) software version
2.2.1. Alignment of the reference sequence with reads were performed using
Bowtie. Quantification of the reads was performed using featureCounts
software program. Differentially expressed genes (DEGs) were identified
using DeSEQ2 in R version  4.1.1. DEGs were then filtered based
on their adjusted p-value. A total of 120744 DEGs were identified with
varying expression in roots and leaves. The threshold value for filtering
was set at 0.1.