Three biological replicates were used for library constructions and sequencing. Each sample was initially treated with Fruit-Mate for RNA purification (Takara) and thereafter the total RNA was isolated with TRIzol Reagent (Thermo Fisher Scientific). An Illumina TruSeq RNA Sample Prep Kit (Illumina) was used to build cDNA libraries. The generated cDNA libraries were sent to a HiSeq2500-PE125 platform (Illumina) to obtain sequence reads. Based on the genome sequences of maize (B73, RefGen_v4), the Tophat and Cufflinks packages were used to assemble the transcripts and to identify differentially expressed genes (DEGs) using DEGseq2 (Trapnell et al., 2012 (link); Love et al., 2014 (link)), and only genes whose levels were at least 2-fold changed with statistical significance (false discovery rate <0.05) were considered to be DEGs. Gene Ontology (GO) analysis and graphing were performed on Omicshare (https://www.omicshare.com/tools/), ImageGP (http://www.ehbio.com/), and agriGO (http://systemsbiology.cau.edu.cn/agriGOv2).
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