RNA sequencing; Function studies of EAR LENGTH1which positive regulates ear length in maize

For RNA-seq analysis, the RNAs extracted from 0.5mm developing ear of ZmEL1-OE and non-transgenic lines with three biological replicates for each genotype, were used for RNA-Seq (Annoroad Gene Technology, Beijing, China). Total RNA was isolated using Quick RNA Isolation Kit (Huayueyang Biotechnology CO., LTD. Beijing, China). A library with insert sizes ranging from 200 to 500bp was prepared using the commercial Illumina library preparation kits (TruSeq Stranded mRNA LT-SetA. RS-122-1201) and was sequenced following the HiSeq X-Ten protocols. Low sequencing quality reads and adapter sequences were removed using the software Trimmomatic-0.36. The paired-end reads were mapped onto the B73 AGPv3.25 reference using the software Tophat2; only those uniquely mapped reads were used to quantify gene expression levels using Cufflinks . The expression data for each gene was normalized using the software DESeq2 before the subsequent analyses. Differential gene expression was determined using edgeR