Gene expression raw count by RNA sequence

Two maize inbred lines with contrasting salt tolerance were used in the present study, of which L2010-3 is a salt-tolerant line and BML1234 is a salt-sensitive line. The seeds from the two lines were surface-sterilized in 10% (v/v) H2O2 for 15 min, rinsed with distilled water and then germinated on filter paper saturated with distilled water. Uniform seedlings with two leaves were transplanted into aerated 1 × Hoagland’s nutrient solution + Na150 for salt stress . The seedlings were then cultured in a growth room with a relative humidity of 70% (14/10 h, day/night) at 26℃. At 0 h (control), 6 h (T-6), 18 h (T-18), and 36 h (T-36) under salt treatment, the mixed roots from three seedlings of each line were individually collected as the samples for transcriptome sequencing, with two biological replicates.According to the manufacturer’s instructions, total RNA of each sample was isolated using the HiPure Plant RNA Maxi Kit purchased from Magen company (http://www.magentec.com.cn). RNA library construction and transcriptome sequencing were performed by the Illumina sequencing platform.Raw sequencing reads were filtered to remove low-quality reads, adaptor-polluted reads, and reads containing Poly-N, which generated clean reads by fastp (Chen et al. 2018). The clean reads were subsequently mapped to the maize reference genome (ZmB73 RefGen_V4) (http://www.gramene.org) via Hisat2. Gene expression levels were determined by Htseq software and were normalized to transcripts per million (TPM) by consumer script.