Transcriptomic Profiling of Gene-Edited Rice

For transcriptomic sequencing, ~500 pedicel samples from the gene-edited lines (S5, Q5, and SQ1) and weedy rice prenatal line (“C9”) were collected at 1, 15, and 25 days after heading, representing the preliminary, middle, and late stages of seed development, respectively. A total of three biological replicates were performed. Total RNA was extracted from the pedicel tissues with an RNA extraction kit (DP432, TIANGEN, Beijing, China) according to the manufacturer’s instructions. After purification with the TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA), the RNA samples were fragmented and used as a template for cDNA synthesis. The obtained cDNA samples were A-tailed, ligated, and sequenced (Table S1) using the Aglient 2100 bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).
Adaptor sequences and low-quality reads were removed using Trimmomatic v0.36 [29 (link)]. High-quality 150 bp paired-end reads were mapped on the reference genome, cultivated rice R498 (Oryza sativa ssp. indica) [30 (link)] with HISAT2 v2.2.1 and StringTie v1.3.3 [31 (link)]. Gene expression levels were represented by the FPKM (fragments per Kb per million reads) values.