FPKM (Fragments per kilobase of exon model per million mapped fragments) value of all detected genes in in WT, rel1, rip2, and rel1 rip2 mutants. ZH11_1, ZH11_2, ZH11_3 represent samples were collected from ZH11 with three independent biological replicates. rel1_1, rel1_2, rel1_3 represent samples were collected from rel1 mutants with three independent biological replicates. rip2_1, rip2_2, rip2_3 represent samples were collected from rip2 mutant with three independent biological replicates. rel1rip2_1, rel1rip2_2, rel1rip2_3 represent samples were collected from rel1rip2 double mutant with three independent biological replicates.

Three replicates of ZH11, rel1, rip2, and rel1rip2 mutant during the seedling stage were used for RNA-sequencing. Leaves of samples were harvested, preserved in liquid nitrogen, and stored at -80 ºC. Transcriptome data were collected by Beijing Novogene Bioinformatics Technology Company. Raw data (raw reads) in fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapters, poly-N, and low-quality reads from the raw data. At the same time, quality parameters of the clean data, including Q20, Q30, GC content, and sequence duplication level, were used for data filtering. All subsequent analyses were conducted using high-quality clean data. Reference genome and gene model annotation files were downloaded from The MSU Rice Genome Annotation Project Database website at http://rice.plantbiology.msu.edu/.