Genome-Wide Transcriptomic Analysis Reveals the Gene Regulatory Network Controlled by SRL1 in Regulating Rice Leaf Rolling

SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glycosylphosphatidylinositol-anchored membrane protein, has been characterized as a gene involved in the regulation of leaf morphology in rice. Mutants of srl1-1 (point mutation) and srl1-2 (transferred DNA insertion) exhibit defects in leaf development resulting in a phenotype with adaxially rolled leaves. To explore the gene regulatory network of leaf development controlled by SRL1 in rice, we created a homozygous SRL1 knock out (KO) line by CRISPR/Cas9, which showed defects in leaf development with adaxially rolling. By comparing the leaf transcriptome of a homozygous SRL1 KO line (srl1-KO) with the control, a total number of 3178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly upregulated, while 1962 genes were downregulated. Further analysis indicated that a group of differentially expressed genes that related to the bulliform cells development (OsZHD1, OsLBD3-7, RFS and ACL1) and the cuticle of leaves (CFL1) may take responsibility for the defects in leaf development for the srl1-KO. Moreover, the downregulation of cellulose synthase (CESA) genes and phenylalanine ammonia-lyase (PAL)/ cinnamoyl-CoA reductase (CCR) gene expressions may lead to the reduction of cellulose/lignin contents in srl1-KO. Our study sheds light on the gene regulatory network controlled by SRL1, the important leaf development-related gene, which could be utilized in future breeding.