Genome-wide transcriptomic analysis reveals the gene regulatory network that controlled by SRL1 in regulating rice leaf rolling

Abstract Background SRL1 (SEMI-ROLLED LEAF 1) also named as CLD1 (CURLED LEAF AND DWARF 1), encoding a putative glyphopholipidininol-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. Results To explore the gene regulatory network of leaf development that 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 3,178 genes were identified as differentially expressed genes, of which 1,216 genes were significantly up regulated, while 1,962 genes were down regulated. Further analyses indicated that, a group of known leaf rolling related genes, which involved in bulliform cells and cuticle development such as OsZHD1, OsLBD3-7, RFS, ACL1, CFL1, SND1, OsCESA5 and OsCESA6 were up or down regulated in the srl1-KO. Conclusions SRL1 might control leaf rolling by regulating a couple of genes that affecting cytological architecture of leaf cells such as bulliforms and cuticle of leaves.