The C2H2 Zinc-Finger protein ELR1 negatively regulates cytokinin metabolism and signaling pathway in rice.

Cytokinins are a class of important plant hormones that are closely associated with processes such as cell division, meristem initiation, and leaf differentiation. Numerous genes involved in cytokinin metabolism and signaling pathways have been reported, and we identified a C2H2 transcription factor that strongly modulates both processes. In this study, we isolated a spontaneous rice mutant displaying wider leaves and thicker roots, thus naming it enlarged leaf and root 1. Through map-based cloning, we mapped ELR1 to chromosome 3 of rice, which encodes a C2H2 zinc-finger protein. It was previously named DROUGHT AND SALT TOLERANCE (DST) or WIDE LEAF 1 (WL1), involved in stress response, leaf and panicle development. Histological analysis revealed that the elr1 mutant exhibits an increased number of vascular bundles and wider leaves, whereas overexpression of ELR1 result in a decreased number of vascular bundles and narrower leaves. Transcriptome analysis demonstrated that ELR1 may participate in stress response and plant hormone metabolism, particularly cytokinin and jasmonic acid. Chromatin Immunoprecipitation Sequencing (ChIP-seq) results showed that ELR1 targets downstream genes involved in cytokinin metabolism, floral morphogenesis, and sulfated peptide signaling pathways. The expression of cytokinin receptor genes is generally up-regulated in elr1 mutant. Taken together, our results reveal that ELR1 plays an important role and acts as a negative regulator in modulating cytokinin metabolism and signaling pathway.