Genome-wide identification and analysis of Catharanthus roseus RLK1-like kinases in rice

A genome-wide survey of Catharanthus roseus receptor-like kinase1-like kinases (CrRLK1Ls) in rice revealed that the pattern of expression by some CrRLK1Ls is controlled by drought or circadian rhythms. This is probably accomplished through the functioning of Gigantea ( OsGI ). Such findings provide a novel angle for using CrRLK1Ls to study the drought-stress response and circadian regulation. The 17 CrRLK1L members of a novel RLK family have been identified in Arabidopsis. Each carries a putative extracellular carbohydrate-binding malectin-like domain. However, their roles in rice, a widely consumed staple food, are not well understood. To investigate the functions of CrRLK1Ls in rice, we utilized phylogenomics data obtained through anatomical and diurnal meta-expression analyses. This information was integrated with a large set of public microarray data within the context of the rice CrRLK1L family phylogenic tree. Chromosomal locations indicated that 3 of 16 genes were tandem-duplicated, suggesting possible functional redundancy within this family. However, integrated diurnal expression showed functional divergence between two of three genes, i.e., peak expression was detected during the day for OsCrRLK1L2, but during the night for OsCrRLK1L3. We found it interesting that OsCrRLK1L2 expression was repressed in osgigantea (osgi) mutants, which suggests that it could function downstream of OsGI. Network analysis associated with OsCrRLK1L2 and OsGI suggested a novel circadian regulation mechanism mediated by OsGI. In addition, two of five OsCrRLK1Ls preferentially expressed in the roots were stimulated by drought, suggesting a potential role for this family in water-use efficiency. This preliminary identification of CrRLK1Ls and study of their expression in rice will facilitate further functional classifications and applications in plant production.