Genome-wide identification and molecular characterization of SlKRP family members in tomato and their expression profiles in response to abiotic stress

The cell cycle has an essential role in the regulation of plant growth, development, and stress responses, which was controlled by the complex of cyclin / cyclin-dependent kinases (CDKs). Kip-related proteins (KRPs) as CDK inhibitors are involved in the precise regulation of cell cycle progression. However, the comprehensive identification of SlKRP family genes in tomato has not been achieved. Here, a total of six SlKRP proteins were identified from the tomato genome and divided into three classes via phylogenetic analysis. Chromosomal localization analysis revealed the interchromosomal segment duplication among SlKRP genes. Analyses on genes structures and conserved motifs indicated that the SlKRP genes were evolutionarily conserved. The subcellular localization analysis showed all SlKRP proteins were located in the nuclei. Six SlKRPs had distinct expression in different tissues. Their expressions were affected by the plant hormones (ABA, IAA, and ethylene) and various abiotic stresses (salt, drought, and low temperature), which were correlated with different cis-acting regulatory elements (CAREs) in the 3-Kb promoter regions of these genes. In addition, co-expression relationship and protein interaction network analysis proved that SlKRP proteins may interact with CDKs and cyclins. To further explore the function of SlKRPs in tomato, VIGS assay was performed to obtain SlKRP5-silenced plants and demonstrated that silencing of SlKRP5 increased the sensitivity to drought stress. These findings provide references for the further functional analysis of KRPs in the future.