Identification of Solanum lycopersicum L. Casein Kinase I-like Gene Family and Analysis of Abiotic Stress Response

TL;DR

This study identifies and analyzes the CKL gene family in tomatoes, revealing their roles in abiotic stress responses and evolutionary relationships.

Contribution

The first systematic identification and analysis of the Solanum lycopersicum CKL gene family and its abiotic stress responses.

Findings

16 SlCKL genes were identified and classified into three subfamilies with uneven chromosomal distribution.

SlCKL genes show high conservation in structure and motifs, with stronger synteny to Arabidopsis and pepper.

SlCKL genes are root-preferential and differentially responsive to drought, salt, heat, cold, and ABA.

Abstract

Background: Casein kinase I-like (CKL) protein is a member of the serine/threonine kinase CKI family and plays a pivotal regulatory role in various eukaryotic cellular processes, including stress responses. Objectives: This study aims to systematically identify the CKL gene family in the tomato genome and investigate its responsiveness to abiotic stress. Methods: Members of SlCKL were identified through genome-wide bioinformatics analysis, and their physicochemical properties, chromosomal localization, gene structure, conserved domains, phylogenetic relationships, cis-acting elements, cross-species collinearity, and tissue expression profiles were comprehensively analyzed. The expression patterns of SlCKL genes under abiotic stress were validated using real-time quantitative PCR. Results: A total of 16 SlCKL genes were identified and classified into three subfamilies (I–III), which are unevenly distributed across nine chromosomes, predominantly clustered at the ends. The gene structure, motifs, and functional domains exhibit high conservation. Collinearity analysis revealed stronger synteny between tomato and Arabidopsis thaliana or pepper compared to rice, maize, or tobacco, suggesting a common ancestral origin. The tissue expression profile indicates that SlCKLs are preferentially transcribed in roots. Promoter analysis and qRT-PCR validation demonstrated differential responses of SlCKLs to various abiotic stresses, such as drought, salt, heat, cold, and ABA treatment. Conclusions: This study represents the first systematic identification of the tomato SlCKL gene family, elucidating its evolutionary relationships, structural characteristics, tissue-specific expression patterns, and differential responsiveness to abiotic stress, thereby providing a critical foundation for further investigation into the molecular mechanisms underlying CKL-mediated abiotic stress adaptation in tomatoes.

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