Genome-wide identification and expression profiling of Pseudo-Response Regulator (PRR) gene family in tomato

Circadian clocks are intrinsic time-keeping mechanisms that facilitate the coordination of development and physiological processes in plants with seasonal and diurnal variations in the environment. Pseudo-response regulator (PRR) genes regulate various essential processes, such as development, flowering time, and the formation of inflorescence architecture in the reproductive stage, principally by regulating transcriptional activity and protein function. The present research focused on genome-wide characterization, phylogenetic, cis-regulatory elements, miRNAs, 3D-sturcutural and expression profiling of the PRR proteins in tomato. Overall, 13 candidate genes were identified on six chromosomes (Chr1, Chr3, Chr4, Chr6, Chr8 and Chr10). Phylogenetic analysis categorized SlPRR gene members into four groups. All genes possess conserved PRR domains with unique sequences within these domains. Additionally, SlPRR genes exhibited diversity in numbers of exons and introns indicating potential functional divergence. Through comparative synteny investigation, it was ascertained that duplication events occurred. Furthermore, miRNAs were predicted to understand post-transcriptional changes in SlPRR genes. The results showed that SlPRR6 and SlPRR13 were targeted by 6 miRNAs each, while SlPRR1 and SlPRR3 were only targeted by 3 miRNAs. Three-dimensional (3D) configurations of 13 PRR proteins were also predicted. PRR genes exhibited differential expression pattern at both vegetative and reproductive stages in different time intervals. This pattern follows the sequence of early morning genes exhibiting the highest expression, followed by evening, and then noon. This implies that SlPRR genes have significant functions in various photoperiod signaling pathways throughout distinct periods during vegetative and reproductive stages. These findings stipulate a comprehensive understanding of the tomato PRR which can be employed for future functional studies of tomato PRR family members and their involvement in the intricate network of the circadian rhythm for regulating growth and development of plants.