Genome-wide analysis and expression profiling of CPK gene families in Sorghum bicolor (L.) Moench reveal their hormone-mediated responses during seed germination

Abstract

Introduction Sorghum (Sorghum bicolor (L.) Moench) is an economically vital crop worldwide for food, forage, and bioenergy production, and also serves as the core raw material for Guizhou-flavored Chinese Baijiu. Pre-harvest sprouting (PHS) severely impairs sorghum grain yield, quality, and industrial economic value. Calcium-dependent protein kinases (CPKs/CDPKs) are plant-specific calcium sensors that exert essential regulatory functions in seed development, dormancy, and germination. Nevertheless, the genome-wide characteristics of the sorghum SbCPK family and their molecular mechanisms underlying seed germination regulation remain largely elusive. Methods In this study, we systematically identified the SbCPK gene family based on the BTx623 v2.1 reference genome, and comprehensively analyzed their physicochemical properties, phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, collinearity, and promoter cis-acting elements. Using the sorghum cultivar `Hongyingzi' as experimental material, we integrated transcriptome profiling and qRT-PCR assays to characterize the tissue-specific expression patterns of SbCPKs and their transcriptional responses to exogenous ABA and ACC (ethylene precursor) treatments Results A total of 30 SbCPK genes were identified across the sorghum genome, which were unevenly distributed on 10 chromosomes and formed 8 tandem duplication clusters. Phylogenetic analysis classified these SbCPKs into four distinct subfamilies, which exhibited high evolutionary conservation with CPK homologs in maize and rice. Gene structures and motif compositions were conserved among the four subfamilies, and abundant cis-elements associated with ABA, ethylene, stress responses and seed development were detected in the promoters of SbCPK genes. Tissue expression profiling revealed that SbCPK5, SbCPK9, SbCPK11, and SbCPK19 were specifically and highly expressed in sorghum embryos. Exogenous ABA significantly inhibited seed germination and upregulated the transcript levels of SbCPK6, SbCPK8, SbCPK9, SbCPK11, and SbCPK21. In contrast, ACC markedly promoted seed germination, specifically induced the expression of SbCPK19, and repressed the expression of multiple other SbCPK members. These results indicate that SbCPK family genes exhibit obvious differential expression in response to ABA and ethylene signals during sorghum seed germination. Discussion Collectively, this study identifies key candidate SbCPK genes associated with seed germination and hormonal signal transduction, providing a fundamental theoretical basis for further elucidating the calcium signaling-mediated molecular regulatory mechanisms of PHS in sorghum.