This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes’ roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.
10 September 2025 in Industrial Crops and Products
Cytosine methylation is a crucial epigenetic modification that responds to various environmental cues, yet the specific mechanisms influencing planting patterns remain incompletely understood. This study reveals significant growth differences between single‐seed (SS) precision sowing and double‐seed (DS) sowing observed 42 days after germination under controlled indoor conditions. These differences were eliminated by the application of the DNA methylation inhibitor 5‐azacytidine (5‐aza), highlighting the role of DNA methylation in these processes. To further investigate the role of DNA methylation in planting pattern, we generated DNA methylation profiles of peanut leaves and roots under both DS and SS planting patterns. The analysis revealed increased CHH methylation in both tissues, caused by the RNA‐directed DNA methylation (RdDM) pathway. Further analysis, including differential methylation, transposable element (TE) analysis and methylation‐related gene analysis, demonstrated tissue‐specific epigenetic responses to planting patterns. Integrating methylome and transcriptome data, we found that DS was associated with hyper‐CHH methylation in WRKY gene promoters in leaves, accelerating leaf senescence. Meanwhile, SS reduced CHH methylation in promoters in roots, upregulating genes involved in flavonoid biosynthesis. This upregulation enhanced root nodule formation and improved stress resistance, resulting in increased concentrations of nitrogen and phosphorus in the roots, as confirmed by metagenomic functional analysis. This research provides novel insights into the epigenetic regulation of plant growth and development.
Rosa hybrida (R. hybrida), a widely cultivated ornamental species, is increasingly threatened by climate-induced abiotic stresses, including heat and drought. Heat shock transcription factors (HSFs) are critical for plant stress responses, yet their roles in R. hybrida remain understudied. In this research, 71 HSF genes were identified from the haplotype-resolved genome of the tetraploid variety ‘Samantha’. These genes were classified into three major classes (HSFA, HSFB, HSFC) and 15 subgroups based on phylogenetic and motif analysis. Gene structure and conserved motifs revealed subgroup-specific functional divergence. Promoter analysis identified abundant hormone- and stress-responsive cis-elements, particularly for abscisic acid (ABA) and jasmonic acid. Synteny analysis suggested that segmental duplication contributed to the RhHSF family’s expansion. Tissue-specific expression profiling revealed distinct roles for HSFs, with HSFB genes predominantly expressed in reproductive tissues and HSFA genes in vegetative organs. Expression under heat and drought stress showed dynamic, subgroup-dependent responses, with HSFC members playing significant roles. Functional assays demonstrated that RhHSF17, induced by both stresses and ABA, localized to the nucleus, and its overexpression in Arabidopsis enhanced drought tolerance. This study provides a comprehensive characterization of the RhHSF gene family, offering insights into their roles in stress tolerance and laying the foundation for future functional research.