Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense

Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut (Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency

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.

Influence of High-Temperature and Intense Light on the Enzymatic Antioxidant System in Ginger (Zingiber officinale Roscoe) Plantlets

Environmental stressors such as high temperature and intense light have been shown to have negative effects on plant growth and productivity. To survive in such conditions, plants activate several stress response mechanisms. The synergistic effect of high-temperature and intense light stress has a significant impact on ginger, leading to reduced ginger production. Nevertheless, how ginger responds to this type of stress is not yet fully understood. In this study, we examined the phenotypic changes, malonaldehyde (MDA) content, and the response of four vital enzymes (superoxide dismutase (SOD), catalase (CAT), lipoxygenase (LOX), and nitrate reductase (NR)) in ginger plants subjected to high-temperature and intense light stress. The findings of this study indicate that ginger is vulnerable to high temperature and intense light stress. This is evident from the noticeable curling, yellowing, and wilting of ginger leaves, as well as a decrease in chlorophyll index and an increase in MDA content. Our investigation confirms that ginger plants activate multiple stress response pathways, including the SOD and CAT antioxidant defenses, and adjust their response over time by switching to different pathways. Additionally, we observe that the expression levels of genes involved in different stress response pathways, such as SOD, CAT, LOX, and NR, are differently regulated under stress conditions. These findings offer avenues to explore the stress mechanisms of ginger in response to high temperature and intense light. They also provide interesting information for the choice of genetic material to use in breeding programs for obtaining ginger genotypes capable of withstanding high temperatures and intense light stress.

Genome-wide identification of R-SNARE gene family in upland cotton and function analysis of GhVAMP72l response to drought stress

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (R-SNAREs) mainly promoted the assembly of the SNARE complex to drive the final membrane fusion step of membrane transport. Previous research on R-SNAREs has mainly focused on development and growth and has rarely been involved in abiotic stress, especially in cotton. Here, we performed a comprehensive analysis of R-SNARE genes in upland cotton. In total, 51 Gh-R-SNARE genes across six phylogenetic groups were unevenly distributed on 21 chromosomes. Cis elements related to plant growth and response to abiotic stress responses were found in the promoter region of Gh-R-SNAREs. Nine Gh-R-SNARE genes were obviously upregulated under drought stress conditions by RNA-seq and qRT-PCR analysis. Among them, GhVAMP72l might be the key candidate gene contributing to drought stress tolerance in cotton by virus-induced gene silencing (VIGS) assay. These results provide valuable insights for the functional analysis of cotton R-SNAREs in response to drought stress and highlight potential beneficial genes for genetic improvement and breeding in cotton.

Genome-wide identification of the CPK gene family in wheat (Triticum aestivum L.) and characterization of TaCPK40 associated with seed dormancy and germination

Calcium-dependent protein kinases (CPKs), important sensors of calcium signals, play an essential role in plant growth, development, and stress responses. Although the CPK gene family has been characterized in many plants, the functions of the CPK gene family in wheat, including their relationship to seed dormancy and germination, remain unclear. In this study, we identified 84 TaCPK genes in wheat (TaCPK1-84). According to their phylogenetic relationship, they were divided into four groups (I-IV). TaCPK genes in the same group were found to have similar gene structures and motifs. Chromosomal localization indicated that TaCPK genes were unevenly distributed across 21 wheat chromosomes. TaCPK gene expansion occurred through segmental duplication events and underwent strong negative selection. A large number of cis-regulatory elements related to light response, phytohormone response, and abiotic stress response were identified in the upstream promoter sequences of TaCPK genes. TaCPK gene expression was found to be tissue- and growth-stage-diverse. Analysis of the expression patterns of several wheat varieties with contrasting seed dormancy and germination phenotypes resulted in the identification of 11 candidate genes (TaCPK38/-40/-43/-47/-50/-60/-67/-70/-75/-78/-80) which are likely associated with seed dormancy and germination. The ectopic expression of TaCPK40 in Arabidopsis promoted seed germination and reduced abscisic acid (ABA) sensitivity during germination, indicating that TaCPK40 negatively regulates seed dormancy and positively regulates seed germination. These findings advance our understanding of the multifaceted functions of CPK genes in seed dormancy and germination, and provide potential candidate genes for controlling wheat seed dormancy and germination.

Combined physiological and transcriptome analysis revealed the response mechanism of Pogostemon cablin roots to p-hydroxybenzoic acid

Pogostemon cablin (patchouli) cultivation is challenged by serious soil sickness, of which autotoxins accumulation is a major cause. p-hydroxybenzoic acid (p-HBA) is one of the main autotoxins of patchouli. However, the molecular mechanism underlying the response of patchouli to p-HBA remains unclear. In this study, RNA-sequencing combined with physiological analysis was used to monitor the dynamic transcriptomic and physiological changes in patchouli seedlings 0, 6, 12, 24, 48, and 96 h after p-HBA treatment. p-HBA stress inhibited root biomass accumulation, induced excessive hydrogen peroxide accumulation and lipid peroxidation, and activated most antioxidant enzymes. Compared with that of the control, the osmotic adjustment substance content was elevated with treatment. Subsequently, 15,532, 8,217, 8,946, 2,489, and 5,843 differentially expressed genes (DEGs) at 6, 12, 24, 48, and 96 h after p-HBA treatment, respectively, were identified in patchouli roots. GO functional enrichment analysis showed that the DEGs were enriched mainly in plasma membrane, defense response, response to chitin, DNA-binding transcription factor activity and abscisic acid-activated signaling pathway. The upregulated genes were involved in glycolysis/gluconeogenesis, cysteine and methionine metabolism, starch and sucrose metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism. Genes associated with MAPK signaling pathway-plant, plant-pathogen interaction, plant hormone signal transduction were downregulated with p-HBA treatment. These pathways are related to root browning and rotting, leading to plant death.

Identification and Expression Analysis of Calcium-Dependent Protein Kinases Gene Family in Potato Under Drought Stress

Calcium-dependent protein kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in stress response and plant growth and development. In this study, the BLAST method was used to search for protein sequences of the potato Calcium-dependent protein kinase gene family. The chromosome location, phylogeny, gene structures, gene duplication, cis-acting elements, protein-protein interaction, and expression profiles were analyzed. Twenty-five CDPK genes in the potato genome were identified based on RNA-seq data and were clustered into four groups (I-IV) based on their structural features and phylogenetic analysis. The result showed the composition of the promoter region of the StCDPKs gene, including light-responsive elements such as Box4, hormone-responsive elements such as ABRE, and stress-responsive elements such as MBS. Four pairs of segmental duplications were found in StCDPKs genes and the Ka/Ks ratios were below 1, indicating a purifying selection of the genes. The protein-protein interaction network revealed defense-related proteins such as; respiratory burst oxidase homologs (RBOHs) interacting with potato CDPKs. Transcript abundance was measured via RT-PCR between the two cultivars and their relative expression of CDPK genes was analyzed after 15, 20, and 25 days of drought. There were varied expression patterns of StCDPK3/13/21 and 23, between the two potato cultivars under mannitol induced-drought conditions. Correlation analysis showed that StCDPK21/22 and StCDPK3 may be the major differentially expressed genes involved in the regulation of malondialdehyde (MDA) and proline content in response to drought stress, opening a new research direction for genetic improvement of drought resistance in potato.