Light-harvesting chlorophyll a/b binding (Lhc) proteins play a key role in the efficiency of the photosynthetic system of plants and participate in the regulation of plant growth, development, and the response to abiotic stress. In this study, 28 PbrLhc genes of the family were identified in the pear Pyrus bretschneideri genome database, which were distributed on 25 of the 27 chromosomes. Phylogenetic relationship analysis demonstrated that PbrLhc proteins could be divided into five subfamilies. Using MEME Suite, PlantRegMap, and Softberry, the conserved motifs, transcription binding sites, and predicated location of all PbrLhc proteins, respectively, were determined. A collinearity relationship using MCScanX software showed that there was a collinearity relationship between different PbrLhc genes. Using the hierarchical clustering method to develop a heat map of gene expression, five genes were found to be down-regulated under irrigation treatment and up-regulated under drought treatment; seven genes were up-regulated under irrigation treatment and down-regulated under drought treatment. Finally, the results of these analyses will provide theoretical basis for future study on the function and differential expression of PbrLhc genes in response to drought stress.

Drought and salt stresses severely constrain apple yield and quality. Using in vitro plantlets of apple ‘ Golden Delicious ’ as experimental materials, we aimed to dissect the stress-responsive mechanisms and provide a basis for the genetic improvement of apple stress resistance. Plantlets under NaCl (salt stress) and PEG (drought stress) treatments, with samples collected at 0, 1, 6, 12 and 24 h post-treatment for transcriptome sequencing. Gene expression levels were quantified as FPKM values to analyze temporal dynamic changes, and Differentially Expressed Genes (DEGs) were screened with |log2(FoldChange)| >1 and padj<0.05. Co-expression analysis was performed to explore the interaction patterns of stress-related genes, coupled with Gene Ontology (GO) (p-value<0.05) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (FDR<0.05) enrichment analyses. The core regulatory network of the “hormone signal-metabolic pathway” in apple in response to salt/drought stresses was identified, with the key nodes of this network clarified as MdAREB3/MdJAZ1 , MdPETE1 , MdSNF1 and MdGH9C2 , which are involved in hormone signal transduction, photosynthesis and carbohydrate metabolism, respectively. Stage-specific expression differences of key DEGs at 0, 1, 6, 12 and 24 h post NaCl/PEG treatments were further characterized via comparison of their expression patterns under the two stress conditions. This study systematically identifies the core regulatory network and its key nodes in apple in response to salt and drought stresses, thereby providing a reliable molecular basis for deciphering stress resistance mechanisms, verifying key gene functions, and the genetic improvement of salt/drought-tolerant apple varieties.

Auxin response factors (ARFs) are an important family of auxin-mediated proteins that have key roles in various physiological and biochemical processes. To the best of our knowledge, no genome-wide identification of the ARF gene family in Arabian jasmine ( Jasminum sambac ) has been conducted to date. During this study, 24 ARF genes were identified in the Arabian jasmine genome. A phylogenetic analysis suggested that the 24 Arabian jasmine ARFs (JsARFs) were clustered into seven groups and distributed on 11 of the 13 Arabian jasmine chromosomes. The promoter regions of these ARF s were rich in cis-responsive elements related to hormone responses, light responses, and biotic and abiotic stresses. A collinearity analysis showed that certain genes arose by duplication, such as JsARF6 and JsARF19 and JsARF7 and JsARF24 . A subsequent analysis of expression profiles based on RNA sequencing data showed that most genes had differential expression patterns among different tissues. The expression levels of 11 genes under indole-3-acetic acid hormone treatment were determined using quantitative real-time polymerase chain reaction, and the results demonstrated that the expression levels of nine JsARF genes were downregulated. Our findings provide valuable information to create the foundation for further functional investigations of the roles of ARF genes in Arabian jasmine growth and development.

C2H2-type zinc finger transcription factors play crucial roles in regulating plant growth and responses to abiotic stresses. Although pear is an economically important fruit crop with available genomic resources, the comprehensive analyses of its C2H2 gene family remain limited. In this study, we performed a genome-wide identification of C2H2 genes in pear, identifying 52 members that were unevenly distributed across 17 chromosomes. The predicted PyC2H2 proteins ranged from 343 to 1764 amino acids in length, with molecular weights between 12.4 and 62.7 kDa. Phylogenetic analysis classified these 52 PyC2H2 proteins into 10 classical clades, where genes with closer evolutionary relationships shared more similar conserved motifs. Collinearity analysis identified 37 collinear gene pairs between Arabidopsis thaliana and pear, suggesting evolutionary conservation. Promoter analysis revealed the presence of various cis-acting elements associated with hormone and stress responses, including Box 4, G-box, and GT1-motif. Additionally, the expression patterns of PyC2H2 genes differed among pear organs. These results provide valuable insights into the potential roles of PyC2H2 genes in drought stress responses and offer a foundation for future molecular breeding of drought-tolerant pear cultivars.

Various CBL-interacting protein kinases (CIPKs) are involved in abiotic stress responses in plants. Despite the economic importance of jasmine (Jasminum sambac L. Aiton) and the availability of genome data, there are few reports analyzing the CIPK gene family. In this study, genome-wide identification of the CIPK gene family in jasmine was conducted, which would provide valuable information for the function analysis of JsCIPKs regarding participation in growth and development and response to salt stress. In the present study, a total of 17 CIPKs were identified, which were unevenly distributed on eight chromosomes. The JsCIPK protein sequences contained 311–781 amino acids, with a molecular weight of 35.05–87.58 kDa. Phylogenetic analysis revealed that the 17 JsCIPKs could be divided into five classical branches. JsCIPK genes with higher homology showed greater similarity between conserved protein motifs. Collinearity analysis demonstrated that 13 gene pairs in Arabidopsis were collinear with the jasmine sequences. Various hormone-related response- and stress-induced elements were observed in the promoter region of JsCIPK genes, such as TC-rich repeats, CARE, etc. Furthermore, the expression of JsCIPK genes varied in different organs. Finally, the expression analyses of eight JsCIPKs under salt stress were performed. A systematic analysis of the CIPK gene family and the effect of salt stress on the expression of eight JsCIPK genes in leaves of jasmine was carried out. The expression of JsCIPK6 and JsCIPK8 was significantly down-regulated and up-regulated by salt treatment, respectively. These findings would lay a foundation for future functional studies of these two genes in jasmine related to salt stress and provide useful resistance genes for the molecular breeding of new varieties of salt-tolerant jasmine.

Background: Tartary buckwheat (Fagopyrum tataricum) serves as an excellent model for studying plant water adaptation mechanisms due to its exceptional drought tolerance. While aquaporins (AQPs) mediate the transmembrane transport of water and solutes in plants, their fine-tuned regulatory networks underlying stress resilience in Tartary buckwheat remain largely elusive. Methods: Here, we combined bioinformatics and transcriptomics to systematically identify 30 highly conserved FtAQP genes at the genome-wide level. Results: Cross-validated by qRT-PCR, our analysis revealed their distinct expression patterns across different organs. Based on our transcriptomic data, we hypothesize that FtAQP family members potentially participate in a coordinated whole-plant water management network through differential spatiotemporal expression. Specifically, the robust transcription of FtAQP8, FtAQP12, and FtAQP28 in roots is associated with the initial water uptake process. As water undergoes long-distance transport, the synergistic upregulation of FtAQP13, FtAQP17, FtAQP20, and FtAQP29 in the stem suggests a potential role in facilitating critical lateral water flow. Furthermore, during reproductive development, FtAQP27 exhibits extreme tissue specificity in floral organs, implying its possible involvement in maintaining local osmotic homeostasis. Furthermore, the promoter regions of FtAQPs are highly enriched with cis-acting elements responsive to light, abscisic acid (ABA), and cold stress, suggesting they are intimately regulated by a coupling of endogenous phytohormones and environmental cues. Conclusions: Ultimately, this study provides valuable insights into the potential molecular basis of multidimensional water regulation in Tartary buckwheat, and identifies candidate genetic targets for improving water use efficiency in dryland agriculture through the precise manipulation of aquaporins. Collectively, while these observational findings provide valuable predictive models, future in vivo experimental validations are required to confirm their exact biological functions.