Search Results (210)

Zinc (Zn) deficiency poses a major global health challenge, and wheat grains generally contain low Zn concentrations. In this study, the wheat cultivar ‘Zhongmai 175’ was identified as zinc-efficient. Hydroponic experiments demonstrated that Zn deficiency induced the secretion of oxalic acid and malic acid in root exudates and significantly increased total root length in ‘Zhongmai 175’. To elucidate the underlying regulatory mechanisms, transcriptome profiling via RNA sequencing was conducted under Zn-deficient conditions. A total of 2287 and 1935 differentially expressed genes (DEGs) were identified in roots and shoots, respectively. Gene Ontology enrichment analysis revealed that these DEGs were primarily associated with Zn ion transport, homeostasis, transmembrane transport, and hormone signaling. Key DEGs belonged to gene families including VIT, NAS, DMAS, ZIP, tDT, HMA, and NAAT. KEGG pathway analysis indicated that phenylpropanoid biosynthesis, particularly lignin synthesis genes, was significantly downregulated in Zn-deficient roots. In shoots, cysteine and methionine metabolism, along with plant hormone signal transduction, were the most enriched pathways. Notably, most DEGs in shoots were associated with the biosynthesis of phytosiderophores (MAs, NA) and ethylene. Overall, genes involved in Zn ion transport, phytosiderophore biosynthesis, dicarboxylate transport, and ethylene biosynthesis appear to play central roles in wheat’s adaptive response to Zn deficiency. These findings provide a valuable foundation for understanding the molecular basis of Zn efficiency in wheat and for breeding Zn-enriched varieties. Full article

The bZIP gene family play a crucial role in plant growth, development, and stress responses, functioning as transcription factors. While this gene family has been studied in several plant species, its roles in the endangered woody plant Phoebe bournei remain largely unclear. This study comprehensively analyzed the PbbZIP gene family in P. bournei, identifying 71 PbbZIP genes distributed across all 12 chromosomes. The amino acid count in these genes ranged from 74 to 839, with molecular weights varying from 8813.28 Da to 88,864.94 Da. Phylogenetic analysis categorized the PbbZIP genes into 12 subfamilies (A-K, S). Interspecific collinearity analysis revealed homologous PbbZIP genes between P. bournei and Arabidopsis thaliana. A promoter cis-acting element analysis indicated that PbbZIP genes contain various elements responsive to plant hormones, stress signals, and light. Additionally, expression analysis of public RNA-seq data showed that PbbZIP genes are distributed across multiple tissues, exhibiting distinct expression patterns specific to root bark, root xylem, stem bark, stem xylem, and leaves. We also performed qRT-PCR analysis on five representative PbbZIP genes (PbbZIP14, PbbZIP26, PbbZIP32, PbbZIP67, and PbbZIP69). The results demonstrated significant differences in the expression of PbbZIP genes under various abiotic stress conditions, including salt stress, heat, and drought. Notably, PbbZIP67 and PbbZIP69 exhibited robust responses under salt or heat stress conditions. This study confirmed the roles of the PbbZIP gene family in responding to various abiotic stresses, thereby providing insights into its functions in plant growth, development, and stress adaptation. The findings lay a foundation for future research on breeding and enhancing stress resistance in P. bournei. Full article

NAC (NAM, ATAF1/2, CUC1/2) is a plant-specific transcription factor (TF) family that plays important roles in various physiological and biochemical processes of plants. However, the NAC gene family in Lagerstroemia indica and its role in anthocyanin metabolism are still unexplored. In our study, a total of 167 NACs were identified in the L. indica genome via genome-wide analysis and bioinformatics techniques. Amino acid sequence analysis showed that all 167 NAC proteins contained a conserved NAM domain. This domain primarily comprised random coils, extended strands, and alpha helices. Most NACs were found on the nucleus and dispersed over 23 of the 24 plant chromosomes. Based on phylogenetic analysis, the NACs can be categorized into ten subgroups. Furthermore, the promoter homeotropic elements predicted the cis-acting elements in the promoters of these genes related to hormones, development, environmental stress response, and other related responses, demonstrating the diverse regulatory mechanisms underlying gene functions. In addition, a co-expression network was established through RNA sequencing. This network helped identify seven key LiNACs, genes related to anthocyanin expression (CHS) and transcription factors (MYB and bHLH). To identify potential anthocyanin regulatory factors present in L. indica petals, protein interaction prediction was performed, which revealed that LiNACs might participate in anthocyanin regulation by interacting with other proteins, such as MYB, ABF, ABI, bZIP, MYC, etc. Our results provided novel insights and could help in the functional identification of LiNACs in L. indica and the regulation of anthocyanin synthesis. Full article

The TGACG motif-binding factor (TGA) family is an important group of basic region/leucine zipper (bZIP) transcription factors in plants, playing crucial roles in plant development and stress responses. This study conducted a comprehensive genome-wide analysis of the TGA transcription factor (TF) family in common wheat (Triticum aestivum L.). A total of 48 wheat TGAs were identified and classified into four subgroups. Collinearity analysis of the TGAs between wheat and other species identified multiple duplicated gene pairs and highlighted the presence of highly conserved TGAs in wheat. Whole-genome and segmental duplications were identified as the primary drivers of TaTGA expansion. Expression pattern analysis indicated that TaTGAs are involved in plant development and responses to abiotic stresses, including drought, heat, and cold treatment. Among these, TaTGA16-2D was significantly upregulated under both drought and heat stresses, showing more than a five-fold increase in expression. Subcellular localization confirmed its nucleus localization. Functional validation through ectopic expression in Arabidopsis demonstrated that transgenic lines overexpressing TaTGA16-2D exhibited significantly improved stress tolerance. Under heat stress, the survival rates of transgenic lines exceeded 34%, compared to less than 18% in wild-type plants. Overall, this study provides valuable insights into the evolution and functional roles of TaTGAs and identifies TaTGA16-2D as a promising candidate to enhance abiotic stress tolerance in wheat via molecular breeding. Full article

Abscisic acid (ABA), a pivotal phytohormone regulating plant growth and stress adaptation, orchestrates abiotic stress responses through the ABA-responsive element-binding factors ABF/AREB/ABI5. Nevertheless, the functional characterization of ABF/AREB/ABI5 homologs in Z. jujuba cv. Dongzao remains unexplored. In this study, we identified seven ZjABF genes distributed across five chromosomes. Domain analyses revealed high structural conservation, particularly within the basic leucine zipper (bZIP) DNA-binding domain. Subcellular localization confirmed nuclear targeting of all seven ZjABF proteins. Phylogenetic classification resolved these factors into three clades (A–C). Cis-regulatory element profiling implicated the involvement of the ZjABFs in hormone signaling, abiotic stress transduction, and photoregulatory pathways. Synteny analyses identified three segmental duplication events within the gene family. Tissue-specific expression patterns indicated critical roles for ZjABF2 and ZjABF3 in fruit maturation, and most of the ABF/AREB/ABI5 genes were highly expressed in the root. Under drought stress, four ZjABF genes exhibited differential expression, with ZjABF2 demonstrating pronounced sensitivity. These findings establish a molecular framework for understanding ZjABF-mediated abiotic stress responses in non-model woody perennials. Full article

Background: Basic (region) leucine zippers (bZIPs) make up one of the largest families and are some of the most prevalent evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. Plant bZIP family members are involved in seed germination, vegetative growth, flower development, light response, and various biotic/abiotic stress response pathways. Nevertheless, a detailed identification and genome-wide analysis of the bZIP family genes in broomcorn millet have not been conducted. Methods: In this research, we performed genome-wide identification, phylogenetic analysis, cis-elements analysis, and expression pattern analysis. Results: 144 bZIP transcription factors were identified from the P. miliaceum genome and classified into eleven subfamilies using a phylogenetic analysis. Motif and bZIP domain sequence alignment analyses indicated that the members in each subfamily were relatively conserved. Furthermore, a promoter analysis revealed that bZIP transcription factor family genes were responsive to multiple hormones and environmental stresses. Additionally, cis-element MYB binding sites were identified in the promoters of most PmbZIP genes. A gene expression analysis showed that 18 PmbZIP genes were differentially expressed during seed germination in salt stress, with 7 being significantly downregulated and 11 upregulated, thus suggesting that these PmbZIP genes may play an important role in the salt stress response and seed germination. Conclusions: Current research provides valuable information for further functional analyses of the PmbZIP gene family and as a reference for future studies on broomcorn millet’s stress response. Full article

Mung bean (Vigna radiata L.) is globally cultivated and has been widely used in the food industries. Other than nutrients, the composition of the volatile organic compounds (VOCs) often influences the quality of mung bean-based products. However, the dynamics of VOCs and the flavor changes during mung bean seed development remain unexplored. This study investigated the VOC and flavor composition in four mung bean varieties by integrating relative odor activity value (ROAV) evaluation and transcriptomic analysis. A total of 65 VOCs were identified, with eucalyptol serving as a key maturity indicator in LL655 and SH-1, while nonanal contributed significantly to the characteristic beany flavor across all varieties. Transcriptomic analysis revealed four downregulated geranylgeranyl diphosphate synthase genes during seed development, leading to terpenoid accumulation patterns. Terpenoids, including trans-beta ocimene and gamma-terpinene, appeared to be regulated by transcription factors (TFs) from the RLK-Pelle, WRKY, AP2/ERF, bHLH, and bZIP families. Additionally, two MYB TFs showed potential roles in modulating the accumulation of phenylpropanoid/benzenoid derivatives. This study provides a comprehensive understanding of the VOC accumulation and flavor variation during mung bean seed development, enriches the knowledge of flavor chemistry in mung bean varieties, and facilitates a theoretical foundation for optimizing and developing mung bean-based products. Full article

The basic leucine zipper (bZIP) gene family constitutes one of the most abundant and conserved transcription factor families in plants, which participates in diverse physiological processes including response to abiotic stress, anthocyanin accumulation, and the regulation of plant growth and development. Although bZIP genes play an important role in plants, comparable studies in mulberry are lacking, particularly regarding their response under abiotic stress conditions. In this study, we identified 56 mulberry bZIP transcription factors and divided these members into 12 groups by phylogenetic analysis. The coding genes of these bZIPs harbor a large number of segmental duplications and are unevenly distributed on 12 chromosomes. We further identified numerous stress responsive elements in the promoter regions of bZIP genes. Furthermore, by analysis of the expression profiles from RNA-seq data, we identified MabZIP43 and MabZIP24 that respond to heat, salt–alkaline, and high light stress. We also found that the gene expression of MabZIP16 was closely related to anthocyanin biosynthesis. As described, we systematically explored the structures and functions of the bZIP gene family in Morus alba. The results imply that the bZIP gene family plays significant roles in stress response and anthocyanin biosynthesis. Three bZIP candidate genes are suggested for genetic engineering to improve the resistance of mulberry to stress and for high-anthocyanin-producing lines. Full article

Enhancing stress tolerance represents a critical objective in the genetic improvement of poplar trees. Populus × euramericana ‘Bofeng 3’ is a nationally certified elite poplar variety that was approved as a premium pulpwood variety for the southern area of Northeastern China. This variety grows quickly, has good yield, and resists frost; however, its weaker drought and salt tolerance limits its broader use in diverse environments. The aim of this study is to understand the genetic basis of the fast growth and stress-adaptation traits of this variety and to provide support for future molecular breeding efforts. We present a chromosome-scale genome assembly of Populus × euramericana ‘Bofeng 3’, totaling 445.53 Mb, of which with 90.39% is anchored to 19 chromosomes, containing 33,309 protein-coding genes and 45.36% repetitive elements. Comparative genomics showed that ‘Bofeng 3’ has expanded gene families related to photosynthesis and metabolism, and contracted families involved in stress responses, distinguishing it from other Populus species. Under drought (9137 leaf, 9403 root differentially expressed genes (DEGs)) and salt stress (2840 leaf, 3807 root DEGs), trend analysis revealed specific expression patterns. Several unique and expanded genes, including those for photosynthetic proteins, peroxidases, gamma-aminobutyric acid metabolism, and disease resistance, showed stress-responsive trends. Weighted gene co-expression network analysis identified five modules (three positive, two negative) that significantly correlated with photosynthetic traits, highlighting key candidates such as bZIP transcription factors and auxin/indole acetic acid genes. This study determined the genetic basis underlying the rapid growth traits of Populus × euramericana ‘Bofeng 3’, while providing genomic resources to establish a robust foundation for future gene editing and molecular breeding studies, including critical candidate genetic resources for developing superior drought- and salt-tolerant poplar varieties via targeted genome editing technologies. Full article

Root-knot nematodes (RKNs), specifically Meloidogyne incognita, are notoriously difficult to eliminate as endophytic nematodes, and cause severe damage to various plants. Cucumber (Cucumis sativus), which is a cash crop widely grown across the world, is often infected by RKNs. ELONGATED HYPOCOTYL5 (HY5), a member of the bZIP transcription factor family, plays a vital role in hormone, nutrient, abiotic stress, biotic stress, and oxygen species (ROS) signaling pathways. However, the involvement of HY5 in the defense against RKNs has rarely been reported. The present study initially explored the response of CsHY5 to RKNs. The results indicated that the hy5 mutant had a higher number of nematodes and galls in the root system and exhibited a higher susceptibility to RKNs compared with the wild type (WT). Particularly, the root-knot nematodes in hy5 plants completed their life cycle more quickly and produced more eggs. The activities of defense-related hormones and antioxidant enzymes were measured, and the results indicated that JA, jasmonoyl-isoleucine (JA-Ile), abscisic acid (ABA), peroxidase (POD), and ascorbate peroxidase (APX) were significantly elevated in the wild type, but were not induced or decreased in the mutant. Through transcriptome sequencing analysis and quantitative real-time PCR (qRT-PCR), it was found that when RKNs infect plants, the key genes of jasmonic acid (JA) synthesis, CsAOC and CsAOS, as well as the key gene of the antioxidant system, CsPOD, were all significantly induced. Nevertheless, this induction effect disappeared in the hy5 mutant. Generally, CsHY5 plays a role in the response of cucumber to RKNs, and its deletion increases the sensitivity of cucumber to RKNs. These results suggest that CsHY5 may affect the resistance of cucumber to RKNs by affecting antioxidant enzyme activities and hormone content. Full article

Zinc (Zn) is an essential micronutrient required for plants to perform various metabolic functions, and plant responses to Zn deficiency have been extensively studied. However, excessive levels of Zn in soil can induce toxic effects in plants, posing a substantial challenge to global agricultural productivity. Consequently, elucidating the response mechanisms of crop plants to excessive Zn toxicity is currently of great significance. In this study, seedlings of maize inbred line B73 were exposed to excessive Zn treatment, and transcriptomic profiling of the roots was conducted at 0, 2, 6, 12, 24, and 48 h post-treatment. In addition to changes in the expression of genes encoding zinc-regulated, iron-regulated transporter-like protein (ZIP), metal tolerance protein (MTP), and yellow stripe-like (YSL) transporter family members involved in Zn transport, we observed that differentially expressed genes (DEGs) were significantly enriched in the phenylpropanoid–lignin metabolic pathway across all treatment stages, including the early (2 and 6 h), middle (12 and 24 h), and late (48 h) stages of Zn treatment. Among the 11 core structural enzyme-encoding genes involved in monolignols biosynthesis from phenylalanine in this pathway, the expression of eight of them was altered by Zn treatment. Additionally, genes encoding peroxidase (POD), which are responsible for the polymerization of monolignols into lignin, demonstrated extensive changes across all treatment stages, particularly at the late stage. The expression levels of these key enzyme genes were further validated using quantitative real-time PCR. Correspondingly, the activity of POD enzymes and the lignin content both significantly increased in Zn treated roots. These findings suggest that the phenylpropanoid–lignin metabolic pathway plays a crucial role in maize root responses to excessive Zn stress. Full article

Rhododendron L., a renowned ornamental species and one of the ten famous flowers in China, is highly regarded for its aesthetic value and extensive applications in landscaping. However, its growth and quality are significantly compromised by drought stress, particularly in regions with dry conditions. To elucidate the drought response mechanisms of Rhododendron, two cultivars, ‘SaKeSiZhiXing’ (SKSZX) and ‘TuRuiMeiGui’ (TRMG), were subjected to natural drought stress, and changes in chlorophyll fluorescence and transcriptomic profiles were examined at 0 days (d), 4 d, and 8 d of drought exposure. An OJIP fluorescence transient (O-J-I-P) analysis revealed a progressive decline in the F_P parameter and an increase in the F_J parameter as drought stress intensified. Additionally, a delayed fluorescence (DF) analysis showed a gradual reduction in the I₁ and I₂ values within the induction and decay curves under prolonged drought conditions. The 820 nm curve indicated the deactivation of a transient phase characterized by a rapid decline, followed by a slow recovery in the modulated reflection (MR) signal. A transcriptomic analysis of leaves identified 24,352, 18,688, and 32,261 differentially expressed genes (DEGs) in SKSZX at 0 d, 4 d, and 8 d of drought treatment, respectively. In contrast, TRMG exhibited more pronounced and earlier drought-induced alterations. These DEGs were primarily enriched in pathways related to phenylpropanoid biosynthesis, plant hormone signaling, photosynthesis, and photosynthesis-antenna proteins. Additionally, 565 transcription factors (TFs) were identified, including bHLH, WRKY, bZIP, MYB-related, MYB, C2H2, and HSF families. The drought-induced changes in TRMG were more substantial and occurred earlier compared to SKSZX, with a greater impairment in the electron transfer capacity at both the donor and acceptor sides of photosystem II (PSII). This study provides valuable insights into the molecular mechanisms underlying drought tolerance in Rhododendron and offers a foundation for molecular breeding strategies aimed at enhancing drought resistance in future cultivars. Full article

The Basic Leucine Zipper (bZIP) transcription factors play a vital role in plant responses to abiotic stress. Despite being studied in various plant species, the function of the bZIP gene family in Soapberry (Sapindus mukorossi Gaertn.), a significant tree species for forestry biomass energy, remains unclear. In this study, we conducted a genome-wide analysis of the bZIP gene family in Soapberry, based on the observation that bZIP transcription factors were enriched in the transcriptome data of Soapberry-grafted stem segments, as revealed by both GO and KEGG analyses. For the first time, we identified 31 SmbZIPs and provided detailed information regarding their physicochemical characteristics, gene structures, protein motifs, phylogenetic relationships, cis-regulatory elements (CREs), and predicted transcriptional regulatory networks. According to our prediction of the SmbZIP-mediated regulatory network and CREs in the promoter region, SmbZIPs may be associated with plant growth and development as well as responses to mechanical wounding stress. By integrating RT-qPCR and RNA-seq analyses, we determined that the expression patterns of SmbZIPs were specific to the graft-healing stages and locations. In conclusion, our study elucidates the potential role of the bZIP gene family in responding to plant wounding stress and facilitating graft healing, thereby providing valuable insights for future functional genomics studies of Soapberry. Full article

Background/Objectives: In perennial plants, developing floral buds survive winter through entering a dormant state, which is induced by low temperature and abscisic acid (ABA). ABA performs vital functions in the dormancy process. ABA-insensitive 5 (ABI5) transcription factor is a key regulator in the ABA signaling pathway. However, little is known about the regulation of ABI5 in the winter dormancy of sweet cherries. Methods: We identified the sweet cherry ABI5 gene and its expression changes using gene cloning and qRT-PCR. Additionally, we validated the interaction between PavABI5 and PavCIG1/2 using Yeast One-Hybrid and Dual-Luciferase Assays. Results: In this study, we identified a basic leucine zipper (bZIP) family gene ABI5 from the sweet cherry, which was closely related to PduABI5 from Prunus dulcis, PpABI5 from Prunus persica, PmABI5 from Prunus mume, and ParABI5 from Prunus armeniaca, through phylogenetic tree analysis. The seasonal expression pattern showed that the PavABI5 level was increased during the winter dormancy stage and induced by exogenous ABA. Specifically, we found that the expression of cherry cold-induced genes (PavCIG1/2) was positively correlated with PavABI5 expression. Furthermore, PavABI5 directly bound to the ABRE elements in the PavCIG1/2 promoters to activate their expression. We further confirmed that the dormancy-associated MADS-box (DAM) genes DAM4 and DAM5 function downstream of the ABA signaling pathway to regulate bud dormancy in sweet cherries. Conclusions: Our findings suggest a putative regulatory model of ABA-mediated bud-dormancy with PavABI5. Full article

Wolfberry (Lycium barbarum L.) is a valued traditional medicinal plant and dietary supplement in China. The basic leucine zipper (bZIP) transcription factor (TF) family is a multifunctional group of regulatory proteins critical to plant biology, orchestrating processes such as growth and development, secondary metabolite biosynthesis, and stress responses to abiotic conditions. Despite its significance, limited information about this gene family in wolfberry is available. In this study, a total of 66 LbabZIP genes were identified, exhibiting a non-uniform distribution across all 12 chromosomes. Phylogenetic analysis divided these genes into 13 subgroups based on comparison with Arabidopsis bZIP proteins. Analysis of gene structures and conserved motifs revealed high similarities within individual subgroups. Gene duplication analysis indicated that dispersed duplication (DSD) and whole-genome duplication (WGD) events were the primary drivers of LbabZIP gene family expansion, with all duplicated genes subject to purifying selection. Cis-regulatory element (CRE) analysis of LbabZIP promoter regions identified numerous elements associated with plant growth and development, hormone signaling, and abiotic stress responses. Gene Ontology (GO) annotation further indicated that the LbabZIP genes are involved in transcriptional regulation, metabolism, and other biological processes. Transcriptome data and quantitative real-time PCR (qRT-PCR) analysis demonstrated tissue-specific expression patterns for several LbabZIP genes. Notably, LbaZIP21/40/49/65 showed significant involvement in wolfberry fruit development. Subcellular localization assays confirmed that these four proteins are nucleus-localized. This comprehensive analysis provides a theoretical foundation for future studies investigating the biological functions of LbabZIP genes, especially their role in wolfberry fruit development. Full article