Search Results (700)

Chinese cabbage is one of the major vegetable crops in northern Asia. Its leaves are the major organ for photosynthesis and production, and leaf color directly influences its yield and quality. Here, we obtained a pale green mutant pgm3. This mutant line was derived from EMS mutagenesis of Chinese cabbage DH line FT. pgm3 exhibited chlorosis and etiolation, delayed growth, reduced photosynthetic pigment content and net photosynthetic rates, and impaired development of the chloroplast inner membrane system. Genetic analysis revealed that the pale green phenotype was controlled by a single recessive nuclear gene, Brpgm3. Mutmap analysis indicated that Brpgm3 is located on a 13.9 Mb region in A03. Within this region, a single SNP (A03: 7194530) with an SNP-index of 1, located in BraA03g015750.3C (BrClpC1), was identified from 40 differential SNPs. KASP genotyping demonstrated that the SNP co-segregated with the pale green phenotype in the F₂ population. Sanger sequencing confirmed a G-to-A SNP in exon 4 of BrClpC1, which resulted in an amino acid substitution from S to G. Furthermore, multiple sequence alignment of homologs from 28 species demonstrated that this mutated residue is highly conserved. BrClpC1 was predominantly expressed in leaves and exhibited the highest transcript abundance among the nine members of the Class I Clp gene family in Brassica rapa. This is the first report identifying ClpC1 in Brassica crops. Our results not only confirmed BrClpC1 as a strong candidate gene for the pale green mutant of Chinese cabbage, but also highlighted BrClpC1 as a target for chloroplast biology research in Brassica crops. Full article

Soybean (Glycine max L.) is an important agricultural crop for human food and animal feed. Soybean yield is severely constrained by abiotic stresses such as salinity and drought, which affect large proportions of arable and irrigated lands worldwide. This necessitates the development of new soybean varieties tolerant to these stress factors. Mutation breeding is an effective approach to improve the stress tolerance of plants due to increased genetic diversity. In this study, two gamma-induced salinity and drought-tolerant soybean mutants (SM1 and SM3-1) were compared with the parental line S04-05 using GO and KEGG pathway enrichment analyses. GO enrichment analyses revealed extensive differential gene expression in the mutant lines under stress conditions, with significant enrichment of pathways related to photosynthesis, hormone signaling, carbohydrate metabolism, and flavonoid and isoflavonoid biosynthesis. Genotype-specific analyses indicated that the SM3-1 mutant exhibited a dynamic regulatory response associated with maintaining the photosynthetic apparatus and chloroplast homeostasis under stress, whereas the SM1 mutant showed an adaptation strategy based on metabolite-mediated osmotic adjustment and ROS scavenging. Compared to the parental variety S04-05, the mutants showed distinct metabolic regulation in phenylpropanoid/isoflavone metabolism, with upregulation of many isoflavone biosynthesis genes under salinity, drought, and untreated conditions, indicating a key and sustained role of this pathway in stress tolerance. Most SNPs identified in the isoflavone biosynthesis pathway consist of moderate-impact and modifier variations. These findings suggest that gamma mutagenesis and subsequent selection processes allow for the development of novel genetic variants that operate through different physiological and metabolic mechanisms but exhibit similar levels of tolerance. In this respect, the study reveals that mutation breeding is a potentially sustainable and effective breeding strategy for increasing abiotic stress tolerance in soybeans. Full article

Lodgepole pine (Pinus contorta Dougl.) exhibits pronounced morphological variation across its range, historically attributed to allopatric differentiation during the Wisconsin glaciation. However, whether genetic divergence aligns with morphological differentiation—a fundamental prediction of allopatric speciation theory—remains untested. We conducted a comprehensive phylogeographic analysis of chloroplast DNA (trnL intron and trnL/trnF spacer) and mitochondrial DNA (nad1 b/c intron) across 31 populations representing all four recognized subspecies to test hypotheses of refugial isolation and to evaluate the genetic basis of current taxonomic classification. Contrary to predictions of allopatric divergence, both organellar genomes showed striking genetic uniformity (π = 0.000178–0.000186; intersubspecific genetic distances: 1.06 × 10⁻⁴ to 3.96 × 10⁻⁴) with no phylogenetic structure corresponding to morphological boundaries. Significant negative neutrality test values (Tajima’s D = −2.26, p < 0.02; Fu and Li’s D* = −4.52, p < 0.02) suggest recent demographic expansion rather than equilibrium divergence. A distinctive 5 bp indel in coastal populations provides molecular evidence for a northern Pacific refugium, and its occurrence in interior populations is consistent with post-glacial pollen-mediated gene flow, though this directionality remains inferential pending nuclear genomic confirmation. These findings suggest that morphological divergence reflects rapid adaptive evolution in heterogeneous environments rather than deep phylogenetic divisions. This pattern exemplifies gene flow-selection balance, in which divergent selection maintains local adaptation despite extensive gene flow—supporting an ecotypic rather than a phylogenetic interpretation of intraspecific diversity. The persistence of morphological variation despite genetic homogeneity indicates strong selection on ecologically important traits, likely driven by variation in fire regimes, differential seed predation, and climate gradients. These results have critical implications for understanding adaptive evolution rates in widespread conifers and for developing conservation strategies that emphasize adaptive processes over taxonomic categories. Full article

The common bean (Phaseolus vulgaris L.cv. BR-104) is the most widely cultivated legume crop and serves as a major dietary protein source worldwide. However, climate change-induced drought poses a severe threat to its productivity by disrupting key physiological and biochemical processes. Therefore, identifying effective strategies to enhance drought resilience in the common bean is of considerable importance. The present study investigates the regulatory role of hydrogen sulfide (H₂S) in improving drought tolerance. Polyethylene glycol (15% PEG) induced drought stress markedly reduced phenotypic changes (leaf area (LA), plant dry weight (PDW), root length (RL), and shoot length (SL) by 18.6, 20.5, 30.3 and 17.5% respectively), photosynthetic efficiency (Fv/Fm by 28.4%), and photosynthetic pigment concentrations (chlorophyll and carotenoids by 25.6 and 36%, respectively), while significantly elevating oxidative stress markers (H₂O₂ and TBARS by 137.1% and 169.8%, respectively), leading to impaired stomatal movement and damaged chloroplast structure. Exogenous H₂S application as sodium hydrogen sulfide (200 µM NaHS; H₂S donor) effectively alleviated drought-induced oxidative damage by boosting endogenous H₂S and GSH levels, upregulating activity of antioxidative enzymes, SOD, APX, and GR, thereby promoting reactive oxygen species (ROS) scavenging, and minimizing lipid peroxidation. Moreover, H₂S maintained photosynthetic efficiency via improved stomatal openings and chloroplast structure, thus sustaining chlorophyll levels and stabilizing photosystem-II functionality. Enhanced proline accumulation following NaHS application led to improved osmotic adjustment, thereby contributing to overall stress tolerance. The use of a H₂S scavenger at 100 µM HT (Hypotaurine) suppressed the mitigating effects of H₂S, confirming the role of H₂S in enhancing drought tolerance in the common bean. Collectively, these findings highlight the potential effect of H₂S as a regulatory signaling molecule to enhance drought resilience in the common bean under drought stress conditions. Further research should explore integrating H₂S-based treatments with breeding programs and agronomic practices to develop sustainable strategies to improve drought resilience in legumes and other staple crops under changing climatic conditions. Full article

Peptide deformylase (PDF) belongs to a conserved enzyme family critical for N-terminal methionine excision (NME), an essential protein maturation process in prokaryotes and eukaryotic organelles (chloroplasts, mitochondria). To explore the potential functions of OsPDFs in Oryza sativa, this study employed bioinformatics approaches and experimental validation to systematically identify and analyze the OsPDF gene family. Three OsPDF genes (OsPDF1A, OsPDF1B, OsPDF1B2) were identified in rice. These genes are exclusively distributed on chromosome 1. The biophysical properties of these proteins showed that OsPDF1A and OsPDF1B are alkaline proteins, while OsPDF1B2 is acidic, and all are hydrophilic with moderate thermostability potential. Synteny analysis revealed closer evolutionary relationships between Oryza sativa and the monocot Triticum aestivum than with dicots, reflecting conserved PDF function in gramineous plants. Analysis of cis-acting elements in the 2000 bp upstream region of OsPDF gene promoters revealed numerous elements associated with abiotic stress response and hormone regulation. Furthermore, quantitative real-time PCR (qRT-PCR) data supported these findings, indicating that OsPDF1A and OsPDF1B were upregulated under low-temperature stress, and all three OsPDF genes were transcriptionally activated by heat, salt and UV-B stresses, indicating their active involvement in rice growth, development, and abiotic stress tolerance. In summary, OsPDFs exhibit significant functions in rice’s stress adaptation, growth, and development. This study not only enhances our understanding of the OsPDF gene family’s genomic, evolutionary, and functional characteristics, but also provides new perspectives and foundational data for further exploring their regulatory mechanisms in protein maturation and abiotic stress responses, as well as their potential applications in rice stress tolerance breeding. Full article

Parameters of reflected light, measured in narrow or broad spectral bands, are widely analyzed for remote and proximal sensing of plant responses to stressors. Specifically, parameters of reflectance in red (R), green (G), and blue (B) spectral bands measured using simple color images can be sensitive to characteristics of plants. The conventional view is that RGB reflectance primarily reveals long-term changes in plants (days, weeks, etc.). In this study, we investigated light-induced changes in RGB reflectance in wheat (Triticum aestivum L.) and pea (Pisum sativum L.) leaves. Illumination increased this reflectance for about 10 min in wheat and about 15–20 min in pea; these changes relaxed after light intensity was decreased. The changes in RGB reflectance were strongly related to the effective quantum yield of photosystem II and non-photochemical quenching of chlorophyll fluorescence under high light intensity; these relations were absent under low light intensity. We hypothesized that changes in both RGB reflectance and photosynthetic parameters were related to the light-induced changes in chloroplast localization. A simple mathematical model of optical properties and photosynthesis in leaves was developed; results of the model-based analysis supported the proposed hypothesis. Experimental analysis of the dynamics of light transmittance additionally supported this hypothesis. Our results thus show that RGB imaging can be sensitive to fast changes in plants. Full article

Viral infections of grapevines reduce plantation productivity and planting material quality, necessitating the development of effective sanitization methods and comprehensive systems for monitoring plant physiological status. This study conducted a comprehensive analysis of the physiological–biochemical status of grapevine microplants (morphometric parameters, activity of key antioxidant enzymes, dehydrogenase activity, pigment composition, and relative copy number of mitochondrial and chloroplast DNA) in microclones of the rootstock Vitis riparia × Vitis berlandieri ‘Kober 5 BB’ in vitro, depending on the presence of viral infection and sanitization using thermo- and cryotherapy. Four plant variants were investigated: healthy (VIRUS FREE), infected (VIRUS), sanitized via thermotherapy (V.F.T.), and cryotherapy (V.F.K.). It was shown that, despite the absence of pronounced suppression of morphometric parameters, viral infection causes a significant increase in total protein content, catalase, polyphenol oxidase, and total dehydrogenase activity in tissues, as well as pigment imbalance (changes in the chlorophyll coefficient) and modulation of the carotenoid profile, along with alterations in the relative copy number of mitochondrial and chloroplast DNA. The relative copy number of mitochondrial and chloroplast DNA decreased in infected plants and was restored to a greater extent after cryotherapy rather than after thermotherapy. The results indicate the formation of stress-related changes (stress imprint) that persist in sanitized microclones and can serve as a multilevel marker system for assessing sanitization efficacy and monitoring the physiological status of grapevine microplants in vitro. Full article

Leaf-color variation in plants should be associated with chlorophyll metabolism and chloroplast development. Here, we characterized a low-temperature-sensitive pakchoi DH line, 1197, which exhibited green leaves at 25 °C, but showed yellowing at 4 °C. Low temperature significantly reduced chlorophyll accumulation and disrupted chloroplast ultrastructure. After transfer from 4 °C to 25 °C for 7 days, yellow leaves partially regreened, and chlorophyll a content increased by 366.67%. RNA-seq analysis identified 3058 core DEGs associated with the yellowing–regreening transition, which were significantly enriched in photosynthesis–antenna proteins, photosynthesis, and porphyrin metabolism pathways. Leaf yellowing was characterized by repression of chlorophyll biosynthesis genes (e.g., CHLD, CHLM, PORC) and induction of degradation genes (SGR1, SGR2, NYC1, PAO), together with widespread downregulation of chloroplast function-related genes. In addition, GLK2, HBI1, NAC047, and NAC029 were identified as candidate regulators of temperature-dependent leaf-color conversion. This study provides candidate molecular insights into low-temperature-induced yellowing and regreening in pakchoi and offers candidate genes for future functional validation and Brassica breeding. Full article

Background: Chlorophyll degradation is a characteristic sign of fruit ripening. However, the chlorophyll degradation pathway during pitaya fruit development remains unexplored. Methods and Results: Here, chlorophyll contents showed a downward trend across the five developmental stages of ‘Jindu No.1’ pitaya peels. Based on the pitaya genome data, twenty chlorophyll degradation genes were identified, including two NYCs, three CLHs, five SGRs, six PAOs, and four RCCRs, spread across eight pitaya chromosomes. In addition, their phylogenetic relationships, conserved motifs, and domains were analyzed using homologous genes from beet and Arabidopsis species. Transcriptomic data and RT-qPCR analyses of these genes suggested that three HuSGRs demonstrated a significant upward trend during pitaya peel maturation. Indeed, the HuSGR1 has the complete gene structure, including the chloroplast transit peptide, SGR domain, and variable C-terminal region. However, HuSGR2 and HuSGR3 contained the N- and C-terminal sequences, respectively, of HuSGR1. They were separated by a 690 bp distance on chromosome 8, forming a gene cluster. Overexpressed HuSGR2 or HuSGR3 alone resulted in a significant decrease in chlorophyll contents in tobacco leaves. Notably, a more obvious reduction of chlorophyll contents was observed when overexpressing them together. Conclusions: Our results show that HuSGR2 and HuSGR3 were involved in accelerating the chlorophyll degradation process, providing new insights into the molecular basis of color formation in pitaya peels. Full article

Granule-bound starch synthase (GBSS) is primarily recognized for its role in amylose production and starch granule formation in plant plastids. While its biochemical function in storage organs has been well documented, its broader contribution to plant growth and stress adaptation remains less defined. To explore these aspects, the maize gene ZmGBSS1 was ectopically expressed in Arabidopsis thaliana and its physiological effects were examined. Subcellular localization assays confirmed that ZmGBSS1 is specifically localized to chloroplasts. Phenotypic analysis of transgenic lines revealed that overexpression of ZmGBSS1 significantly altered early seedling development, promoted root elongation, and accelerated flowering, with flowering occurring approximately four days earlier than in wild-type plants. Changes in development were accompanied by increased starch accumulation, elevated amylose levels, and a higher abundance of enlarged starch granules within chloroplasts. Under drought and PEG-induced osmotic stress, transgenic plants maintained improved growth performance and recovery capacity, together with greater proline accumulation and chlorophyll retention. These physiological advantages coincided with more rapid starch utilization and clear rises in transcripts for proline synthesis enzymes (AtP5CS1, AtP5CS2) and starch-degrading proteins (AtBAM1, AtBAM3, AtDPE1). Collectively, these findings suggest that ZmGBSS1 not only regulates starch biosynthesis but also plays a crucial role in coordinating plant development and drought stress responses, highlighting its potential for improving stress tolerance through metabolic regulation. Full article

ZmSIG2A is a nuclear-encoded plastid sigma factor 2A in maize (Zea mays L.) that is essential for plastid gene transcription and chloroplast biogenesis. As a key regulator of chloroplast development and function, ZmSIG2A may also contribute to the coordination of plant growth and environmental adaptation; however, its roles in root development and stress responses remain largely unclear. We compared two ZmSIG2A mutants, eal1-1 (hypomorphic) and ems110 (nonsense). eal1-1 had increased root number and longer roots, while ems110 had normal root number but shorter roots and failed to mature. The zmsig2a^Val480del transcript was upregulated in eal1-1, and the root-promoting effect of OsSIG2A in rice suggests a conserved role in monocot root growth. DAP-seq indicated that zmsig2a^Val480del targets are involved in metabolism, transport, signaling, and antioxidants, with Chr4 peak clustering near multiple LRR-RLKs, suggesting a ZmSIG2A–LRR-RLK module in root development and stress integration. Physiologically, eal1-1 showed increased antioxidant enzyme activities and reduced MDA, indicating enhanced ROS scavenging, while ems110 exhibited decreased enzyme activities and elevated MDA, indicating compromised ROS detoxification. Upstream, Y1H and dual-luciferase assays demonstrated that the Mediator subunit ZmMed31 positively regulates transcription from the ZmSIG2A promoter. Given Mediator’s role in bridging transcription factors and the core transcriptional machinery, ZmMed31 likely links hormone-responsive transcription factors to the ZmSIG2A regulatory network. Collectively, we propose a stress-responsive ZmMed31–ZmSIG2A–LRR-RLK module that underpins maize root development and drought adaptation, offering mechanistic insight and potential targets for stress-resilient breeding. Full article

Mitogen-activated protein kinase kinase kinases (MAPKKKs) play important roles in plant responses to abiotic stresses; however, the function of SiMAPKKK17 in mediating drought tolerance in foxtail millet remains unclear. In this study, the expression pattern, subcellular localization, and biological function of SiMAPKKK17 were investigated to clarify its role in the drought stress response. Tissue expression analysis showed that SiMAPKKK17 was expressed across developmental stages and in multiple organs, with the highest transcript level observed at the booting stage and comparatively higher expression in vegetative tissues, including roots, stems, and leaves. Subcellular localization analysis demonstrated that SiMAPKKK17 was localized to both the plasma membrane and the nucleus, suggesting potential involvement in membrane-associated signal transduction and nuclear regulatory processes. To evaluate its function, foxtail millet lines overexpressing SiMAPKKK17 were generated and subjected to drought stress. Compared with wild-type plants, the overexpression lines exhibited enhanced drought tolerance, as indicated by greener and more upright upper leaves, higher aboveground fresh weight, greater plant height, and larger leaf area under drought conditions. Transcriptome analysis of OE4 and WT plants under drought stress identified 3919 upregulated genes and 2965 downregulated genes in OE4 compared with WT. These differentially expressed genes were mainly enriched in chloroplast-related cellular components, as well as biological processes and metabolic pathways related to cellular amide metabolism, ion transport, carbon metabolism, photosynthesis, carbon fixation, purine metabolism, and amino acid biosynthesis. Taken together, these results indicate that SiMAPKKK17 acts as a positive regulator of drought tolerance in foxtail millet, potentially through modulation of photosynthesis- and metabolism-related pathways. This study provides evidence for the molecular mechanisms underlying drought tolerance in foxtail millet and identifies SiMAPKKK17 as a promising candidate gene for the development of drought-resistant cultivars. Full article

Hopea celebica Burck is an endangered dipterocarp endemic to Sulawesi, Indonesia, occurring in two ecologically contrasting habitats: karst and ultrabasic forests. These environments differ markedly in soil composition and topography, potentially driving ecological specialization and genetic divergence. To investigate the genetic variation and genetic structure of this species, we applied newly developed microsatellite (SSR) markers, together with the chloroplast DNA sequences of the trnL–trnF region. Genotypes at 15 SSR loci were determined for 255 individuals collected from six populations covering the range of the species’ distribution across karst and ultrabasic forests. Genetic diversity was consistently higher in karst than in ultrabasic populations. DIYABC and VarEff analyses revealed a historical bottleneck and earlier recovery in the karst populations. Analysis of molecular variance (AMOVA) revealed that 35% of the genetic variation was partitioned between habitat types (F_RT = 0.345, p = 0.001). Bayesian clustering (STRUCTURE), principal coordinate analysis (PCoA), and UPGMA dendrograms consistently showed two distinctive clusters corresponding to habitat type. Chloroplast haplotypes differed between populations in the karst and ultrabasic forests. These results suggest that populations in the karst and ultrabasic forests have undergone a long history of differentiation without migration. The strong habitat-related genetic structure likely reflects ecological isolation and early-stage speciation. We recommend treating the karst and ultrabasic populations as distinct conservation units to preserve the evolutionary potential and adaptive capacity of H. celebica under ongoing environmental change. Full article

Yeyong mustard is a mustard vegetable belonging to the Brassicaceae family and the Brassica genus. This study assembled, annotated, and analyzed the chloroplast genome of Brassica juncea L., aiming to clarify its systematic evolutionary relationship with other cruciferous plants. The study used the Illumina NovaSeq 6000 platform to sequence the entire chloroplast genome of leaf mustard, and systematically analyzed its genome structure, repeat sequences, nucleic acid diversity, and codon preferences using bioinformatics methods. At the same time, the phylogenetic relationships were constructed by combining the leaf chloroplast genome sequences of other cruciferous plants. The results showed that the chloroplast genome of leaf mustard had a total length of 153,490 bp and a GC content of 36.36%, exhibiting a typical tetrad structure; a total of 132 coding genes were annotated, including 87 mRNA genes, 37 tRNA genes, and eight rRNA genes, and no pseudogenes were found. Codon preference analysis shows that leucine (Leu) has the highest frequency of use, with 32 codons having a relative synonymous codon usage (RSCU) greater than 1, mostly ending in A or U; there are 37 scattered repetitive sequences and 315 simple repetitive sequences in the genome. Ka/Ks analysis showed that the chloroplast genes of leaf mustard were subjected to purification selection as a whole, while genes such as nadhF and petD showed positive selection, which is speculated to be related to adaptive evolution. The results of the phylogenetic analysis further confirm that the chloroplast genome of leaf mustard has a typical tetrad structure and is relatively conserved. It is most closely related to mustard greens in terms of evolutionary relationship, followed by Brassica plants such as nori and turnip, and is also closely related to Brassica plants such as European rapeseed. This study elucidated the conservative characteristics and evolutionary patterns of the chloroplast genome in mustard leaves, providing theoretical support for the phylogenetic research of the Brassicaceae family and the development and utilization of germplasm resources. Full article

In this study, we dissect the genetic effects of two major rice heading date genes, Heading date 1 (Hd1) and Grain number, plant height, and heading date 7 (Ghd7), in the regulation of six photosynthesis-related traits: the chlorophyll a/b contents, net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), and transpiration rate (Tr). Using two sets of near-isogenic lines (Z43 and Z44) derived from a Zhenshan97/Milyang46 cross, functional Hd1 increased the chlorophyll contents but decreased the photosynthesis-related parameters; however, functional Ghd7 consistently inhibited all six traits. More importantly, there is a significant epistatic interaction between them: Hd1 only enhances the photosynthetic capacity under the non-functional background of ghd7 but intensifies its photosynthesis inhibition under the functional background of Ghd7. Transcriptome analysis showed that functional Ghd7 mainly down-regulated the expression of genes related to photosynthesis and chloroplast development, and the inhibitory effect was significantly enhanced in the presence of functional Hd1. GO enrichment analysis further confirmed that the chlorophyll synthesis, photosystem assembly, and electron transfer pathways were downregulated in the bifunctional allele combination. Although Hd1 promotes chlorophyll accumulation, it reduces the actual photosynthetic efficiency, indicating that it has different regulatory paths for chlorophyll synthesis and photosynthetic function. Both physiological and molecular evidence showed that the Hd1-Ghd7 module coordinated the regulation of the heading date and photosynthetic capacity, forming a trade-off relationship between “early heading–high photosynthesis” and “late heading–low photosynthesis”. This study reveals the pleiotropy of genes at the heading stage and provides a theoretical basis for the optimization of the source–sink balance in high-yield rice breeding. Full article