This study aimed to optimize gamma irradiation for in vitro mutagenesis in two Begonia rex cultivars by determining lethal doses (LD25, 50, 75) and evaluating morpho-physiological responses and oxidative stress using the IBRv2 index. The in vitro-derived callus from leaf explants of two Begonia rex cultivars (“Jurassic” and “Silver King”) were exposed to seven gamma radiation doses (0.0, 10, 20, 30, 40, 50, and 100 Gy) in a 2 × 7 factorial completely randomized design with three replicates. Data were analyzed by two-way ANOVA followed by Duncan’s multiple range test (P < 0.05). Based on regenerated plantlet survival, the estimated LD25, LD50, and LD75 values for “Jurassic” were 43.05, 86.10, and 129.15 Gy, respectively, whereas the corresponding values for “Silver King” were 15.00, 60.00, and 105.00 Gy. Moreover, an increment in gamma radiation dose detrimentally affected plant height, root number, root length, leaf area, leaf number, growth index, and proliferation percentage. The quantities of total phenolic content (TPC) varied from 0.02 mg GAE/ g DW (for “Silver King” at 10 Gy) to 0.54 mg GAE/ g DW (for “Jurassic” at 40 Gy or 100 Gy). The highest ratios of total anthocyanin contents (TAC) were observed for “Jurassic” and “Silver King” cultivars at 40 Gy (1.35 and 1.65 times higher than controls). Both control and treated regenerated shoots of “Jurassic” showed maximum DPPH-assisted radical scavenging activity at 10, 40, and 100 Gy (92.9
The phloem protein 2 (PP2), one of the major phloem proteins, is known to be involved in the transport of nutrients, RNA, and defense; however, the molecular basis of its RNA-binding activity and its role in antiviral defense remain poorly understood. In the present study, we investigated the domains responsible for RNA-binding properties and defense-related functions of PP2 in interactions with apple scar skin viroid (ASSVd) and cucumber mosaic virus (CMV). The cucumber PP2 (CsPP2) was divided into four RNA-binding domains (RBD1-4), and their interactions with ASSVd RNA were analyzed. This study revealed that both the C-termini and the conventionally predicted single RNA-binding domain interact with ASSVd RNA. To investigate the role of the ASSVd-PP2 interaction function by using AtPP2-A1 (the closest homolog of CsPP2) T-DNA knockout mutants, we found that the PP2 protein plays an important role in phloem-based defense in contrast to the long-distance movement of RNA. The AtPP2-A1 gene knockout mutants showed high disease severity and accumulation of ASSVd and reduced expression of the phloem defense marker gene PDF1.2 compared with wild-type plants, indicating a role for PP2 in phloem-based defense. and. In the protoplast study, we found that the PP2 protein does not affect the replication of ASSVd. Like ASSVd, AtPP2-A1 mutants exhibited enhanced susceptibility to cucumber mosaic virus (CMV), symptom severity, and increased viral accumulation. Overall, these findings showed that PP2 functions as an unconventional RNA-binding protein and plays an important role in restricting virus and viroid accumulation through phloem-associated defense mechanisms.
Fig (Ficus carica L.) is a major fruit crop in the Mediterranean Basin, and Türkiye is one of the world’s leading producers. However, fig populations in transitional zones between Mediterranean and continental climates remain poorly characterized compared with those from coastal areas. This study aimed to characterize phenotypic and SSR fingerprint-based variation within a targeted collection of fig genotypes from surveyed sites in the Konya-Karaman transition zone and to identify candidate genotypes for further conservation and agronomic evaluation. A total of 47 female fig genotypes were evaluated using 46 standardized phenotypic and physicochemical traits and 20 SSR markers. Substantial phenotypic variation was observed in key fruit traits, including fruit weight (11.22–68.17 g), fruit width (27.49–53.85 mm), fruit length (22.85–56.09 mm), total soluble solids (16.47–29.90
The “terrestrial island” effect of the karst landscape in southwest China drives plant diversification, with Petrocodon (Gesneriaceae) being a highly specialized representative. Frequent taxonomic revisions and severe morphological convergent evolution obscure its intrageneric phylogeny. Given the low resolution of traditional markers for radiated taxa and the scarcity of molecular data from the Guizhou karst plateau, we analyzed 19 Petrocodon complete chloroplast genomes (plastomes) to characterize genomic structures, resolve interspecific relationships, and identify highly variable candidate markers. We newly assembled 13 plastomes and comparatively analyzed them with six re-annotated public sequences. Ranging from 152,378 to 153,621 bp in length, all plastomes exhibited a typical quadripartite structure containing 131–132 functional genes. They displayed a significant A/T bias, with preferred codons (relative synonymous codon usage, RSCU > 1) strongly terminating in A/U. Sliding window analysis identified 12 highly variable regions as mutational hotspots based on nucleotide diversity (Pi), with ycf1 and ndhF-rpl32 exhibiting the highest nucleotide diversity as the most informative candidate markers. Selection pressure analysis revealed that, despite an overall background of strong purifying selection, the ndhK and atpF genes exhibited elevated evolutionary rates, indicating relaxed purifying selection. Phylogenomic analysis strongly supported the monophyly of Petrocodon, delineating three geographically associated clades (Clades I–III) within our current sampling. Notably, Clade I exhibited distinct geographical endemism. Within Clade III, topological conflicts, extremely short branch lengths, and the non-monophyly of varieties among closely related species suggested a complex history of extremely short internal branches consistent with rapid diversification. This study reveals highly conserved plastome structures among the sampled Petrocodon species. While primarily reflecting ancestral neutral mutational pressures, the pronounced A/T bias may incidentally confer metabolic advantages in nitrogen-poor habitats. Concurrently, the accelerated evolution of ndhK and atpF suggests a potential trend of photoprotective optimization against environmental extremes. Our backbone phylogeny aligns with clade distributions, which is consistent with the hypothesis that karst habitat isolation contributes to speciation among the sampled taxa. Extensive morphological homoplasy exposes traditional taxonomic limitations. Consequently, our whole-plastome data robustly support the monophyly and phylogeny of sampled Petrocodon, including former genera (Calcareoboea, Tengia). These resources and candidate markers aid in elucidating radiation mechanisms and conserving karst biodiversity.
Salinity stress significantly affects the establishment and productivity of pea, a salinity-sensitive cool-season legume, necessitating efficient early-stage screening for tolerant genotypes. A set of 33 pea genotypes were initially screened in vitro under six NaCl concentrations (50–300 mM) using the salt injury index (SII) to determine the optimum salinity level for screening, based on eight seedling traits. An average SII value of 0.5 across the traits identified 100 mM NaCl as the optimal level for differentiating the tolerance, with a mean reduction of 57.8
Laccase (LAC) genes play important roles in plant lignin biosynthesis, cell wall formation, growth and development, and responses to biotic and abiotic stresses. However, the LAC gene family has not been systematically characterized in cucumber (Cucumis sativus). In this study, 34 CsLAC genes were identified in the cucumber genome through hidden Markov model searches and conserved-domain validation. The corresponding CsLAC proteins were classified into six subfamilies, and members within the same subfamily generally showed similar motif compositions and exon–intron structures. The CsLAC genes were unevenly distributed across all seven cucumber chromosomes, with chromosome 1 containing the largest number of members. Intragenomic analysis identified one tandem duplication pair and eight putative whole-genome or segmental duplication pairs, while 27 syntenic gene pairs were detected between cucumber and Arabidopsis thaliana. Ka/Ks ratios below 1 for all analyzed duplicated gene pairs suggested that purifying selection has been the predominant evolutionary force acting on the CsLAC family. Promoter analysis revealed numerous cis-acting elements associated with light responses, hormone signaling, stress responses, and plant development. Protein–protein interaction prediction suggested that CsLAC23, CsLAC19, and CsLAC21 may represent relatively highly connected nodes within the inferred interaction network. Expression profiling revealed distinct tissue-, developmental stage-, and treatment-associated transcript patterns among CsLAC genes. Several genes showed broad transcript accumulation, whereas others exhibited tissue- or stage-preferential patterns and distinct temporal responses to heat, salt, and pathogen treatments. qRT-PCR analysis of eight selected CsLAC genes, with six genes examined under each stress treatment, showed temporal expression trends generally consistent with the transcriptome-derived profiles. Overall, this study provides a comprehensive genome-wide characterization of the cucumber LAC gene family and describes their diverse expression patterns under salt and heat stress. In particular, CsLAC22, CsLAC29, and CsLAC31 were identified as candidate genes that may be involved in responses to both stresses. These findings provide a valuable resource for future functional studies of CsLAC genes and may facilitate the genetic improvement of stress tolerance in cucumber.
Rice production through conventional transplanting is becoming increasingly difficult because of limited water resources and labor shortages. Dry direct-seeded rice (DSR) offers a practical alternative with lower water and labor requirements. However, the success of DSR depends on suitable genotype selection and efficient nitrogen (N) management. Therefore, this study was conducted to assess the influence of genotype, N rate, and split application schedule on yield and agronomic efficiency under temperate conditions. A field experiment was carried out under dry direct-seeded conditions using three temperate rice genotypes: Shalimar Rice-3 (SR-3), Shalimar Rice-4 (SR-4), and SKAU-484 (SK-484). Three nitrogen rates (0, 120, and 150 kg N ha⁻¹) were tested in combination with three split-application schedules (3, 4, and 5 splits). Data were recorded on crop phenology, grain and protein yield, thermal indices, and nitrogen-use efficiency. Significant differences were observed among genotypes and nitrogen treatments. SR-3 produced the highest grain yield (6.4 t ha⁻¹), which was 14
Establishing medicinal and groundcover species like Portulaca oleracea L. in urban green walls requires innovative approaches to overcome restrictive environmental conditions. This study evaluated the morphophysiological, biochemical, and antioxidant responses of purslane grown in an outdoor green wall to the individual and interactive effects of metallic nanoparticles (silver: N1; titanium dioxide: N2; and combined: N3) and Magnet Pellet treatments (Level 1: M1; Level 2: M2; and control: M3). The interaction between nanoparticles and Magnet Pellet significantly influenced most of the evaluated plant traits. Combined applications markedly enhanced canopy coverage, survival duration, and visual quality compared with the control. Under the significant NPs × Magnet Pellet interaction, the N1M1 treatment combination yielded the highest growth index (25,000 cm3), representing a 595
Auxin response factors (ARFs) are plant-specific transcription factors (TFs) that regulate organogenesis, vascular differentiation, and stress responses. However, the ARF family in Solanum americanum, a stress-tolerant wild relative of major Solanaceous vegetable crops, remains largely unexplored. Using the S. americanum reference genome, we identified 18 ARF genes by combining HMM profile searches with homology-based alignment. We then analyzed chromosomal distribution, physicochemical properties, gene structure, conserved protein domains and motifs, promoter cis-elements, phylogeny and collinearity, tissue-specific expression (root, stem, leaf, flower, and fruit), and transcriptional responses to cold, drought, and salt stresses. Three representative genes were further examined by transient 35S: GFP subcellular localization. Most SaARF proteins contain the canonical B3 and Auxin_resp domains, and several also harbor the C-terminal PB1 domain, which enables homotypic and heterotypic protein interactions. Phylogenetically, SaARFs cluster with ARFs from Arabidopsis and major Solanaceae crop species (S. lycopersicum, S. melongena, S. tuberosum, and Capsicum annuum), and exhibit extensive collinearity with Solanaceae genomes. Gene expression analyses revealed organ-preferential expression patterns and stress responsiveness; in particular, several SaARFs are enriched in reproductive organs, and multiple members are rapidly induced or repressed by salt, drought, or cold. Subcellular localization placed all three tested proteins in the nucleus. This study provides the first genome-wide characterization of the ARF family in S. americanum, refines our understanding of ARF evolution, and provides candidate genes for future functional studies on stress tolerance and fruit quality in cultivated Solanaceous vegetables.
The expansion of poisonous weed Stellera chamaejasme resulting from unreasonable grazing practices is altering plant composition and soil properties in degraded grasslands in Inner Mongolia. However, the impacts of S. chamaejasme encroachment on plant carbon density and the vertical changes in soil organic carbon (SOC) in grasslands are poorly understood, which hinders the accurate estimation of C stocks in degraded grasslands. This study compared three vegetation degradation types (degraded grassland with S. chamaejasme encroachment (SS), degraded grassland without S. chamaejasme encroachment (NS), and non-degraded natural grassland (CK) in Inner Mongolia typical steppe during the early growing season. We aimed to elucidate the differences in plant carbon stocks, the vertical patterns of SOC fractions across 0–50 cm layers, and their underlying driving mechanisms. During the early growing season of typical steppe, SS maintained plant carbon density comparable to CK via higher plant aboveground biomass and plant belowground carbon content, whereas total SOC density (0–50 cm) was similarly reduced in both degraded types. Moreover, SS induced a distinct vertical SOC redistribution. Compared to NS, SS showed significantly elevated SOC in the topsoil (0–10 cm), similar levels at 10–20 cm, and significantly lower contents among 20–50 cm. In particular, the SS plot exhibited significantly higher particulate organic carbon (POC) in the first two soil layer (0–20 cm). Furthermore, partial least squares path modeling indicated that the mechanisms controlling SOC also shifted with depth, moving from plant-driven POC inputs in the surface (0–20 cm) to mineral-associated organic carbon (MAOC) stabilization below 30 cm governed by soil properties. Our findings highlight that S. chamaejasme encroachment represents a unique degradation pathway that significantly alters carbon storage patterns during the early growing season of typical steppe in Inner Mongolia. Increases in plant and topsoil carbon density due to S. chamaejasme encroachment must be interpreted with caution, given the potential trade-offs with deeper soil carbon pools and long-term ecosystem stability.
Ginseng, a traditional precious Chinese herb of high medicinal value, has ginsenoside as its main active medicinal ingredient. Modern pharmacological studies have confirmed that ginsenoside plays a crucial role in treating various diseases and daily healthcare. While the catalytic pathway in ginsenoside biosynthesis has been extensively studied, its regulatory mechanism remains poorly understood. In this study, the regulatory mechanism of ginsenoside synthesis was investigated from the perspective of inducer regulation combined with transcription factor regulation. Methyl Jasmonate (MeJA), as an important phytohormone, is widely involved in plant growth and development, resistance to adversity, secondary metabolite synthesis and other biological processes. Here, 11,789 differentially expressed genes of ginseng in response to MeJA induction were obtained by transcriptome sequencing and analysis of ginseng adventitious roots with different durations of MeJA induction (0, 6, 12, 24, 36, 48, 60, 72, 84, 96, 108, and 120 h), which were then subjected to Gene Ontology (GO) functional annotation and classification of functional genotypes, and obtained the The overall characteristics of ginseng adventitious roots in response to MeJA induction were obtained. Further, the dynamic temporal characteristics of ginseng adventitious roots in response to MeJA induction were obtained by comparing the phenotypes of ginsenoside content, the number of differentially expressed genes, GO functional annotations, and functional gene types at different induction time points. Finally, gene modules that were significantly associated with the phenotype of ginsenoside content were obtained from the above differentially expressed genes using weighted gene co-expression network analysis (WGCNA) analysis, and the functionally important genes among them were identified and analysed in the interaction network. The above study results will lay a theoretical groundwork for comprehensively and deeply interpreting MeJA’s dynamic regulatory mechanism, offer information for researching ginsenoside synthesis and regulatory mechanisms, and provide a database for identifying important functional genes in ginsenoside synthesis and studying the molecular mechanism. This is of great value and significance for the development of ginseng basic research.
Black rice (Oryza sativa L. indica), is valued for its rich nutritional value and unique phytochemical composition. It is a significant source of anthocyanins, that contribute to its characteristic dark purple hue, along with other essential nutrients. The endophytic microbiome plays a pivotal role in plant growth, nutrient acquisition and the biosynthesis of health-promoting metabolites (antioxidants). Modulation of the endophytic bacterial community through beneficial microbial inoculants offers a promising strategy for improving crop productivity and functional quality. However, field-based evidence linking microbiome dynamics with black rice plant growth, antioxidant potential, and soil biological activity remains limited. A field experiment was conducted to evaluate the effects of a consortium of endophytic plant growth-promoting bacteria consisting of Bacillus subtilis, AMR1; Kluyvera sp. PO2S7; Enterobacter sp. SES19 on black rice. Plants were inoculated with the bacterial consortium, and plant growth, yield, antioxidant attributes (TPC, TFC, DPPH, and anthocyanin), and soil enzyme activities were assessed. The endophytic bacterial community was profiled using 16 S rRNA amplicon sequencing, followed by diversity, taxonomic, functional, and correlation network analyses to investigate microbiome modulation and its association with plant physiological and biochemical traits. The consortium promoted plant growth, mitigated stress responses, enhanced antioxidant activity, soil fertility and improved the yield of black rice (Oryza sativa L.) compared to single bacterial inoculation and uninoculated control plants. Stress enzyme activities, including catalase, peroxidase, and superoxide dismutase, were notably reduced, indicating alleviation of oxidative stress. Simultaneously, antioxidant activity such as total polyphenol content (TPC), total flavonoid content (TFC) in plant tissues was enhanced by 56.63
Perilla frutescens (L.) Britton is an important medicinal plant with considerable potential for the production of valuable bioactive metabolites. This study investigated the induction and growth of hairy roots through two sequential experiments designed to optimize hairy root induction and biomass production. In the first experiment, the effects of explant type (leaf, cotyledon, hypocotyl, and stem internode) and co-cultivation period (48 and 72 h) on hairy root induction were evaluated using the R. rhizogenes ATCC 15834 strain. Cotyledon explants co-cultivated for 48 h achieved the highest transformation efficiency (66
Barley is a crucial crop worldwide, but it faces significant production challenges due to limited adaptable varieties, poor management practices, and environmental factors. Food barley varieties often struggle in unfamiliar environments, leading to crop loss. To address this issue, a study was conducted to evaluating the adaptability, performance, and yield stability of released high-performing food barley varieties over two years across 17 diverse environments during the 2023–2024 cropping years. A multi-environment trial (MET) involving 20 released food barley genotypes was conducted during the 2023–2024 main cropping years across 17 environments using a randomized complete block design with three replications. Grain yield data were analyzed using combined analysis of variance (ANOVA), Additive Main Effects and Multiplicative Interaction (AMMI), AMMI Stability Value (ASV), Yield Stability Index (YSI), and Genotype plus Genotype × Environment (GGE) biplot analyses to assess genotype performance, stability, adaptability, and test environment suitability. Combined ANOVA and AMMI revealed highly significant (P < 0.0001) effects for all sources of variation. In the ANOVA, environment, year, genotype, environment × year, genotype × environment interaction (GEI), genotype × year, and genotype × environment × year accounted for 33.06
DNA methylation is an important epigenetic mechanism involved in plant growth, development, and responses to environmental cues. Although Cannabis sativa exhibits notable floral sex plasticity and ethylene-induced feminization has significant agricultural importance, the DNA methylation machinery associated with this process has not been systematically investigated. An in-silico genome-wide analysis identified ten DNA methylation-related genes in the C. sativa genome, comprising six cytosine-5 DNA methyltransferases (C5-MTases) and four DNA demethylases (dMTases). Phylogenetic, gene structure, conserved domain, and motif analyses demonstrated that these gene families are highly conserved and share structural features with homologues from other plant species. Promoter analysis revealed numerous cis-regulatory elements associated with light, phytohormone, and stress responses, including ethylene-responsive motifs. Functional validation by quantitative expression profiling revealed distinct transcriptional differences between male and female flowers and dynamic changes in the expression of several methyltransferase and demethylase genes during ethephon-induced feminization. These transcriptional changes were accompanied by altered expression of flowering- and sex-associated genes, including AGL11, SOC1, SQUAMOSA1, LFY, AP3, Men8, SHT, and bHLH91, throughout floral development. This study provides the first comprehensive characterization of DNA methyltransferase and DNA demethylase gene families in C. sativa. The expression patterns observed during ethephon-induced feminization identified candidate genes for future investigations into DNA methylation-associated regulatory pathways causing floral development and sex plasticity in C. sativa.
Cayenne development is not limited to improving production but also offers opportunities to reach new consumer markets through its aesthetic value. Consequently, cayenne cultivation can be directed towards both functional and ornamental purposes to bolster household food resilience. Therefore, this study aimed to identify the characteristics that make ornamental cayenne desirable to consumers by evaluating F5 cayenne breeding lines through complementary agronomic and consumer preference assessments of the ornamental cayenne. The study utilized Alpha Lattice design, involving 25 genotypes selected from a F4 generation alongside three check varieties, resulting in 28 combinations per replicate. The plants were grown in two replicates, each containing three incomplete blocks. Agronomic data were initially analyzed using Best Linear Unbiased Prediction (BLUP) under an alpha-lattice design, followed by correlation analysis. The correlated traits were transformed into family indices and fitness values, which were subsequently integrated through principal component analysis (PCA) and the Weighted Average of Absolute Scores (WAAS) to construct the agronomic index (AI) of each selected lines. Preference assessment involving 45 panelists who evaluated the visual appeal of the selected lines based on AI. The optimal agronomic traits identified for selection included canopy width, stem diameter, fruit number, and yield, all of which exhibited high heritability, which is crucial in fitness-WAAS selection. The fitness-WAAS analysis indicated that lines G25 (0.78) and G13 (0.46) had higher indices than the best check variety, Bara (0.44). Based on the standard deviation to relative check variety, six lines were recommended in the preference analysis, with line G25 (0.75) being the most promising, followed by the other five. These lines are recommended for yield potential evaluation and multi-location trials using a participatory breeding concept. Although further refinement through metabolomic, transcriptomic, and molecular analyses is required, this approach provides a systematic framework for selecting ornamental cayenne lines by integrating agronomic performance and consumer preferences while offering a preliminary indication of the visual characteristics preferred by panelists.
Water scarcity and declining soil fertility necessitate the adoption of sustainable agricultural practices that enhance crop productivity while maintaining soil health. Mulching is an effective strategy for regulating soil temperature, conserving soil moisture, and improving crop performance. This study was conducted during the 2022 Rabi season at the experimental farm of Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K) to evaluate the effects of different mulching materials on soil temperature, soil moisture dynamics, growth, and yield of broccoli (Brassica oleracea var. italica L.). The experiment was laid out in a randomized complete block design with three replications, comprising five mulching treatments (control, white plastic, black plastic, silver plastic, and organic mulch), with soil measurements recorded at three depths (5, 10, and 15 cm). Silver plastic mulch significantly improved soil moisture retention (30.61
Reverse transcription quantitative PCR (RT-qPCR) is widely used to quantify gene expression, but reliable normalization requires reference genes with stable expression in the species, tissues, and experimental conditions being examined. Cuphea hookeriana is an ornamental shrub whose wider landscape application is limited by poor cold tolerance. However, no validated reference genes have been reported for RT-qPCR normalization in this species. In this study, twelve candidate reference genes were selected from a C. hookeriana leaf transcriptome generated during a 5 °C low-temperature time course and deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA1117973. The candidates comprised elongation factor 1-alpha (EF1α), DnaJ heat shock protein (DNAJ), cyclophilin (CYP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), 18 S ribosomal RNA (18 S rRNA), eukaryotic initiation factor 2 (EIF2), tubulin (TUB), protein phosphatase 2 A (PP2A), acyl carrier protein (ACP), ubiquitin (UBQ), and ubiquitin-conjugating enzyme (UBC). Their expression stability was evaluated in roots, stems, leaves, and flowers and in leaves exposed to 5 °C for 0, 12, 24, 36, and 48 h. The amplification efficiencies ranged from 92.41
Moringa stenopetala is an important multipurpose tree recognized for its nutritional, medicinal, and socioeconomic value. Although widely utilized by communities in southern Ethiopia, the species remains underutilized and has a relatively restricted natural distribution, occurring mainly in southern Ethiopia and northern Kenya. Understanding the potential impacts of climate change on its habitat suitability is essential for supporting conservation, sustainable utilization, and agroforestry planning. This study assessed the current and future habitat suitability of Moringa stenopetala in Ethiopia using an ensemble species distribution modelling approach. Seven modelling algorithms, namely boosted regression trees, random forest, generalized linear model, generalized additive model, maximum entropy, support vector machine, and multivariate adaptive regression splines, were integrated into an ensemble model and evaluated using five-fold cross-validation. The ensemble model showed high predictive performance, with mean Area Under the Curve and True Skill Statistic values of 0.97 and 0.85, respectively. Precipitation seasonality, precipitation of the coldest quarter, soil pH, and isothermality were the most influential variables determining habitat suitability. Under current climate conditions, suitable habitat for M. stenopetala was estimated at 40,136.80 km2, representing approximately 3.6
