Search Results (809)

Salt stress severely impairs rice (Oryza sativa L.) germination and seedling establishment. Exogenous spermidine (Spd) has been shown to regulate stress tolerance in plants, but whether it acts during rice germination and seedling establishment under salt stress remains unclear. Here, rice seeds (cv. Jindao 919) were exposed to 75 mM NaCl with different Spd concentrations (0–1.4 mM), and physiological, biochemical, and transcriptomic responses were evaluated. The findings showed that salt stress had a pronounced inhibitory effect on both seed germination and seedling development. Exogenous Spd effectively alleviated these negative effects, with the most significant improvements observed at 1.0–1.2 mM: germination rate increased by 3.98–8.52%, seedling root length increased by 17.74–37.68%, soluble sugar content increased by 29.83–230%, and SOD and POD activities increased by 29.81–40.3% and 18.45–44.0%, respectively, while MDA content decreased by 36.28–40.3%. Further transcriptomic analysis identified a total of 1835 differentially expressed genes (DEGs). KEGG enrichment analysis revealed these genes were concentrated in key pathways including terpenoid biosynthesis, phenylpropanoid biosynthesis, and amino sugar and nucleotide sugar metabolism, thus alleviating the negative impact of salt stress on rice germination and seedling development. These pathways are closely related to gibberellin metabolism, lignin biosynthesis, and amino sugar metabolism, further revealing the regulatory role of Spd. Overall, 1.0–1.2 mM Spd was most effective in alleviating salt stress by synergistically regulating antioxidant defense, osmoregulation, and metabolic reprogramming, enhancing rice’s overall stress tolerance. This study provides theoretical guidance for precise regulation of Spd concentration to improve rice performance in saline-alkaline soils, and reveals the sustained promoting effects of Spd across various developmental stages of rice and its underlying molecular mechanisms. Full article

Salt and low temperature are serious abiotic stresses and important constraints to agricultural productivity across the globe. These abiotic stresses negatively affect plant growth and physiological, biochemical, and molecular processes. Glycine betaine (GB) is an important osmoprotectant that enables plants to resist salinity, low temperature, and drought. GB can be synthesized in many organisms, including animals, plants, and bacteria. In higher plants, GB is synthesized through two-step oxidation of choline. However, rice, an important food crop, cannot synthesize GB. Thus, conferring the ability to synthesize GB to rice through genetic engineering is of great significance for enhancing its tolerance to abiotic stress. Recently, an enzyme, GSDMT (glycine, sarcosine, and dimethylglycine methyltransferase) was found in a diatom, Talassiosira pseudonana, and found able to catalyze the three successive methylation steps of glycine to form GB. This biosynthetic pathway for GB synthesis is also the simplest in living organisms. Here, the optimized codon of the TpGSDMT gene sequence was synthesized and cloned into an overexpression vector, pBWA(V)HS, which contains a CaMV 35S promoter, and then, the constructed vector was transferred into rice (Oryza sativa L. ssp. Japonica). The GB content in transgenic rice showing overexpression of TpGSDMT was significantly increased, and these transformants exhibited markedly enhanced tolerance to salt and low temperature. These results indicate that the TpGSDMT gene can be used for the genetic improvement in crop plants’ resistance to salinity and low temperature. Full article

Salinity is one of the primary limiting factors in the rice production system in northeast Thailand due to the presence of underground salt rocks, and the situation is expected to deteriorate further in the future since rice is particularly susceptible to salinity. In this study, 382 indigenous lowland rice germplasms were evaluated for salt tolerance under hydroponic conditions at the seedling stage. The stress condition was induced by adding NaCl from 2 dS/m to 22 dS/m. Twenty-two varieties (group 1) were selected based on low leaf salinity scores in 2019 and 2020. Ten varieties, LLR050, LLR054, LLR106, LLR216, LLR309, LLR365, LLR377, LLR402, LLR441, and LLR449, were selected from leaf salt injury scores under hydroponic conditions in 2021 and 2022. The response of ten selected varieties was investigated under both hydroponic and soil media at the seedling stage, as well as soil culture at the tillering and flowering stages. The results revealed that LLR054, LLR365, and LLR216 exhibited low leaf injury scores (less than 4.0) at both the seedling and tillering stages. At the seedling stage, most varieties demonstrated high Na+ accumulation in the root, while high accumulation in the shoot was observed at the tillering stage. Varieties LLR054 and LLR441 displayed low leaf damage scores, root sodium accumulation at the seedling stage, and shoot sodium accumulation at the tillering stage, similar to the tolerant check variety Pokkali. Additionally, LLR365 and LLR216 showed high shoot sodium accumulation but low leaf damage scores at the tillering stage. At the flowering stage, LLR050 and LLR449 maintained high yields and filled seeds per panicle under salt stress. Therefore, early-stage LLR054, LLR441, LLR365, and LLR216 had high tolerance and LLR050 and LLR449 maintained high yields, and these varieties are potential sources of salt tolerance for future rice breeding programs. Full article

Leaves represent an important organ in plant photosynthesis, and moderately rolled leaves would be beneficial in establishing an ideal plant architecture and thereby increasing rice yields. In this study, a stable inherited rolled leaf mutant was obtained via ethyl methanesulfonate (EMS) mutagenesis from japonica variety WYJ27, which was named rll2 (rolling leaf 2). rll2 showed a leaf-rolling phenotype at the seedling stage, which increased with growth. Compared with the wild type, the leaves at all levels of rll2 were significantly shorter and narrower, and the leaf-rolling index gradually decreased from the highest leaf to the third-highest leaf. Semi-thin sections showed that the bulliform cells of rll2 were significantly larger than those of the wild type, and the number of cells was significantly higher than that of the wild type. Genetic analysis showed that rll2 is controlled by a pair of recessive nuclear genes. Map-based cloning revealed that RLL2 encodes a conserved and plant-specific calpain-like cysteine proteinase. RLL2 was mainly expressed in young roots, shoots, spikelets, and panicles. Transcriptome sequencing showed that a total of 104 genes were differentially expressed in the wild type and rll2. Moreover, several transcription factor genes were significantly altered in the rll2 mutant. Taken together, our findings indicate that RLL2 plays an important role in leaf rolling by regulating bulliform cells, which may be useful in breeding rice with an ideal plant architecture. Full article

In rice (Oryza sativa L.), the short-chain dehydrogenase protein OsABA2 plays a crucial role in regulating abscisic acid (ABA) biosynthesis. However, little is known about the other proteins that interact with OsABA2 to regulate ABA biosynthesis. Using yeast two-hybrid screening, we identified a novel OsABA2 interacting protein OsPP2C55, which contains a serine/threonine phosphatase (family 2C) catalytic domain. The yeast two-hybrid (Y2H) assay and firefly luciferase complementary imaging (LCI) assay confirmed these interactions. Subsequent studies revealed that saline–alkaline stress significantly downregulated OsPP2C55 gene expression. Meanwhile, we constructed ospp2c55 CRISPR gene knockout (ospp2c55-KO) plants using Agrobacterium genetic transformation. Compared with wild-type plants, ospp2c55-KO plants under saline–alkaline stress exhibited significantly elevated OsABA2 protein levels, leading to substantial increases in ABA content. In addition, ospp2c55-KO plants demonstrated heightened sensitivity to ABA during seed germination. Moreover, ospp2c55-KO plants improved the survival rate and stress-related indices of rice seedlings under saline–alkaline stress, and upregulated the expression of genes related to adversity stress (OsNCED1, OsNCED3, OsABA2, OsSODCc2, and OsCatB). We found that OsPP2C55 plays a negative regulatory role in ABA biosynthesis and saline–alkaline stress tolerance in rice. Full article

This study examined the effects of dielectric barrier discharge (DBD) plasma and copper oxide nanoparticles (CuO NPs) on rice seed quality, seedling growth, and fungal inhibition. Sanpatong 1 rice seeds were treated with DBD plasma at three exposure durations (0.4, 0.6, and 0.8 s/cm) and coated with CuO NP solutions at five concentrations (0, 0.02, 0.04, 0.06, and 0.08 M). The experiment followed a split-split-plot design within a randomized complete block design (RCBD), with storage time (0, 2, 4, and 6 months) as the main plot factor. Plasma etching improved seed surface wettability, while CuO NPs increased copper uptake and promoted growth at 0.04–0.06 M but caused toxicity at 0.08 M. Combined treatments suppressed Rhizopus sp. and Rhizoctonia solani, though Aspergillus spp. were less affected. Seed quality declined after six months of storage, likely due to oxidative stress. The best results were obtained with 0.6 s/cm plasma and 0.06 M CuO NPs, maximizing germination, vigor, and seedling growth without toxicity, demonstrating their potential as practical tools for improving rice seed quality and pathogen management. Full article

Studying hypoxia in rice is particularly important because oxygen deficiency during germination severely limits seedling establishment. Understanding the molecular and physiological mechanisms underlying hypoxic tolerance is therefore crucial for improving rice yield stability under flooded or waterlogged conditions. Progress in developing rice cultivars that thrive under flooding and low oxygen (hypoxic) conditions has been limited over the past two decades due to a lack of tolerant plant varieties and a limited understanding of genetic mechanisms. This study evaluated hypoxia tolerance in the Cheongcheong Nagdong Double Haploid (CNDH) rice population, along with their parent lines, for hypoxia tolerance. Significant phenotypic differences were identified, with the Cheongcheong and CNDH lines CNDH13, CNDH35, and CNDH91 showing strong hypoxia tolerance, while Nagdong and CNDH lines CNDH14-2, CNDH43, and CNDH50-1 were susceptible to hypoxia. Root length was unaffected by hypoxia, while shoot length and fresh weight were key tolerance indicators. Comprehensive quantitative trait loci (QTL) analysis based on logarithm of the odds (LOD) scores above 3.0 identified three QTLs associated with hypoxia tolerance, indicating significant genetic control: qSL-8 and qSL-10 (shoot length) and qFW-2 (fresh weight). The gene expression analysis performed under hypoxic conditions highlighted that 35 candidate genes within these QTL regions exhibited differential regulation: Os02g0184200, Os08g0430200, Os08g0431900, and Os08g0432500 were upregulated, whereas Os08g0439100, Os10g0343400, Os10g0395400, and Os10g0405600 were downregulated in both resistant and susceptible lines. Os08g0431900 displayed significant expression changes correlating with hypoxia resistance. Phylogenetic and protein–protein interaction analyses revealed that Os08g0431900 is highly conserved and interacts with proteins involved in stress responses, suggesting that these proteins are crucial in hypoxia tolerance. These findings provide valuable insights into the genetic basis of hypoxia tolerance and identify key genes for future breeding programs to develop hypoxia-resistant rice varieties. Full article

The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil’s pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks. Full article

Amending reservoir sediments with organic matter provides a sustainable alternative to conventional rice (Oryza sativa L.) seedling substrates, simultaneously reducing dependence on agricultural soils and promoting the recycling of dredged sediments and agricultural by-products. Preliminary tests showed that adding rice husk (RH) improved the porosity and water retention of the sediments while preventing surface cracking. This study further examined the effects of RH and rice husk biochar (RHB) on sediment fertility and rice seedling growth. Seedlings were grown for 15 days in a fine- or coarse-texture sediment amended with 0, 5, 10, or 20% (w/w) RH or RHB. A 10% amendment was identified as the optimal ratio for promoting seedling growth (increasing ca. 20% biomass). Nitrogen (N) availability was the primary factor influencing seedling performance, outweighing the effects of salinity and phosphorus availability. Compared with RH, RHB amendment resulted in lower substrate available N, likely due to greater losses through denitrification and ammonia volatilization, leading to reduced growth. In contrast, RH amendment maintained higher levels of available N, resulting in greater shoot biomass and higher leaf chlorophyll concentrations. Overall, amending reservoir sediments with 10% RH provides the most effective substrate formulation, offering a practical and sustainable strategy for rice seedling production. Full article

Rice (Oryza sativa L.) is a salt-sensitive crop, where even moderate soil salinity (electrical conductivity ≥ 3.5 dS/m) can cause significant yield reduction. During the seedling stage, the underdeveloped root system has limited capacity for salt uptake and translocation, making root system architecture (RSA) a crucial trait for enhancing salinity tolerance. In this study, we used 165 individuals from the 3K Rice Genome Project to comprehensively measure multidimensional root morphological traits at the early seedling stage under salt stress, thereby overcoming the limitations of conventional methods that mainly rely on root length and biomass. We identified 78 quantitative trait nucleotides (QTNs) associated with eight root morphological traits through genome-wide association studies (GWAS) of 3VmrMLM. Among these, 12 QTNs co-localized within genomic regions of previously cloned salt tolerance-related genes. Additionally, six salt-tolerant lines were selected based on significantly increased root volume (RV) and surface area (SA), suggesting that their adaptive mechanism under salinity involves optimized spatial root distribution rather than radial thickening. Our findings show that high-resolution root scanning-based phenotyping provides a reliable platform for screening and breeding salt-tolerant rice varieties, offering valuable indicators for assessing seedling-stage salt tolerance. Full article

SHORT INTERNODE (SHI)-Related Sequence (SRS) transcription factors play crucial roles in plant growth, development, and stress responses and have been extensively studied in various plant species. However, the molecular functions and regulatory mechanisms of SRS genes in the economically important tropical fruit crop pitaya (Hylocereus undatus) remain poorly understood. This study identified 9 HuSRS genes in pitaya via bioinformatics analysis, with subcellular localization predicting nuclear distributions for all. Gene structure analysis showed 1–4 exons, and conserved motifs (RING-type zinc finger and IXGH domains) were shared across subclasses. Phylogenetic analysis classified the HuSRS genes into three subfamilies. Subfamily I (HuSRS1–HuSRS4) is closely related to poplar and tomato homologs and subfamily III (HuSRS6–HuSRS8) contains a recently duplicated paralogous pair (HuSRS7/HuSRS8) and shows affinity to rice SRS genes. Protein structure prediction revealed dominance of random coils, α-helices, and extended strands, with spatial similarity correlating to subfamily classification. Interaction networks showed HuSRS1, HuSRS2, HuSRS7 and HuSRS8 interact with functional proteins in transcription and hormone signaling. Promoter analysis identified abundant light/hormone/stress-responsive elements, with HuSRS5 harboring the most motifs. Transcriptome and qPCR analyses revealed spatiotemporal expression patterns: HuSRS4, HuSRS5, and HuSRS7 exhibited significantly higher expression levels in callus (WG), which may be associated with dedifferentiation capacity. In seedlings, HuSRS9 exhibited extremely high transcriptional accumulation in stem segments, while HuSRS1, HuSRS5, HuSRS7 and HuSRS8 were highly active in cotyledons. This study systematically analyzed the characteristics of the SRS gene family in pitaya, revealing its evolutionary conservation and spatio-temporal expression differences. The research results have laid a foundation for in-depth exploration of the function of the SRS gene in the tissue culture and molecular breeding of pitaya. Full article

To solve the problems of large root damage and incomplete seedling blocks (SBs) in rice machine transplanting, this study numerically optimized the root blanket-cutting device for rice blanket seedling cutting and throwing transplanters based on the discrete element method (DEM) and multi-body dynamics (MBD) coupling method. A longitudinal sliding cutter (LSC)–substrate–root interaction model was established. Based on the simulation tests of Center Composite Design and response surface analysis, the sliding angle and cutter shaft speed of the LSCs arranged at the circumferential angles (CAs) of 0°, 30°, and 60° were optimized. The simulation results indicated that the LSC arrangement CA significantly affected the cutting performance, with the optimal configuration achieved at a CA of 60°. Under the optimal parameters (sliding angle of 57°, cutter shaft speed of 65.3 r/min), the average deviation between the simulated and physical tests was less than 11%, and the reliability of the parameters was verified. A seedling needle–substrate–root interaction model was established. The Box–Behnken Design method was applied to conduct simulation tests and response surface optimization, focusing on the picking angle, needle width, and rotary gearbox speed. The simulation results showed that the picking angle was the key influencing factor. Under the optimal parameters (picking angle of 20°, seedling needle width of 15 mm, rotary gearbox speed of 209 r/min), the average deviation between the simulated and physical tests was less than 10%, which met the design requirements. This study provides a new solution for reducing root injury, improving SB integrity, and reducing energy consumption in rice transplanting, and provides theoretical and technical references for optimizing transplanting machinery structure and selecting working parameters. Full article

The coupling of partial root-zone drying (PRD) with nitrogen forms exerts an interactive “water-promoted fertilization” effect, which enhances rice (Oryza sativa L.) growth and development, improves water use efficiency (WUE), mediates the expression of aquaporins (AQPs), and alters root water conductivity. In this study, gene cloning and CRISPR-Cas9 technologies were employed to construct overexpression and knockout vectors of the OsPIP2;1 gene, which were then transformed into rice (cv. Meixiangzhan 2). Three water treatments were set: normal irrigation (CK); partial root-zone drying (PRD); and 10% PEG-simulated water stress (PEG), combined with a nitrogen form ratio of ammonium nitrogen (NH₄⁺) to nitrate nitrogen (NO₃⁻) at 50:50 (A50/N50) for the coupled treatment of rice seedlings. The results showed that under the coupled treatment of PRD and the aforementioned nitrogen form, the expression level of the OsPIP2;1 gene in roots was upregulated by 0.62-fold on the seventh day, while its expression level in leaves was downregulated by 1.84-fold. Overexpression of OsPIP2;1 enabled Meixiangzhan 2 to maintain a higher abscisic acid (ABA) level under different water conditions, which helped rice reduce water potential and enhance water absorption. Compared with the CK treatment, overexpression of OsPIP2;1 increased the superoxide dismutase (SOD) activity of rice under PRD by 26.98%, effectively alleviating tissue damage caused by excessive accumulation of O₂⁻. The physiological and biochemical characteristics of OsPIP2;1-overexpressing rice showed correlations under PRD and A50/N50 nitrogen form conditions, with WUE exhibiting a significant positive correlation with transpiration rate, chlorophyll content, nitrogen content, and Rubisco enzyme activity. Overexpression of OsPIP2;1 could promote root growth and increase the total biomass of rice plants. The application of the OsPIP2;1 gene in rice genetic engineering modification holds great potential for improving important agricultural traits of crops. This study provides new insights into the mechanism by which the AQP family regulates water use in rice and has certain significance for exploring the role of AQP genes in rice growth and development as well as in response to water stress. Full article

Damping-off disease hinders rice seedling growth and reduces yield. Current control methods, such as seed or soil sterilization, rely on chemicals that cause environmental pollution and promote pathogen resistance. As a sustainable alternative, we targeted the damping-off resistance-related gene OsDGTq1 using CRISPR/Cas9. Field experiments first verified OsDGTq1’s significance in resistance. The CRISPR/Cas9 system, delivered via Agrobacterium-mediated transformation, was used to edit OsDGTq1 in rice cultivar Ilmi. Lesions from major damping-off pathogens, Rhizoctonia solani and Pythium graminicola, were observed on G₀ plants. All 37 regenerated plants contained T-DNA insertions. Among them, edits generated by sgRNA1-1, sgRNA1-2, and sgRNA1-3 resulted in the insertion of two thymine bases as target mutations. Edited lines were assigned names and evaluated for agronomic traits, seed-setting rates, and pathogen responses. Several lines with edited target genes showed distinct disease responses and altered gene expression compared to Ilmi, likely due to CRISPR/Cas9-induced sequence changes. Further studies in subsequent generations are needed to confirm the stability of these edits and their association with resistance. These results confirm that genome editing of OsDGTq1 alters resistance to damping-off. The approach demonstrates that gene-editing technology can accelerate rice breeding, offering an environmentally friendly strategy to develop resistant varieties. Such varieties can reduce chemical inputs, prevent pollution, and minimize seedling loss, ultimately enhancing food self-sufficiency and stabilizing rice supply. Full article

Pre-harvest sprouting (PHS) reduces the quality and quantity of crop seeds. PHS can be imposed through the embryo or husk pathway of cereal crops. Most reported PHS seeds are imposed via the embryo pathway. Here, we generated transgenic rice plants overexpressing rice melatonin 2-hydroxylase (OsM2H), which catalyzes the hydroxylation of melatonin to 2-hydroxymelatonin (2-OHM). OsM2H overexpression (M2H-OE) showed PHS under paddy conditions. Germination assays revealed that intact seeds harvested at 26 and 36 days after heading (DAH) showed PHS, whereas dehusked seeds did not, indicating husk-imposed PHS. Overproduction of 2-OHM was observed in M2H-OE seeds compared to wild-type control. In addition, M2H-OE lines produced more hydrogen peroxide than the wild-type. 2-OHM-induced reactive oxygen species resulted in the induction of OsGA3ox2, a gibberellin (GA) biosynthesis gene, and repression of OsGA2ox3, a GA degradation gene, in caryopses at 2 DAH, but in the induction of the ABA degradation gene OsABA8ox3 in intact seeds at 26 DAH. In addition, M2H-OE seedlings were longer and showed increased levels of hydrogen peroxide and OsGA3ox2 expression versus the wild-type. This is the first report showing that 2-OHM can induce PHS via the husk pathway in rice seeds through the induction of GA biosynthetic and ABA degradation genes. Full article