Rice Seedlings Research Articles

Mechanism of microbial action of the inoculated nitrogen-fixing bacterium for growth promotion and yield enhancement in rice (Oryza sativa L.)

The use of nitrogen-fixing bacteria in agriculture is increasingly recognized as a sustainable method to boost crop yields, reduce chemical fertilizer use, and improve soil health. However, the microbial mechanisms by which inoculation with nitrogen-fixing bacteria enhance rice production remain unclear. In this study, rice seedlings were inoculated with the nitrogen-fixing bacterium R3 (Herbaspirillum) at the rhizosphere during the seedling stage in a pot experiment using paddy soil. We investigated the effects of such inoculation on nutrient content in the rhizosphere soil, plant growth, and the nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere. The findings showed that inoculation with the R3 strain considerably increased the amounts of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the rhizosphere by 14.77%, 27.83%, and 22.67%, respectively, in comparison to the control (CK). Additionally, the theoretical yield of rice was enhanced by 8.81% due to this inoculation, primarily through a 10.24% increase in the effective number of rice panicles and a 4.14% increase in the seed setting rate. Further analysis revealed that the structure of the native nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere were altered by inoculation with the R3 strain, significantly increasing the α-diversity of the communities. The relative abundance of key nitrogen-fixing genera such as Ralstonia, Azotobacter, Geobacter, Streptomyces, and Pseudomonas were increased, enhancing the quantity and community stability of the nitrogen-fixing community. Consequently, the nitrogen-fixing capacity and sustained activity of the microbial community in the rhizosphere soil were strengthened. Additionally, the expression levels of the nitrogen absorption and transport-related genes OsNRT1 and OsPTR9 in rice roots were upregulated by inoculation with the R3 strain, potentially contributing to the increased rice yield. Our study has revealed the potential microbial mechanisms through which inoculation with nitrogen-fixing bacteria enhances rice yield. This finding provides a scientific basis for subsequent agricultural practices and is of critical importance for increasing rice production and enhancing the ecosystem services of rice fields.

Methyl jasmonate enhances rice tolerance to alkaline stress via the auxin pathway

Soil alkalization is a major challenge for global crop production. This study reveals a novel defense mechanism in rice seedlings against alkaline stress, involving methyl jasmonate (MeJA) and auxin pathways. Under alkaline stress (15 mM Na2CO3), rice seedlings exhibited elevated levels of endogenous MeJA and upregulation of JA-responsive genes. Pre-treatment with MeJA (50 µM) significantly improved seedling survival, growth, and mitigated root damage under alkaline stress. This treatment also upregulated genes associated with cell death suppression (OsBI1) and stress tolerance (OsJRL, OsNAC). Notably, MeJA pre-treatment increased auxin (indole-3-acetic acid, IAA) levels in roots, and upregulated genes involved in IAA synthesis (OASA1, OASA2) and auxin signaling (Aux/IAA, ARFs). Blocking auxin transport with N-1-naphthylphthalamic acid intensified root damage under alkaline stress and diminished the protective effect of MeJA. These results highlight the crucial role of MeJA-induced activation of auxin pathway in enhancing rice tolerance to alkaline stress, and provide valuable insights for developing strategies to improve crop resilience in alkaline soils.

Silicon-Mediated Arsenic Tolerance: Restriction of Arsenic Uptake and Modulation of Antioxidant Defense System in Rice Seedlings

Silicon-Mediated Arsenic Tolerance: Restriction of Arsenic Uptake and Modulation of Antioxidant Defense System in Rice Seedlings

Exogenous Uniconazole promotes physiological metabolism and grain yield of rice under salt stress.

Salt stress severely inhibit plant growth and development. Uniconazole has been considered to significantly increase plant stress tolerance. However, the mechanism by which Uniconazole induces salt tolerance in rice seedlings and its impact on yield is still unclear. In this study, the effects of exogenous Uniconazole on morphogenesis, physiological metabolism, and yield of rice seedlings under salt stress were analyzed using the salt-tolerant rice variety HD961 and the salt-sensitive rice variety 9311. The results showed that salt stress significantly inhibited rice growth, disrupted the antioxidant system and pigment accumulation, and reduced photosynthesis, and yield. There were corresponding percent decreases of 13.0% and 24.1% in plant height, 31.6% and 55.8% in leaf area, 65.7% and 85.3% in root volume, respectively for HD961 and 9311. spraying However, compared to salt stress, the US treatment increased the percentage to 4.7% and 139.0% in root volume, 7.5% and 38.0% in total chlorophyll, 4.5% and 14.3% in peroxidase (POD) of leaves, 14.4% and 54.2% in POD of roots, 18.7% and 22.7% in catalase (CAT) of leaves, and 22.6% and 53.9% in CAT of roots, respectively, for HD961 and 9311. In addition, it also significantly enhanced photosynthesis at the reproductive stage, promoted the transport of carbohydrate to grains. And US treatment significantly increased the percentage to 9.0% in panicle length, 28.0% in panicle number per hole, 24.0% in filled grain number, 3.0% in 1000-grain weight, and 26.0% in yield per plant, respectively, for HD961, compared to salt stress. In summary, applying Uniconazole at the seedling stage can alleviate the damage induced by NaCl stress on rice by regulating the physiological metabolism of rice plants. This reduces the negative effects of salt stress, enhance salt tolerance, and boost rice production.

Endophytic consortium exhibits varying effects in mitigating cadmium toxicity in rice cultivars with distinct cadmium accumulation capacities

Cadmium (Cd)-contaminated rice is the main source of Cd exposure that threatens food safety and human health. While plant growth-promoting bacteria (PGPB) have been reported to reduce Cd toxicity in rice, the effect of endophytic consortium is less understood compared to the single strain. Here, we reported that the PGPB consortium consisting of Cd-tolerant endophytic bacteria Pseudomonas sp. 4N2 and Bacillus sp. TB1 increased extracellular polymeric substance secretion and demonstrated a higher Cd removal rate compared to individual 4N2 and TB1. Further, two rice cultivar, namely the low-Cd-accumulating (LA) cultivar 728B and the high-Cd-accumulating (HA) cultivar BB, were inoculated with the 4N2-TB1 consortium. As expected, the consortium had a more pronounced effect on 728B, from which the endophytic bacteria were screened. The 4N2-TB1 consortium was found to facilitate the growth of rice seedlings and enhance their antioxidation activity. Moreover, the consortium significantly reduced Cd transfer coefficient from root to shoot through Cd immobilization in rice roots, resulting in a reduction from 30 % to 6 % in 728B and from 31 % to 13 % in BB. Furthermore, alpha-diversity analysis indicated an increased diversity and richness of the root bacterial community after 4N2-TB1 inoculation. Also, redundancy analysis confirmed a positive correlation between rice biomass and Cd content with a specific assemblage of bacteria including Bacillus and Leifsonia. These results demonstrated that the 4N2-TB1 consortium may alleviate Cd stress in rice cultivars through recruiting PGPB and Cd-binding bacteria on the root surface, thus strengthening the immobilization of Cd in rice roots.

Ammonium mitigates cadmium toxicity by activating the bZIP20-APX2/CATA transcriptional module in rice seedlings in an ABA-dependent manner

The amelioration of cadmium (Cd2+) toxicity in plants by ammonium (NH4+) has been widely investigated. However, the molecular mechanisms underpinning this amelioration have remained ambiguous. Here, we found that NH4+ significantly reduces Cd2+ accumulation and enhances antioxidant capacity by increasing ABA accumulation, which, in turn, improves Cd2+ tolerance in rice seedlings. A combination of qPCR, yeast-one-hybrid and dual-luciferase assays, and CUT&RUN-qPCR methods demonstrates that OsbZIP20 directly binds to the promoters of OsAPX2 and OsCATA, activating their transcription, and we show that the process requires phosphorylation modification of OsbZIP20 by OsSAPK9. Under Cd2+ stress, Osbzip20 and Ossapk9 mutants show reduced peroxidase and catalase activities, higher H2O2 accumulation, and reduced Cd2+ tolerance. In sum, our results elucidate a novel mechanism by which NH4+ enhances Cd2+ resistance, through ABA-SAPK9-bZIP20-APX2/CATA, offering a new strategy for improving Cd2+ resistance in rice.

Synergistic interaction between brassinosteroid and jasmonate pathways in rice response to cadmium toxicity

Brassinosteroids (BRs) and jasmonic acid (JA) are known to be involved in regulating plant responses to cadmium (Cd) stress. However, their specific roles and interaction in this process remain unclear. In this study, we discovered that exogenous BR alleviated Cd-mediated growth inhibition of rice seedlings. Enhanced Cd tolerance was also observed in m107, a BR-overproduction mutant. Phenotypic analysis of genetic materials involved in BR signaling confirmed the positive role of BR in regulating rice response to Cd toxicity. OsDLT, a key component in the BR signaling pathway, was found to be crucial for BR-mediated Cd tolerance. Further analysis demonstrated that activation of the BR pathway reduced the accumulation of Cd and reactive oxygen species (ROS) by modulating the expression of genes associated with Cd transport and ROS scavenging. Interestingly, transcriptome analysis indicated that the JA pathway was enriched in OsDLT-regulated differently expressed genes (DEGs). Gene expression and hormone assays showed that BR promoted the expression of JA pathway genes and JA levels in plants. Moreover, BR-induced tolerance was compromised in the JA signaling-deficient mutant osmyc2, suggesting that BR-mediated Cd resistance depends on the activation of the JA signaling pathway. Overall, our study revealed the synergistic interaction between BR and JA pathways in rice response to Cd stress, providing insights into the complex hormonal interplay in plant tolerance to heavy metals.

A proposed plant classification framework for smart agricultural applications using UAV images and artificial intelligence techniques

Utilizing Wireless Sensor Networks (WSNs), Internet of Things (IoTs) sensors, and Unmanned Aerial Vehicles (UAVs), in conjunction with optimization techniques and machine learning algorithms, can present a novel approach to Precision Agricultural (PA) crops. Agriculture has transitioned from traditional legacy systems to incorporate advanced smart technologies. Several complex farming problems are utilized to promote a variety of UAV sensing and Artificial Intelligence (AI) algorithms in PA applications of smart agriculture, especially in developing countries. This paper proposes the design of a conceptual UAV sensing system for crop management using a novel classification framework. UAV-based image datasets can be implemented and expanded to various types of crops. In addition, it can classify various types of rice species and detect weed farms as it consists of a multistage process for identifying and monitoring different crops. The proposed classification framework is evaluated using three different real UAV image datasets compared with Naive Bayes, Decision Tree (DT), Bagging, and Random Forest (RF) techniques. The classification performance metrics obtained are as follows: i) the WeedNet dataset with 100 % F1-score, 100 % recall, 100 % precision, and 100 % accuracy; ii) the Rice Seedling dataset with 99.5 % F1-score, 99.5 % recall, 99.5 % precision, and 99.5 % accuracy; and iii) the Rice Varieties dataset with 97.99 % F1-score, 97.99 % recall, 98.14 % precision, and 97.99 % accuracy. The success rates achieved by the proposed classification framework outperform those of other recent state-of-the-art techniques, demonstrating its efficacy in crop management applications.

Assessment of the utilization of modern agricultural machinery in rice production and its problems: A case from San Leonardo, Philippines

This study examines the relationship between the utilization of modern agricultural machinery and the business technical aspect of rice production of paddy field farmers in San Leonardo, Nueva Ecija, Philippines. The objective of this study is to assess the effectiveness of modern machinery on the business technical aspect of the farmers and the paddy field owners. The study utilized descriptive analysis to assess the use of modern agricultural machinery in rice production and its problems. The design was quantitative, using percentage, frequencies, and weighted mean. The results revealed that the majority of respondents have been operating for 11 to 20 years, owned 1 hectare of land that cultivate 2 times a year and harvest 86 rice sacks per hectare. Rice cultivation is happened during wet and dry season. To maximizing the land, farmers can try other crops while waiting for the season of rice cultivation. In agricultural mechanization, it concluded that plowing machines helps remove clods from the soil, transplanting rice seedlings and applying chemicals using machine can saves time. Harvester machine is suitable in small and large farmland for harvesting and may help farmers to save time, effort and total cost requirements. Local Government Unit to support through grants and funding the local rice farmers in maximizing utilization of machines that shows positive effect.

Multiomics Analysis of the Mechanism by Which Gibberellin Alleviates S-Metolachlor Toxicity in Rice Seedlings.

S-metolachlor is a selective pre-emergence herbicide used in dryland. However, it is challenging to employ in paddy fields due to its phytotoxic effects on rice. As a common phytohormone, Gibberellin-3 (GA3) is inferred to have the ability to alleviate herbicide phytotoxicity. This study first quantitatively verified the phytotoxicity of s-metolachlor to rice and then demonstrated the mitigative effect of GA3 on these adverse reactions. Furthermore, a transcriptome of rice seedlings subjected to different treatments was constructed to assemble the reference genes, followed by comparative metabolomics and proteomics analyses. Metabolomics revealed an enrichment of flavonoid metabolites in the group of adding GA3, and these flavonoids can eliminate ROS in plants. Proteomics analysis indicated that differential proteins were enriched in the phenylpropanoid biosynthesis pathway responsible for the synthesis of flavonoids and that the functions of most differential proteins are associated with peroxidase. The proteome, combined with the transcriptome, revealed that the expressions of proteins and genes was related to the POD activity in the group of adding GA3. It was speculated that the elimination of ROS is key to alleviating the stress of s-metolachlor on rice growth. It was inferred that the mechanism of GA3 in alleviating the phytotoxicity of the substance s-metolachlor is by increasing the activity of the POD and influencing the growth of rice seedlings through the restoration of flavonoid synthesis. In this study, we screened GA3 as a safener to alleviate the phytotoxicity of s-metolachlor on rice. On this basis, the mechanism of alleviating phytotoxicity was studied. The application range of s-metolachlor might be expanded, providing a new supplementary method for weed control and herbicide resistance management.

Comparative Study of the Productivity and Some Economical Aspects of the Conventional Rice and Rice-Fish Farmings Systems in Agonlin-Lowé Village, Adjohoun, Bénin

The main idea of this work was to compare the productivities of rice farming systems and rice rice- fish polyculture in the same fish ponds. The experiment was conducted in six (06) different compartments with a total area of 300 m² between March and August 2022. The test was carried out with 600 fry including 400 fingerlings of Oreochromis niloticus and seedlings of rice (Variety IR 841). The initial average weights of fish in rice-fish culture without food supply and with food supply were respectively 9.7 g and 9.8 g. After 72 days, the variations of the physico-chemical parameters showed no significant difference between the compartments. In rice-fish farming, in the compartments without food supply, the average yield was 2.17 t/ha and in the compartments with food supply this average was 2.33 t/ha against 2.04 t/ha in the rice fields. In the associated culture, food intake was favorable with a mass gain of 6.9 g compared to 1.4 g obtained in the second pound. Also, the rice yields and the growth performance of fish O. niloticus were significantly (p > 0.05) higher than those obtained in conventional rice cultivation. Also monitoring the growth of farmed fish must continue in order to assess the performance achieved as well as the financial benefits for good promotion of the sector.

The Diterpene Isopimaric Acid Modulates the Phytohormone Pathway to Promote Oryza sativa L. Rice Seedling Growth.

Many plant secondary metabolites are active and important in the regulation of plant growth. Certain plant-derived diterpenes are known to promote plant growth, but the pathways by which this promotion occurs are still unknown. Activity screening revealed that the plant-derived diterpene isopimaric acid exhibits growth-promoting activity in rice (Oryza sativa L.) seedlings. Furthermore, 25 μg/mL of isopimaric acid promoted the growth of 15 self-incompatible associated populations from different rice lineages to different extents. Quantitative analyses revealed a significant decrease in the concentration of the defense-related phytohormone abscisic acid (ABA) following treatment with isopimaric acid. Correlation analysis of the phytohormone concentrations with growth characteristics revealed that the length of seedling shoots was significantly negatively correlated with concentrations of 3-indole-butyric acid (IBA). Moreover, the total root weight was not only negatively correlated with ABA concentrations but also negatively correlated with concentrations of isopentenyl adenine (iP). These data suggest that isopimaric acid is able to influence the phytohormone pathway to balance energy allocation between growth and defense in rice seedlings and also alter the correlation between the concentrations of phytohormones and traits such as shoot and root length and weight. We provide a theoretical basis for the development and utilization of isopimaric acid as a plant growth regulator for rice.

Combined effects of polyamide microplastic and sulfamethoxazole in modulating the growth and transcriptome profile of hydroponically grown rice (Oryza sativa L.)

The use of reclaimed water from wastewater treatment plants for irrigation has a risk of introducing micropollutants such as microplastics (MPs) and antimicrobials (AMs) into the agroecosystem. This study was conducted to investigate the effects of single and combined treatment of 0.1 % polyamide (PA ∼15 μm), and varying sulfamethoxazole (SMX) levels 0, 10, 50, and 150 mg/L on rice seedlings (Oryza sativa L.) for 12 days. The study aimed to assess the impact of these contaminants on the morphological, physiological, and biochemical parameters of the rice plants. The findings revealed that rice seedlings were not sensitive to PA alone. However, SMX alone or in combination with PA, significantly inhibited shoot and root growth, total biomass, and affected photosynthetic pigments. Higher concentrations of SMX increased antioxidant enzyme activity, indicating oxidative stress. The roots had a higher SMX content than the shoots, and the concentration of minerals such as iron, copper, and magnesium were reduced in roots treated with SMX. RNA-seq analysis showed changes in the expression of genes related to stress, metabolism, and transport in response to the micropollutants. Overall, this study provides valuable insights on the combined impacts of MPs and AMs on food crops, the environment, and human health in future risk assessments and management strategies in using reclaimed water.

Rich-silicon rice husk ash increases iron plaque formation and decreases cadmium and arsenic accumulation in rice seedlings

Combined Cd (cadmium) and As (arsenic) pollution in cultivated land affects the safety of crops production and endangers human health. Rice (Oryza sativa L.) is a crop that uptakes Si (silicon), and Si can effectively promote rice growth and mitigate heavy metal toxicity. This study examined the effect and mechanism of Si-rich amendment (HA) prepared by aerobic combustion of rice husk on Cd and As accumulation in iron plaque and rice seedlings via hydroponic experiments. HA enhanced the vitality of rice growth because of its Si content and increased the amount of amorphous fraction iron plaques, furthermore, Cd content was decreased while the As was increased in both amorphous fraction and crystalline fraction iron plaques, resulting in the contents of Cd and As decreases by 10.0%–38.3% and 9.6%–42.8% for the shoots, and by 13.4%–45.2% and 9.9%–20.0% for the roots, respectively. In addition, X-ray diffraction and X-ray photoelectron spectroscopy illustrated significantly more Fe2O, MnO2 and MnO in the iron plaque after HA supply and the simultaneous existence of Mn–As and Mn–Si compounds. This result revealed less Cd from iron plaque and more As retention with HA supply, reducing the amount of Cd and As up taking and accumulation by rice seedlings. HA is beneficial to rice growth and reduce the absorption of heavy metals in plants. At the same time, HA is environmentally friendly, it can be used for the remediation of paddy fields contaminated by Cd and As.

Assessing the physiological responses and uptake patterns of lanthanum and yttrium in rice and Phytolacca americana L.

The effects of rare earth elements (REEs) on plant physiology and bioaccumulation characteristics vary significantly. As a result, considerable attention has been directed towards the effects and toxicity of REEs on plants. REEs migrate and transform in the environment and are absorbed by plant roots. However, different plants exhibit varying capacities to absorb REEs, leading to diverse impacts on their growth. In our study, we subjected seedlings of rice and Phytolacca americana L. to a gradient of lanthanum and yttrium (La + Y) concentrations to evaluate the physicochemical effects and uptake patterns of these elements. We meticulously measured variables such as biomass, root length, and elemental concentrations of La and Y, as well as macronutrients (P, Na, K, Mn, Fe, Mg, Ca) and micronutrients (Cu, Zn) to decode the physiological responses to varying levels of La + Y exposure. Based on the known dualistic nature of REEs interaction with plants, our results reveal that the threshold of REEs to different plants is different, and this conclusion can serve well for the formulation of rare earth pollution remediation strategies. Importantly, the accumulation of La and Y in P. americana L. roots was significantly greater than in rice roots, by an order of magnitude, reflecting the unique uptake capacities of hyperaccumulators. Additionally, this research found that nutrient dynamics and the absorption patterns of La and Y within the plants diverged, suggesting that La uptake in P. americana L. may occur via Ca2+ ion channels. These insights enhance our understanding of REE-plant interactions and have broader implications for agriculture and environmental health.

Root phenotype detection of rice seedling under nitrogen conditions based on terahertz imaging technique

Root phenotype detection is the basis for screening of dominant root and improving of seed breeding. The efficiency of root phenotype detection is restricted by the concealment and complexity of crop roots. In this paper, a new method based on terahertz imaging technology was proposed to detect the phenotypic characteristics of rice root and quantitatively predict root nitrogen content. First, the terahertz imaging spectral data of rice root were preprocessed with de-overlapping, reconstruction, enhancement, and segmentation. Then, the phenotypic characteristics of root length, diameter and surface area of rice roots were extracted according to the refinement algorithm. In addition, three linear regression models were fitted between root phenotype and root nitrogen content. Finally, Convolutional Neural Network (CNN), Genetic Algorithm-Back Propagation Neural Network (GA-BPNN), and Sparrow Search Algorithm-Support Vector Regression (SSA-SVR) were used to predict nitrogen content in rice roots by training and testing terahertz time domain data. Compared with two kinds of root phenotypic analysis software, the average errors of root length, diameter and root surface area calculated in this paper were 10.68 %, 7.29 % and 3.49 %, respectively. The fitting determination coefficients between root length, root surface area and the root nitrogen content were 0.88 and 0.87 after removing three groups of high-nitrogen data and one group of contrast data. The prediction accuracy of SSA-SVR model was 0.99 and the root mean square error was 0.05. Studies show that terahertz imaging technique can provide an effective analytical way for qualitative analysis of root phenotype.

An efficient and generalisable approach for mapping paddy rice fields based on their unique spectra during the transplanting period leveraging the CIE colour space

As one of the most important staple foods globally, rice sustains nearly half of the world's population. Accurate and timely paddy rice mapping is, thus, essential for rice-related policy-making to ensure food security in the context of anthropogenic, environmental and climate changes. However, paddy rice mapping remains a challenging task since it usually has similar spectral characteristics to other land covers. In this research, for the first time, an entirely new approach, called RiceTColour, was proposed for mapping rice fields within the Commission Internationale de l'Eclairage (CIE) colour space based on their unique spectra during the rice transplanting period as observed in remotely sensed imagery. We demonstrate that transplanted rice fields, representing a mixture of soil, water and rice seedlings, consistently exhibit relatively low spectral values in both SWIR and NIR bands across various geographical locations, leading to their unique dark green colours in the false-colour image composed of SWIR, NIR and Red bands. Based upon this, we transformed these three spectral bands into the CIE colour space where paddy rice was found to be readily and completely separated from the other land covers. Straightforward, but specific classification criteria were established within the CIE colour space to differentiate paddy rice from the other land covers. The proposed RiceTColour, thus, represents a new approach for paddy rice identification, that is mapping paddy rice using the CIE colour space based upon the previous underexplored remotely sensed spectra of paddy fields during the transplanting season. The effectiveness of the proposed method was investigated over five rice-planting regions distributed across different geographical regions, characterised by different climates, rice cropping intensities, irrigation schemes and cultural practices. Specifically, the mapping criteria established in a training site (S1) were directly generalised to the other four sites (S2 to S5) for paddy rice mapping. Experimental results demonstrated that the RiceTColour method consistently achieved the most accurate and balanced classifications across all five sites compared with four benchmark comparators: a SAR-based method, an index-based method and two supervised classifier-based methods. In particular, the RiceTColour method performed relatively stable, producing an overall accuracy exceeding 95% in the training site (S1) as well as the four generalised sites (S2 to S5), which is an encouraging result. Such efficient yet stable rice mapping results across various rice-planting regions suggest a very strong generalisation capability of the proposed RiceTColour method. In consideration of the relatively large planting area of paddy rice fields globally, the proposed parameter-free, efficient, and generalisable RiceTColour method, thus, holds great potential for widespread application in various rice-planting areas worldwide.

Genome-Wide Association Studies Reveal That the Abietane Diterpene Isopimaric Acid Promotes Rice Growth through Inhibition of Defense Pathways.

Plants are an important source for the discovery of novel natural growth regulators. We used activity screening to demonstrate that treatment of Nipponbare seeds with 25 μg/mL isopimaric acid significantly increased the resulting shoot length, root length, and shoot weight of rice seedlings by 11.37 ± 5.05%, 12.96 ± 7.63%, and 27.98 ± 10.88% and that it has a higher activity than Gibberellin A3 (GA3) at the same concentration. A total of 213 inbred lines of different rice lineages were screened, and we found that isopimaric acid had different growth promotional activities on rice seedlings of different varieties. After induction with 25 μg/mL isopimaric acid, 15.02% of the rice varieties tested showed increased growth, while 15.96% of the varieties showed decreased growth; the growth of the remaining 69.02% did not show any significant change from the control. In the rice varieties showing an increase in growth, the shoot length and shoot weight significantly increased, accounting for 21.88% and 31.25%. The root length and weight significantly increased, accounting for 6.25% and 3.13%. Using genome-wide association studies (GWASs), linkage disequilibrium block, and gene haplotype significance analysis, we identified single nucleotide polymorphism (SNP) signals that were significantly associated with the length and weight of shoots on chromosomes 2 and 8, respectively. After that, we obtained 17 candidate genes related to the length of shoots and 4 candidate genes related to the weight of shoots. Finally, from the gene annotation data and gene tissue-specific expression; two genes related to this isopimaric acid regulation phenotype were identified as OsASC1 (LOC_Os02g37080) on chromosome 2 and OsBUD13 (LOC_Os08g08080) on chromosome 8. Subcellular localization analysis indicated that OsASC1 was expressed in the plasma membrane and the nuclear membrane, while OsBUD13 was expressed in the nucleus. Further RT-qPCR analysis showed that the relative expression levels of the resistance gene OsASC1 and the antibody protein gene OsBUD13 decreased significantly following treatment with 25 μg/mL isopimaric acid. These results suggest that isopimaric acid may inhibit defense pathways in order to promote the growth of rice seedlings.

Transfer of antibiotic resistance genes from soil to rice in paddy field

The global spread and distribution of antibiotic resistance genes (ARGs) has received much attention whereas knowledge about the transmission of ARGs from one matrix to another is still insufficient. In this study, the paddy fields fertilized with chemical fertilizer, swine compost, and no fertilizer were investigated to assess the transfer of ARGs from soil to rice. Soil and plant samples were collected at day 0, 7, 30 and 79 representing various stages of paddy growth. High throughput qPCR was applied to quantify ARGs using a set of 144 primers. Gene copy number of ARGs measured in soil initially decreased and then increased in soil with no fertilizer and chemical fertilizer, indicating that crop planting and flooding conditions did influence the ARGs profiles in soil. Application of swine compost significantly enhanced the relative abundance and gene copy number of ARGs in paddy soil. Rice seedlings contained substantial amount of ARGs and their relative abundance continually decreased after transplant. Compared with initial stage, detection frequencies of ARGs increased in soil without swine compost at harvest time (day 79), indicating the transmission of ARGs from irrigation water to soil. Detection frequencies of ARGs increased in soil and rice root with swine compost at harvest time, indicating the transfer of ARGs from swine compost to soil and rice root. There was no significant difference in abundance and diversity of ARGs in rice grains with these three different fertilizations. The source of the ARGs in rice grain still needs further exploration.

Co-exposure to Organophosphate esters (OPEs) and Cadmium alleviated their accumulation in rice (Oryza sativa L.) by inhibiting transports' transcription

Combined contamination of Organophosphate esters (OPEs) and heavy metal has been concerning on their potential threaten to human health through food chain. In order to estimate effects of OPEs and heavy metal's combined contamination on crop, the growth of rice seedlings, pollutant accumulations and their involved in transcript regulation pathway under OPEs and Cd contamination were investigated. In results, only single OPEs pollution improved the biomass of rice, while single Cd pollution inhibited the growth of plants. Although the combined contaminations of OPEs and Cd also showed negative effect for plant growth, OPEs could alleviate the negative effect of Cd on rice. The Octanol-water partition coefficients (log Kow) of OPEs were positively correlated with root concentration factor (RCF) values in the trend line and negatively correlated with shoot concentration factor (SCRF) and translocation factor (TF). OPEs and Cd inferred with each other's accumulations in plants through reducing RCF, SCRF and TF. After addition of Cd, the expressions of OsTIL, OsLTP4, OsLTPL1, and OsMLP423 genes involved in OPEs accumulation were downregulated. Moreover, the presence of Cd also affected the binding sites and binding energy of the four proteins with OPEs. Meanwhile, the expression of OsNramp1, OsNramp5, OsHMA2, OsGS1, and OsPCS1 genes involved in Cd accumulation and toleration were also downregulated after addition of OPEs. These results suggested that OPEs and Cd directly repressed each other gene transcript involved in accumulation and toleration process.