Rice Seeds Research Articles

RSG-YOLOV8: Detection of rice seed germination rate based on enhanced YOLOv8 and multi-scale attention feature fusion.

The lack of obvious difference between germinated seeds and non-germinated seeds will cause the low accuracy of detecting rice seed germination rate, remains a challenging issue in the field. In view of this, a new model named Rice Seed Germination-YOLOV8 (RSG-YOLOV8) is proposed in this paper. This model initially incorporates CSPDenseNet to streamline computational processes while preserving accuracy. Furthermore, the BRA, a dynamic and sparse attention mechanism is integrated to highlight critical features while minimizing redundancy. The third advancement is the employment of a structured feature fusion network, based on GFPN, aiming to reconfigure the original Neck component of YOLOv8, thus enabling efficient feature fusion across varying levels. An additional detection head is introduced, improving detection performance through the integration of variable anchor box scales and the optimization of regression losses. This paper also explores the influence of various attention mechanisms, feature fusion techniques, and detection head architectures on the precision of rice seed germination rate detection. Experimental results indicate that RSG-YOLOV8 achieves a mAP50 of 0.981, marking a 4% enhancement over the mAP50 of YOLOv8 and setting a new benchmark on the RiceSeedGermination dataset for the detection of rice seed germination rate.

Using single-sample networks and genetic algorithms to identify radiation-responsive genes in rice affected by heavy ions of the galactic cosmic radiation with different LET values

IntroductionHeavy ions of the galactic cosmic radiation dominate the radiation risks and biological effects for plants under spaceflight conditions. However, the biological effects and sensitive genes caused by heavy ions with different linear energy transfer (LET) values have not been thoroughly studied.MethodsTo comprehensively analyze the biological effects of heavy ions with different LET values on rice under spaceflight conditions, we utilized the Shijian-10 recoverable satellite (SJ-10) to transport the dehydrated rice seeds on a 12.5-day mission in a 252 km low Earth orbit (LEO), and obtained rice plants hit by individual heavy ions with LET values ranging from 18 keV/μm to 213 keV/μm. The transcriptome and methylation sequencing were conducted on above plants, and a bioinformatics pipeline based on single-sample networks (SSNs) and genetic algorithms (GA) was developed to analyze the multi-omics expression profiles in this work. Note that SSNs can depict the gene interaction patterns within a single sample. The LET regression models were constructed from both gene expression and interaction pattern perspectives respectively, and the radiation response genes that played significant roles in the models were identified. We designed a gene selection algorithm based on GA to enhance the performance of LET regression models.ResultsThe experimental results demonstrate that all our models exhibit excellent regression performance (R2 values close to 1), which indicates that both gene expressions and interaction patterns can reflect the molecular changes caused by heavy ions with different LET values. LET-related genes (genes exhibiting strong correlation with LET values) and radiation-responsive genes were identified, primarily involved in DNA damage and repair, oxidative stress, photosynthesis, nucleic acid metabolism, energy metabolism, amino acid/protein metabolism, and lipid metabolism, etc. DNA methylation plays a crucial role in responding to heavy ions stressors and regulates the aforementioned processes.DiscussionTo the best of our knowledge, this is the first study to report the multi-omics changes in plants after exposure to heavy ions with different LET values under spaceflight conditions.

Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen.

Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, X. protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118=MTCC 13396=CFBP 9164=ICMP 25181 as the type strain. PPL117, PPL124, PPL125 and PPL126 are other strains of the species.

Exogenous Riboflavin Application at Different Growth Stages Regulates Photosynthetic Accumulation and Grain Yield in Fragrant Rice

Fragrant rice has high market value and is popular among consumers because of its pleasant fragrance. Plant growth regulators and trace elements can influence the yield and physiological indices of fragrant rice. Riboflavin, a vital component of plant vitamins, plays a crucial role in plant growth and development, and it is a water-soluble vitamin that is essential for sustaining normal photosynthesis and metabolic processes. However, the effects of riboflavin on nutrient accumulation and yield formation in fragrant rice have rarely been reported. Therefore, to further increase the yield and quality of fragrant rice, this study investigated the impact of the foliar application of riboflavin at different growth stages on nutrient accumulation and yield formation in two different genotypes of fragrant rice via a pot experiment. The experimental design consisted of three treatment groups, i.e., the T0 treatment group (control), which was sprayed with water; the T1 treatment group, which was sprayed at the booting stage; and the T2 treatment group, which was sprayed at the flowering stage; in all of these groups, 20 mg·L−1 riboflavin solution was used. The results revealed that the yields of the T1 and T2 treatments increased by 6.56–7.25% and 10.52–13.80%, respectively, compared with those of T0, which was attributed mainly to the increase in 1000-grain weight and grain filling. Furthermore, foliar spraying of riboflavin significantly increased the chlorophyll content, which resulted in the increased production of more total starch, soluble sugars, and sucrose and facilitated their transportation to the seeds. Moreover, applying riboflavin directly to the leaves increased the activity levels of the sucrose synthase (SS) and sucrose phosphate synthase (SPS) enzymes. Among the three treatments, the T2 treatment had the most pronounced effect. The results revealed that the foliar application of riboflavin could increase photosynthesis and promote the production of nonstructural carbohydrates, thereby increasing the total aboveground biomass of fragrant rice by 17.00–20.91% and 21.07–72.91% under the T1 and T2 treatments, respectively. Additionally, spraying riboflavin promoted rapid increases in the weight of fragrant rice seeds. In conclusion, foliar spraying of riboflavin during the flowering stage of aromatic rice can effectively enhance photosynthetic accumulation and yield, which is a promising physiological regulation strategy and provides new theoretical guidance for high-yield cultivation practices.

Transgenic rice with microbial high-temperature-resistant β-glucosidase gene significantly improved 2-acetyl-1-pyrroline content and edible quality.

The content of 2-acetyl-1-pyrroline (2-AP) directly affects the aroma and taste of rice. Δ1-Pyrroline and methylglyoxal are the precursors of 2-AP synthesis, and β-glucosidase plays an important role in the synthesis of methylglyoxal. In this study, β-glucosidase gene cloned from Pyrococcus furiosus was molecularly modified to obtain the high-temperature-resistant β-glucosidase gene 371-β-glucosidase (T371A), which was transformed into kitaake varieties (Oryza sativa L. subsp. japonica) by Agrobacterium-mediated transformation method, and transgenic rice with heterologous expression of T371A was obtained. Experiments were conducted in transgenic rice to investigate whether this gene had an effect on the synthesis of 2-AP. Under the optimum reaction temperature of 50°C and cooking temperature of 100°C, the enzyme activity of β-glucosidase in transgenic rice seeds was prominently increased by 260-280% and 419-426% over that of the control, respectively. The content of 2-AP in transgenic rice seeds significantly increased by 75-105% under normal temperature and high-temperature cooking conditions compared with the control. It was also found that transgenic rice increased the content of methylglyoxal and decreased the expression of betaine aldehyde dehydrogenase (BADH2). The high-temperature-tolerant β-glucosidase gene obtained in this study provides an innovative technical strategy for molecular breeding of high-edible aroma crops and has wide application potential. © 2024 Society of Chemical Industry.

Effect of environmental factors on seed germination and seedling emergence of weedy rice (Oryza sativa f. spontanea) in China

Abstract Weedy rice (Oryza sativa f. spontanea Auct. ex Backer) is a troublesome annual weed from the Gramineae family and infests rice (Oryza sativa L.) fields globally, with a notable presence in China. However, limited information is available regarding the effects of diverse environmental factors on its germination and emergence. A better understanding of the seed biology and ecology of weedy rice is crucial for developing effective weed management strategies. Experiments were conducted to evaluate the effects of temperature, light, soil burial depth, wheat (Triticum aestivum L.) crop residue amount, salt stress, osmotic stress, and radiant heat on the germination and seedling emergence of weedy rice. Weedy rice exhibited robust germination (>98%) when exposed to varying day/night temperatures (20/15 to 35/30 C) and remained unaffected by light conditions. Seedling emergence was not influenced within the top 5-cm soil layer, where 100% of the seedlings emerged. However, emergence decreased as the soil burial depth increased, eventually resulting in no emergence from a burial depth of 11 cm. The soil burial depth required for 50% of the maximum emergence was 8.3 cm. Seedling emergence ranged from 97% to 100% across different amounts of the wheat straw residue cover (0 to 10,000 kg ha−1). The sodium chloride concentration and osmotic potential required for 50% were 230.8 mM and −0.5 MPa, respectively. No germination was observed when weedy rice seeds were exposed to >110 C pretreatment (radiant heat for 5 min), indicating that residue burning could reduce infestation of weedy rice. The insights gained from this study contribute valuable knowledge to enhance the integrated management of weedy rice in China.

Microbial biosurfactant-mediated green synthesis of zinc oxide nanoparticles (ZnO NPs) and exploring their role in enhancing chickpea and rice seed germination

Malnutrition is one of the greatest challenges faced by humanity, which may be addressed by improving crop productivity to ensure food security. However, extensive use of synthetic fertilizers can lead to soil fertility degradation. This study highlights the potential of combining nanotechnology with biotechnology to enhance the germination rates of commercially important crop seeds. Bacterial biosurfactant extracted from a newly isolated Klebsiella sp. strain RGUDBI03 was used as a reducing and capping agent for the synthesis of zinc oxide nanoparticles (ZnO NPs) through a simple method. Extensive characterization of ZnO NPs through electron microscopic analysis showed well-dispersed, homogeneous NPs with a size range of 2–10 nm. High-resolution transmission electron microscopy (HR-TEM) images also revealed molecular fringes of 0.26 nm in single crystal ZnO NPs, with approximately 50% of the NPs exhibiting a size range of 2–4 nm. X-ray diffraction (XRD) results of ZnO NPs indicated the presence of (100), (002), (101), (102), (200), and (112) planes, confirming their crystalline nature. The presence of C = C–H, C = C, C–H, and C = C groups in both the bacterial biosurfactant and ZnO NPs, as depicted by Fourier-transform infrared spectroscopy (FTIR) spectra, confirmed the function of the biosurfactant as a reducing and capping agent. The nano-primed chickpea (Cicer arietinum) and rice (Oryza sativa) seeds showed an increase in water uptake rate, 89% and 92% respectively, compared to the control (73% and 44%), leading to an enhanced germination rate of 98% and 76%, compared to their respective controls (80% and 30%) under optimized conditions. Additionally, the nano-primed seeds exhibited higher levels of α-amylase activity in both seeds (0.37 mg/g for chickpea and 2.49 mg/g for rice) compared to the control. Notably, the ZnO NP priming solution exhibited no cytotoxicity on red blood cells and earthworms (Eudrilus eugeniae), indicating their non-cytotoxic and eco-friendly nature for future field trials.

Biofilmed-PGPR: Next-Generation Bioinoculant for Plant Growth Promotion in Rice under Changing Climate

The exopolysaccharide matrix of the diazotrophic cyanobacteria was used to integrate the phosphorus (P) and potassium (K) solubilizing bacteria for enhanced survival of the plant growth-promoting bacteria and, ultimately, survival of bacteria in the rhizosphere for better plant growth. A new biofilm-based formulation comprising the diazotrophic cyanobacteria Anabaena AMP2, phosphorus-solubilizing Bacillus megaterium var. phosphaticum PB1, and potassium-solubilizing Rhizobium pusense KRBKKM1 was tested for efficacy in rice. The growth medium with half-strength BG-11 medium supplemented with 3% glucose showed best for biofilm formation under in vitro conditions. Analysis of the methanolic extract of the cyanobacterial-bacterial biofilm (CBB) showed antioxidants, such as 2-methoxy phenol and pentadecane, which are proven to improve plant-microbe interactions and plant growth promotional activity, respectively. Treatment of rice seeds with CBB extract at 10 mL or 20 mL/100 g showed significant enhancement in germination percentage and seedling length. Therefore, a pot culture experiment with the CBB formulations was carried out, and different growth and yield parameters were recorded. Principal component analysis showed that the plant growth, yield, soil dehydrogenase activity, and soil chlorophyll content were positively correlated with rice plants amended with vermiculite-based CBB at 2 kg/hm2 followed by a spray with aqueous CBB formulation at 5 mL/L on 15 and 30 d after the rice transplanting (T6) grown with a 25% reduced level of NPK chemical fertilizers than the recommended dose. Further, Pearson correlation analysis showed that yield was positively correlated with soil dehydrogenase (r = 0.92**) and soil chlorophyll content (r = 0.96**). We concluded that CBB could be used as a novel biofilm-based bio-inoculant to increase rice productivity and crop fitness as a component in integrated nutrient management and sustainable organic farming strategies with reduced chemical fertilizers.

Design and Testing of a Branched Air-Chamber Type Pneumatic Seed Metering Device for Rice

To meet the diverse seeding requirements of super hybrid rice, common hybrid rice, and conventional rice—which vary from 1 to 3 seeds, 2 to 4 seeds, and 5 to 8 seeds per hole, respectively—this study developed a branched air-chamber type pneumatic seed metering device for rice. The device utilizes an air chamber control board to manage the branched air chamber casing, enabling precise adjustments to the seeding quantity. This study presents a theoretical analysis of the seed metering device’s operation and its critical components. Structural parameter optimization was conducted using Ansys-Fluent (2021 R1) software, followed by multi-objective optimization of operational parameters through bench testing. Simulation results indicated that optimal vacuum pressure in the seed metering disc pores reached a maximum of 857 Pa with a chamber depth of 22 mm, an angle of 100°, and a cavity depth of 25 mm, achieving a minimal coefficient of variation of 0.86%. Bench test results showed that for seeding targets of 1 to 3 rice seeds per hole, the optimal operational parameters were: two openings, a working vacuum of 1355 Pa, and a rotor speed of 32.78 r/min, resulting in a missed seeding rate of 4.70%, a qualification rate of 85.81%, and a re-seeding rate of 9.49%. For targets of 2 to 4 seeds per hole, the best parameters included three openings, a working vacuum of 1357 Pa, and a speed of 32.87 r/min, with a missed seeding rate of 4.60%, a qualification rate of 85.59%, and a re-seeding rate of 9.81%. For 5 to 8 seeds per hole, optimal parameters were six openings, a vacuum of 1339 Pa, and a rotor speed of 31.07 r/min, yielding a missed seeding rate of 4.09%, a qualification rate of 87.27%, and a re-seeding rate of 8.64%. These findings demonstrate that the branched air-chamber type pneumatic seed metering device effectively meets the varied direct seeding requirements of rice, enhancing the adaptability of pneumatic seed metering devices to different seeding quantities in rice and potentially informing the design of pneumatic seeders for other crops.

PENINGKATAN PEREKONOMIAN PETANI MELALUI PEMBUATAN BENIH PADI KELAS SEBAR (EXTENSION SEED)

The economy of farmers in Indonesia can be said to not be in good condition. Only a small number of farmers have been financially successful. The government's role in improving the welfare of farmers has been carried out by paying great attention to the agricultural sector. Sukoharjo Regency is a major contributor to the regional economy through the agricultural sector. In order for the economy of farmers in Sukoharjo Regency to be optimal, training is provided on making rice seeds in the distribution class. The method used in the community service program is through Asset Based Community Development (ABCD). Training and counseling are carried out for the "Ngudi Rejeki" farmer group as a partner. Making good seeds will make plants grow well and the harvest is maximized. Maximum harvest results will directly improve the economy of farmers and increase purchasing power. Deflation in various regions can be suppressed by improving the economy from below, especially farmers.

Cell Wall Invertases from Maternal Tissues Modulate Sucrose Flux in Apoplastic Pathways During Rice Anther and Seed Development.

Efficient sucrose transport and metabolism are vital for seed and pollen development in plants. Cell wall invertases (CINs) hydrolyze sucrose into glucose and fructose, maintaining a sucrose gradient in the apoplast of sink tissues. In rice, two CIN isoforms, OsCIN1 and OsCIN2, were identified as being specifically expressed in the anthers but not in pollen. Functional analyses through genetic crosses and mutant characterization showed that oscin1/2 double mutants exhibit a sporophytic male-sterile phenotype and produce shrunken seeds. This suggests that CIN activity is essential for proper pollen development and seed formation in rice. Observation of the progeny genotypes and phenotypes from various genetic crosses revealed that the phenotype of oscin1/2 seeds is determined by the genotype of the maternal tissue, indicating the critical role of CIN function in the apoplast between maternal and filial tissues for sucrose transport and metabolism. The CIN activity in the anthers and seeds of wild-type rice was found to be significantly higher-over 500-fold in the anthers and 5-fold in the seeds-than in the leaves, highlighting the importance of CIN in facilitating the efficient unloading of sucrose. These findings suggest that the fine-tuning of CIN activity in the apoplast, achieved through tissue-specific expression and CIN isoform regulation, plays a key role in determining the carbohydrate distribution across different tissues. Understanding this regulatory mechanism could provide opportunities to manipulate carbohydrate allocation to sink organs, potentially enhancing crop yields.

Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome.

To explore the rice seed microbiome, our objective was to isolate novel strains of Xanthomonas, a plant-associated bacterium with diverse lifestyles. Four isolates, anticipated to be Xanthomonas based on morphological features of yellow colonies, were obtained from healthy rice seeds. Phylo-taxono-genomic analysis revealed that these isolates formed monophyletic lineages belonging to a novel species within the genus Luteibacter. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization confirmed their distinct species status. We propose Luteibacter sahnii sp. nov. as a novel species, with PPL193T = MTCC 13290T = ICMP 24807T = CFBP 9144T as the type strain and PPL201, PPL552, and PPL554 as other constituent members. The fatty acid profile of the type strain is dominated by branched fatty acids like Iso-C15:0, consistent with other members of the genus. The novel species displays non-pathogenic attributes and exhibits plant probiotic properties, protecting rice plants from the leaf blight pathogen X. oryzae pv. oryzae. Production of Indole-3-Acetic Acid (IAA) and genomic regions encoding anti-microbial peptides emphasize its potential contributions to plant hosts. This study underscores the importance of employing a combination of phenotypic and genotypic methods in culturomics to enhance our understanding of rice seed microbiome diversity.

Seed Priming with Dynamically Transformed Selenium Nanoparticles to Enhance Salt Tolerance in Rice.

Seed priming with nanomaterials is an emerging approach for improving plant stress tolerance. Here, we demonstrated a mechanism for enhancing salt tolerance in rice under salt stress via priming with nonstimulatory nanoparticles such as selenium nanoparticles (SeNPs), distinct from stimulatory nanomaterials. Due to the dynamic transformation ability of SeNPs, SeNP priming could enhance rice salt tolerance by mediating the glutathione cycle to eliminate excess reactive oxygen species (ROS). During priming, SeNPs penetrated rice seeds and transitioned into a soluble form (99.9%) within the embryo endosperm. Subsequently, the soluble selenium (Se) was transported to rice roots and metabolized into various Se-related derivatives, including selenomethionine (SeMet), Na2SeO3 (Se IV), selenocysteine (SeCys2), and methylselenocysteine (MeSeCys). These derivatives significantly enhanced the root activities of key enzymes such as glutathione peroxidase (GSH-PX), glutathione reductase (GR), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) by 24.97%, 47.98%, 16.23%, 16.81%, and 14.82%, respectively, thus reinforcing the glutathione cycle and ROS scavenging pathways. Moreover, these alterations induced transcriptional changes in rice seedlings, with genes involved in signal transduction, transcription factors (TFs), ROS scavenging, and protein folding being upregulated, activating signal perception and self-repair mechanisms. These findings offer valuable insights for the agricultural application of nanomaterials.

OsNAL11 and OsGASR9 Regulate the Low-Temperature Germination of Rice Seeds by Affecting GA Content

Low temperatures cause serious threat to rice seed emergence, which has become one of the main limiting factors in the production of direct seeding rice. It is of great importance to study the genes controlling low-temperature tolerance during seed germination and to mine the possible regulatory mechanism for developing new rice varieties with immense low-temperature germination ability. In the current research study, two types of mutants of nal11 and gasr9, derived from the WT (wild type) ZH11, were used for the analysis of low-temperature germinability. The results showed that the nal11 and gasr9 mutants displayed no significant difference in germination rate with ZH11 at room temperature, but the mutants showed significantly lower germination rates, germination potential and germination index, and slowed seedling growth in the simulated direct seeding experiments at low temperatures compared to ZH11. Additionally, the activity of POD, SOD, CAT, and anti-superoxide anion radial activity were significantly reduced, but the levels of MDA and H2O2 were significantly higher in the nal11 and gasr9 mutant seeds that were germinated at low temperatures compared to ZH11. Further analysis revealed that the levels of total active GA, especially GA4 and GA7, were significantly lower in the nal11 and gasr9 mutants than that in ZH11 during low-temperature germination. Based on qRT-PCR analysis, the expression levels of some GA synthesis-related genes were higher, whereas some were lower in the nal11 and gasr9 mutants than those in ZH11, however, the GA metabolism-related genes OsGA2ox8 and OsGA2ox10 and the GA signaling negative regulator gene SLR1 were significantly up-regulated in both nal11 and gasr9 mutants at several time points during low-temperature germination. This may explain the lower GA levels in the nal11 and gasr9 mutants. Furthermore, the interaction between the OsNAL11 and OsGASR9 proteins was confirmed by Y2H, LUC, and Co-IP assays. This study provides preliminary insights into the regulatory mechanism of the OsNAL11 and OsGASR9 genes, which control the low-temperature germination of rice seeds by affecting the GA pathway. Our study will provide the basis for further mining the molecular mechanisms of low-temperature germination in rice and valuable theoretical reference for breeding varieties with strong low-temperature germinability.

EFISIENSI TEKNIS DAN FAKTOR YANG MEMPENGARUHI PRODUKSI PADI LOKAL SIGUPAI DI KABUPATEN ACEH BARAT DAYA (Technical Efficiency and Factors Affecting the Production of Local Sigupai Rice in Aceh Barat Daya Regency)

Sigupai rice is highly sought after and has significant economic value. Despite its popularity, the production of Sigupai rice remains relatively low. This study aims to identify the factors influencing the production, technical efficiency, and sources of inefficiency in Sigupai rice farming in West Aceh District. Data was collected from all 31 Sigupai rice farmers in the region and analyzed using the stochastic frontier Cobb-Douglas production function. The results indicate that Sigupai rice farming has achieved a technical efficiency level of 0.80. Land area, seed quantity, and fertilizer were found to significantly influence rice production. However, farmers' age, experience in cultivating Sigupai rice, and education did not have a significant impact on technical inefficiency.To improve the efficiency of Sigupai rice farming, it is recommended to optimize input utilization, including proper land planning and soil management. Additionally, the use of certified Sigupai rice seeds and efficient fertilization techniques can contribute to increased productivity.

Assessment of Trichoderma Species Isolated From Volcanic Soil of a Durian Field in Sisaket Province, Thailand for Plant Growth Promotion and Biocontrol Potential

Trichoderma species are ubiquitous saprophytic fungi commonly found in soil, with potential as fungal biocontrol agents for plant disease control and growth promotion. This research aimed to assess the attributes of Trichoderma sp. as plant growth promoters, focusing on nitrogen fixation, siderophore production, plant nutrient solubilization and indole-3-acetic acid production. Out of 19 isolates tested, 6 (T05, T19, T25, T27, T28 and T33) showed superior plant growth promotion abilities. These isolates were further evaluated for their capacity to enhance the germination of Khao Dawk Mali 105 rice seeds. Seeds were soaked in a suspension of conidia at a concentration of 1×1012 conidia/mL, and germination rates were measured. The germination rate ranged between 77.67 - 86.67 %, statistically significantly higher than the control rate of 33.33 %. Among the isolates, T05 exhibited the highest promotion of plant growth, evidenced by root length (7.27 cm), shoot length (8.50 cm), fresh weight (0.54 g) and dry weight (0.27 g), all significantly different from the control. Additionally, the potential of isolates to inhibit the fungal pathogen Colletotrichum sp. MN-3 was assessed using a dual culture method, with T35 showing the highest inhibition percentage (60.90 %). Morphological classification and nucleotide sequencing of the ITS1-5.8S-ITS2 region of rDNA gene identified the isolates as T. harzianum, T. reesei, T. asperellum and T. longibrachiatum. These findings underscore the effectiveness of Trichoderma sp. in promoting plant growth and suppressing plant pathogenic fungi. HIGHLIGHTSSix Trichoderma isolates (T05, T19, T25, T27, T28 and T33) exhibited superior plant growth promotion abilities. These isolates significantly enhanced germination rates of Khao Dawk Mali 105 rice seeds compared to the method. Among the isolates, T05 showed the greatest promotion of plant growth, as evidenced by root length, shoot length, fresh weight and dry weight. Trichoderma isolates demonstrated potential for inhibiting the fungal pathogen Colletotrichum sp. MN-3. Morphological classification divided the Trichoderma sp. into 4 groups, and species identification through nucleotide sequencing revealed T. harzianum, T. reesei, T. asperellum and T. longibrachiatum. GRAPHICAL ABSTRACT

The presence of a significant endophytic fungus in mycobiome of rice seed compartments

Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed’s compartment, indicating that the compartment can affect the distribution of the seed microbial community.

YOLOrot2.0: A novel algorithm for high-precision rice seed size measurement with real-time processing

We present YOLOrot2.0, an automated algorithm for measuring the dimensions of rice seeds, which holds significant importance in evaluating grain quality and genetic breeding research. The current methods for rice seed measurement exhibit various limitations, such as the need for seed preprocessing and selection, specialized equipment for measurement, and prolonged measurement time. To address these issues, YOLOrot2.0 introduces the following improvements: Firstly, it utilizes an anchor-free detection algorithm to optimize the detection of rotated targets. Secondly, the utilization of the Kalman Filter IoU loss function, which combines the horizontal bounding box and smooth L1 loss function, accelerates the convergence speed of the network. Moreover, the YOLOv8 architecture was adjusted by modifying certain convolutional layers and the Context to Fusion module to enhance the detection capabilities for smaller targets. Finally, YOLOrot2.0 enables direct processing of the entire image, eliminating the need for image partitioning and resulting in substantial time and processing savings. Experimental results demonstrate that YOLOrot2.0 achieves an mAP (mean average precision) score of 0.95, surpassing other comparative algorithms. Additionally, YOLOrot2.0 provides highly accurate measurements of seed length and width, closely aligned with ground truth values. Notably, YOLOrot2.0 achieves real-time detection by achieving an average detection time of only 11.5 ms for images sized 3000×4000 pixels.

Characterization of differences in seed endophytic microbiome in conventional and organic rice by amplicon-based sequencing and culturing methods.

In this paper, we studied the differences in the endophytic microbial composition of rice seeds grown in conventional and organic farming systems. Our results demonstrate a greater bacterial diversity in conventional farming, while organic farming showcases a higher fungal diversity. Additionally, our research reveals the ability of seed bacterial endophytes to inhibit the growth of three fungal pathogens responsible for causing seedling blight in rice. This study provides valuable insights into the potential use of beneficial seed microbial endophytes for developing a novel microbiome-based strategy in the management of rice diseases. Such an approach has the potential to enhance overall plant health and improve crop productivity.

Anthocyanin can improve the survival of rice seeds from solar light outside the international space station

A purple-pigmented (purple) rice seeds containing an anthocyanin, a major class of flavonoids, and their isogenic non-pigmented (white) seeds were exposed outside of the international space station (ISS) to evaluate the impact of anthocyanin on seed viability in space. The rice seeds were placed in sample plates at the exposed facility of ISS for 440 days, with the bottom layer seeds exposed to space radiation and the top layer seeds exposed to both solar light and space radiation. Though the seed weight of both purple and white seeds decreased after exposure to outer space, growth percentages after germination of purple and white seeds in the top layer were 55 and 15 %, respectively, compared to those in the bottom layer 100 and 70 %, respectively. RNA analysis revealed that 1,590 and 1,546 seed-stored mRNAs (long-lived mRNAs) were degraded in the white seeds of the top and the bottom layers, respectively, whereas those of the purple seeds in the top and bottom layers were 548 and 303, respectively. These results suggest that anthocyanin protected seeds and safeguarded long-lived mRNAs from solar light and space radiation to increase the seed viability.