Germination Of Rice Research Articles

Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping

BackgroundRice is one of the most important food crops in the world, and with the development of direct seeding methods for rice, exposure to anaerobic stress has become a major factor limiting its growth.ResultsIn this experiment, we tested the tolerance to anaerobic germination of rice varieties NIP and HD84, and they were used as parents to construct a DH (doubled-haploid) population. The transcriptomes of NIP (highly tolerant) and HD86 (intolerant), and their progeny HR (highly tolerant) and NHR (intolerant) were sequenced from normal and anaerobic environments. The differentially-expressed genes (DEGs) were subjected to GO (Gene ontology), KEGG (Kyoto Encyclopedia of Genes and Genomes), and WGCNA analyses. QTL mapping of the DH population identified tolerance to anaerobic germination-related chromosomal segments. The transcriptome results from 24 samples were combined with the anaerobic stress QTL results for 159 DH population lines to construct a metabolic network to identify key pathways and a gene interaction network to study the key genes. Essential genes were initially subjected to rigorous functional validation, followed by a comprehensive analysis aimed at elucidating their potential utility in domestication and breeding practices, particularly focusing on the exploitation of dominant haplotypes.ConclusionThe results show that pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) are the starting signals of energy metabolism for coleoptile length growth, the auxin transporter EXPA is the determining signal for coleoptile length growth. The pivotal genes Os05g0498700 and Os01g0866100 exert a negative regulatory influence on coleoptile length, ultimately enhancing tolerance to anaerobic germination in rice. Analyses of breeding potential underscore the additional value of Os05g0498700-hyp2 and Os01g0866100-hyp2, highlighting their potential utility in further improving rice through breeding programs. The results of our study will provide a theoretical basis for breeding anaerobic-tolerant rice varieties.

Effect of Hormonal Priming on Seed Germination and Initial Growth of Cambodian Rice in Salt Stress Condition

Effect of Hormonal Priming on Seed Germination and Initial Growth of Cambodian Rice in Salt Stress Condition

Trichoderma spp. isolates stimulate rice seedling growth of Sertani 13 variety

Trichoderma has become one of the most studied filamentous fungi to be used as a greener and more sustainable solution for improving the production and growth of numerous crops, due to its capability to form symbiotic associations with plants. This study aimed to evaluate the effect of Trichoderma isolates obtained from the rhizosphere of organic rice fields in Sukabumi, Indonesia, in enhancing rice germination and seedling growth. A laboratory experiment used a completely randomized design consisting of seed treatments of 21 Trichoderma isolates (T1-T21) and a control treatment without Trichoderma (C). The inoculation was employed to elucidate any potential effects of Trichoderma isolates. Results showed that five isolates, i.e., T5, T7, T9, T10, and T14 stimulated the highest seedling vigor index, root and shoot length, and fresh weight and dry weight. These findings exhibited the potential of these five isolates as plant growth-promoting fungi to improve rice seedling growth and contribute to our understanding of the role of symbiotic fungi in sustainable rice crop production. Keywords: plant growth promoting fungi; seed treatment; plant-microbe interactions, symbiotic fungi

Evaluation of anaerobic germination and submergence tolerance in rice (Oryza sativa L.) suitable for direct seeded condition

Evaluation of anaerobic germination and submergence tolerance in rice (Oryza sativa L.) suitable for direct seeded condition

Symphonies of Growth: Unveiling the Impact of Sound Waves on Plant Physiology and Productivity.

The application of sound wave technology to different plant species has revealed that variations in the Hz, sound pressure intensity, treatment duration, and type of setup of the sound source significantly impact the plant performance. A study conducted on cotton plants treated with Plant Acoustic Frequency Technology (PAFT) highlighted improvements across various growth metrics. In particular, the treated samples showed increases in the height, size of the fourth expanded leaf from the final one, count of branches carrying bolls, quantity of bolls, and weight of individual bolls. Another study showed how the impact of a 4 kHz sound stimulus positively promoted plant drought tolerance. In other cases, such as in transgenic rice plants, GUS expression was upregulated at 250 Hz but downregulated at 50 Hz. In the same way, sound frequencies have been found to enhance the osmotic potential, with the highest observed in samples treated with frequencies of 0.5 and 0.8 kHz compared to the control. Furthermore, a sound treatment with a frequency of 0.4 kHz and a sound pressure level (SPL) of 106 dB significantly increased the paddy rice germination index, as evidenced by an increase in the stem height and relative fresh weight. This paper presents a complete, rationalized and updated review of the literature on the effects of sound waves on the physiology and growth parameters of sound-treated plants.

A multi-omics study revealed the effect of pulsed light treatment on germinated brown rice: Promotion of sprouting efficiency and gamma-aminobutyric acid enrichment

Physical fields are increasingly proposed in the production of germinated grain foods, thus shorting the preparation cycle of high value-added sprouted grain foods. Here, pulsed light treatment (PLT) with 300 times at a single energy of 400 J was found to significantly promote the shoot length and gamma-aminobutyric acid (GABA) content in 8 varieties of germinated brown rice (GBR). Functional annotation analysis showed that the brown rice germination was promoted by the biosynthesis of phenylalanine, carbohydrate metabolism, and energy metabolism pathway. Moreover, PLT influenced the genes and metabolites involved in the GABA shunt and the polyamine degradation pathway, promoting the accumulation of GABA. Transcription factor OsbZIP56 was closely related to the transcript level of regulatory gene for germination and GABA enrichment. Furthermore, overexpression of OsbZIP56 in rice significantly promoted germination and GABA accumulation. These findings would be significant for improving the germination efficiency of edible seeds, promoting accumulation of active ingredients, and exploring gene functions in food materials.

STUDY OF THE EFFECT OF BACTERIA OF THE GENUS BACILLUS ON THE CULTURE OF RICE AND CORN SEEDS IN VITRO

The aim of the study was to investigate the effect of bacteria strains Bacillus megaterium ONU500, Bacillus velezensis ONU553, Bacillus pumilus ONU554, Bacillus subtilis ONU559 on the germination and growth of rice and corn seeds under sterile conditions. Materials and methods. Three-day cultures of the four strains were grown on LB liquid nutrient medium in a thermostat at 28 °C and the seeds of model plants were sterilized according to the standard scheme. The seeds were placed in 1% solutions of bacterial suspensions (106 CFU/ml) of each strain and inoculated for 1 hour. Results. The experiment results on both model plants indicate significant potential of the bacteria B. megaterium ONU500, B. velezensis ONU553, B. pumilus ONU554 as growth and development stimulators for plants. B. subtilis ONU559 is recommended for further study and clarification of its impact on plants in subsequent research. Conclusion. The most positive, stimulating effect on the indicators of germination, growth, and development of rice and corn seeds is exerted by inoculation with the strain B. megaterium ONU500 (for rice: increase in shoot length by 36.5%, root by 29%; for corn: 50% and 69% respectively). Further study of the influence of B. velezensis ONU553 is promising for rice cultivation, and for corn – B. pumilus ONU554.

Biocompatible silver nanoparticles as nanopriming mediators for improved rice germination and root growth: A transcriptomic perspective

Silver nanoparticles (AgNPs) have an important role in agriculture since they have several applications that are essential for the enhanced yield of crops. Furthermore, they act as nano-pesticides, delivering a proper dose to the target plants without releasing unwanted pesticides into the environment. Upholding the sustainable nano agriculture, biocompatible silver nanoparticles were synthesised utilising Piper colubrinum Link. leaf extract. Different characterization methods (TEM, EDX and XRD) revealed that AgNPs were successfully formed and coated with phytochemicals that constituted the plant extract. Enhanced root development during the early post-germination phase is crucial for the success of direct seeding in rice cultivation. The effects of AgNPs on the growth of plant roots are poorly understood. In this work, Piper colubrinum mediated AgNPs-primed Oryza sativa L. seeds, at various concentrations (0, 50, 80, 100, and 150 mg/L), exceeded typical hydro-primed controls in terms of germination and seedling growth. Oryza sativa L. treated with AgNPs at a concentration of 80 mg/L enhanced root elongation. Additionally, exposure to AgNPs significantly enhanced the content of chlorophyll. The Kyoto Encyclopedia of Genes and Genomes (KEGG) study revealed that the identified pathways like Aromatic amino acid biosynthesis genes, Fatty acid biosynthesis genes, and Carotenoid biosynthesis genes were the most enriched. Some of the genes associated with root growth and development like glucosyltransferases, Glutathione pathway genes, Calcium-ion binding pathway genes, Peroxidase precursor and Nitrilase-associated protein were up regulated. Overall, AgNPs treatments promoted seed germination, growth, chlorophyll content and gene expression patterns, which might be attributable to the beneficial effects of AgNPs on rice.

OsSCYL2 is Involved in Regulating ABA Signaling-Mediated Seed Germination in Rice.

Seed germination represents a multifaceted biological process influenced by various intrinsic and extrinsic factors. In the present study, our investigation unveiled the regulatory role of OsSCYL2, a gene identified as a facilitator of seed germination in rice. Notably, the germination kinetics of OsSCYL2-overexpressing seeds surpassed those of their wild-type counterparts, indicating the potency of OsSCYL2 in enhancing this developmental process. Moreover, qRT-PCR results showed that OsSCYL2 was consistently expressed throughout the germination process in rice. Exogenous application of ABA on seeds and seedlings underscored the sensitivity of OsSCYL2 to ABA during both seed germination initiation and post-germination growth phases. Transcriptomic profiling following OsSCYL2 overexpression revealed profound alterations in metabolic pathways, MAPK signaling cascades, and phytohormone-mediated signal transduction pathways, with 15 genes related to the ABA pathways exhibiting significant expression changes. Complementary in vivo and in vitro assays unveiled the physical interaction between OsSCYL2 and TOR, thereby implicating OsSCYL2 in the negative modulation of ABA-responsive genes and its consequential impact on seed germination dynamics. This study elucidated novel insights into the function of OsSCYL2 in regulating the germination process of rice seeds through the modulation of ABA signaling pathways, thereby enhancing the understanding of the functional significance of the SCYL protein family in plant physiological processes.

A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination

The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.

Slow-release Fertilizer Application on Silk (Falcataria moluccana Miq.) and Rice (Oryza sativa L.) Plant Growth and Yield in Agroforestry System

The aim of this experiment is to evaluate the impact of chitosan-NPK slow-release fertilizer (CS-NPK SRF) on the germination and growth of silk tree and rice in different planting patterns, as well as to assess the nutrient release rate of the SRF. The germination test followed a complete randomized design, incorporating a single factor (fertilizer type), namely no fertilizer (F0), SRF CS 0.5% weight 0.03 g (F1), SRF CS 0.5% 0.01 g (F2), SRF CS 0.7% 0.03 g (F3), SRF CS 0.7% 0.01 g (F4), and conventional NPK fertilizer (F5). The growth test utilized a 2-factor split-plot design, with the primary factor being the planting pattern (sengon/rice monoculture-SM/RM and sengon-rice agroforestry-AF) and the second factor being the fertilizer type. Results indicate that F2 and F4 yielded the highest germination and growth values in both plants, although not significantly different from F0. These findings suggest that CS-NPK SRF has the potential to enhance plant growth. The AF pattern exhibited lower growth compared to SM/RM, attributed to plant competition. CS-NPK SRF demonstrated a slower nutrient release (47.65% N; 85.01% P; 31.80% K) compared to conventional fertilizers. This slow release could potentially reduce nutrient loss to the environment while enhancing plant nutrient absorption.

Effects of iron oxide nanocoatings on the seed germination, seedling growth, and antioxidant response of aromatic rice grown in the presence of different concentrations of rice straw extracts

Effects of iron oxide nanocoatings on the seed germination, seedling growth, and antioxidant response of aromatic rice grown in the presence of different concentrations of rice straw extracts

Iron-lanthanum supported on graphite sheets for As(III) removal from aqueous solution: kinetics, thermodynamic and ecotoxicity assessment.

Graphene-based material is widely used to remove arsenic from water due to its layered structure with high surface area. Here, we have successfully synthesized Fe-La bimetallic modified graphite sheet materials to more efficiently remove As(III) from aqueous solution. The results showed that Fe-La-graphite sheets (FL-graphite sheets) have a larger specific surface area (194.28 m2·g-1) than graphite sheets (2.80 m2·g-1). The adsorption capacity of FL-graphite sheets for As(III) was 51.69mg·g-1, which was higher than that of graphite sheets (21.91mg·g-1), La-graphite sheets (26.06mg·g-1), and Fe-graphite sheets (40.26mg·g-1). The FL-graphite sheets conformed to the Freundlich and Dubinin-Radushkevich isotherm, and the maximum adsorption capacity was 53.62mg·g-1. The removal process obeys intra-particle diffusion and pore diffusion for As(III). The results of batch adsorption experiments and characterization analyses demonstrated that oxidation, ligand exchange, and inner sphere complexation mechanisms involved in the adsorption of FL-graphite sheets to As(III) in comparison with graphite sheets. In addition, electrostatic attraction mechanism was found vital in the adsorption. Ecotoxicity assessment revealed that FL-graphite sheets have little influence on rice germination and growth, but reduced the toxicity of As(III) to rice. Therefore, the FL-graphite sheets have good practical application value in purifying As(III) polluted water with litter ecotoxicity.

Phytohormone and energy metabolism of rice germination and coleoptile growth during submergence by RNA-seq and LC-MS/MS analysis

Rice is one of the main food crops to guarantee the world's food security. Although rice is a semi-aquatic crop, long-term flooding stress can also inhibit growth and reduce yield and quality. Especially during the germination period, the germination rate of rice was inhibited by flooding stress, which resulted in the low emergence rate. Therefore, in this study, rice lines or cultivars with flood tolerance (C11) and flood sensitivity (KY60) were screened, and analyzed the response mechanisms during seed germination at different time points of waterlogging stress through transcriptome and metabolome sequencing. Compared with C11, waterlogging stress significantly inhibited the germination and coleoptile growth of KY60. Certain pathways, including plant hormones, energy metabolism, and carbohydrate metabolism, were identified as significantly involved in the flooding stress response in rice. The plant hormone-related DEGs (IAA, SAUR, ARF, LOX) and metabolites (IAA, JA, GA, and SA) were identified to up-regulate gene expression levels and significantly up-accumulate phytohormone content in C11 to resist waterlogging stress. However, the ABA signaling pathway-related genes (ZHD, PLY) and ABA content were decreased in C11 under submerged conditions. It is beneficial for C11 to promote seed germination and coleoptile elongation under flooding conditions. A total of 150 DEGs (AMY, PGLR) and 58 related compounds were identified as involved in the energy metabolism and carbohydrate metabolism of rice after flooding stress. Candidate key genes and metabolite compounds were identified by combined RNA-Seq and LC-MS/MS correlation network analysis. This study provided insights to explore the flood-tolerance mechanism of rice and laid the foundation for the cultivation of new varieties of flood-tolerance rice.

Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice.

Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non-invasive micro-test technology results showed that OsHAK9 restricted K+ efflux in salt-exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice.

A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination

Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.

AMPK activator 991 specifically activates SnRK1 and thereby affects seed germination in rice.

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) and AMP-activated protein kinase (AMPK) are highly conserved. Compound 991 is an AMPK activator in mammals. However, whether 991 also activates SnRK1 remains unknown. The addition of 991 significantly increased SnRK1 activity in desalted extracts from germinating rice seeds in vitro. To determine whether 991 has biological activity, rice seeds were treated with different concentrations of 991. Germination was promoted at low concentrations but inhibited at high concentrations. The effects of 991 on germination were similar to those of OsSnRK1a overexpression. To explore whether 991 affects germination by specifically affecting SnRK1, germination of an snrk1a mutant and the wild type under 1 μM 991 treatment was compared. The snrk1a mutant was insensitive to 991. Phosphoproteomic analysis showed that the differential phosphopeptides induced by 991 and OsSnRK1a overexpression largely overlapped. Furthermore, SnRK1 might regulate rice germination in a dosage-dependent manner by regulating the phosphorylation of three phosphosites, namely S285-PIP2;4, S1013-SOS1, and S110-ABI5. These results indicate that 991 is a specific SnRK1 activator in rice. The promotion and inhibition of germination by 991 also occurred in wheat seeds. Thus, 991 is useful for exploring SnRK1 function and the chemical regulation of growth and development in crops.

CALMODULIN-LIKE16 and PIN-LIKES7a cooperatively regulate rice seedling primary root elongation under chilling.

Low-temperature sensitivity at the germination stage is a challenge for direct seeding of rice in Asian countries. How Ca2+ and auxin (IAA) signaling regulate primary root growth under chilling remains unexplored. Here, we showed that OsCML16 interacted specifically with OsPILS7a to improve primary root elongation of early rice seedlings under chilling. OsCML16, a subgroup 6c member of the OsCML family, interacted with multiple cytosolic loop regions of OsPILS7a in a Ca2+-dependent manner. OsPILS7a localized to the endoplasmic reticulum membranes and functioned as an auxin efflux carrier in a yeast growth assay. Transgenics showed that presence of OsCML16 enhanced primary root elongation under chilling, whereas the ospils7a knockout mutant lines showed the opposite phenotype. Moreover, under chilling conditions, OsCML16 and OsPILS7a-mediated Ca2+ and IAA signaling and regulated the transcription of IAA signaling-associated genes (OsIAA11, OsIAA23, and OsARF16) and cell division marker genes (OsRAN1, OsRAN2, and OsLTG1) in primary roots. These results show that OsCML16 and OsPILS7a cooperatively regulate primary root elongation of early rice seedlings under chilling. These findings enhance our understanding of the crosstalk between Ca2+ and IAA signaling and reveal insights into the mechanisms underlying cold-stress response during rice germination.

Application of the thermal time model to assess the effects of priming treatments on seed germination of rice (Oryza sativa) cultivars in response to temperature

Application of the thermal time model to assess the effects of priming treatments on seed germination of rice (Oryza sativa) cultivars in response to temperature

Genetic Assessment of Germplasms for Anaerobic Germination in Rice

The present study was planned using portray method to screen rice germplasm lines for anaerobic germination (AG) by assessing seedling parameters. Among 266 lines studies, 121 exhibited variable germination % of 100‒17 under AG condition. Germplasm lines viz., RDR 7555, WGL 915, CSR 27, RGP 103, IRTON 103, IET 23993, RGP 60 and MTU NS1 were with highest germination capability (100%). Longest seedling length was recorded in WGL 915 (33.1 cm), RGP 57 (31.8 cm) and CSR 27 (31.2 cm). Seedling vigour index was maximum in lines WGL 915 (3310), RGP 57 (3180) and CSR 27 (3120). Genotypes CSR 27 (22.5 cm), WGL 915 (23.3 cm), RGP 57 (23.1 cm), RGP 103 (21.5 cm) and IRTON 103 (20.7 cm) are possessing highest tolerance to AG conditions with elongated shoot length. Highest root length was recorded in WGL 915 (9.8 cm), CSR 27 (8.7 cm), RGP 57 (8.7 cm), Indursamba (8.5 cm) and RGP 103 (8.1 cm). Highest heritability, genetic advance, PCV and GCV were recorded for seedling vigour index clearly highlights the importance of trait for simple selection. Highest significant positive correlation was observed between the seedling length and seedling vigour index (0.93**) followed by germination % and seedling vigour index (0.88**). Seedling length and germination % are important traits for seedling establishment in direct seeded rice under AG conditions. The 121 Germplasm lines were grouped into four clusters, cluster 3 and 4 has genotypes with above standard germination % (80%), highest seedling length (33.1‒20.3 cm) and high vigour index (3310‒2030). Present day task for plant breeders is to identify rice germplasm lines tolerant for anaerobic germination and to introgress the trait into the superior variety for development of rice pre-breeding lines with tolerance to anaerobic conditions and high yield [1].