How does rice cope with too little oxygen during its early life?

Effects of Planting Methods and Varieties on Rice Quality in Northern China

With the continuous improvement in living standards, consumers' demand for rice quality has been increasingly growing. This study analyzed the quality characteristics of different rice varieties under various cultivation methods. This study examined the rice variety Liaoxing 21 (LX21), the upland rice variety Han 9710 (H9710), and the hybrid rice variety Liaoyou 7362 (LY7362) from Liaoning Province to evaluate the effects of transplanting (TP) and direct seeding (DS) on processing, appearance, nutritional, and tasting quality. The results indicated that the planting method (PM) had a relatively minor impact on processing quality. Compared to TP, DS significantly increased grain length (GL) by 1.19%, grain width (GW) by 2.69%, appearance (A) by 2.61%, stickiness (Ss) by 7.15%, degree of balance (DB) by 3.19%, apparent amylose content (AAC%) by 6.20%, fa by 0.66%, fa/fb3 by 5.34%, and protein content (PC) by 19.93%. However, DS significantly reduced the grain length/width ratio (GL/W) by 1.03%, chalky grain rate (CGR) by 46.00%, chalkiness (CH) by 52.76%, and fb3 by 4.23%. Compared to DS, TP resulted in a higher peak viscosity (PV), final viscosity (FV), and pasting temperature (PaT), whereas setback (SB) was lower. Among the tested varieties, LX21 exhibited superior milled rice rate (MRR), head rice rate (HRR), GL, GL/W, A, Ss, DB, taste value (T), and FV compared to H9710 and LY7362, while demonstrating significantly lower CGR, CH, hardness (H), fa, trough viscosity (TV), and peak time (PeT). Under the same planting conditions, the conventional rice variety LX21 demonstrated excellent processing, appearance, and taste quality, whereas H9710 exhibited favorable nutritional quality and Rapid Visco Analyzer (RVA) characteristics. Meanwhile, we also analyzed the correlation between temperature/light conditions and nutritional quality, as well as RVA profiles. The results showed that variations in temperature and light were closely associated with amylopectin accumulation and starch pasting properties. This study highlights the findings that selecting the appropriate PMs and japonica rice varieties can effectively enhance overall rice quality. In the medium maturing regions of Liaoning Province, adopting DS with medium-early maturing japonica rice varieties offers an optimal production strategy for achieving high quality, high yield, and efficient utilization of temperature and light resources.

Genome-wide association study to identify candidate genes for submergence tolerance during rice seed germination

KEY MESSAGE

Submergence tolerance QTLs for rice germination were identified via a genome-wide association study, and a new causal gene, LOC_Os06g17260, was identified. Submergence stress is a major obstacle limiting the application of direct seeding in rice cultivation. Rapid bud and root growth helps plants establish a stronger growth base and improve their submergence tolerance. Therefore, mining genes for bud length (BL) and root length (RL) helps in the development of varieties that are adaptable to submergence and improve seedling emergence and yield of direct-seeded rice. In this study, a genome-wide association study of BL and RL was performed on a diverse rice collection consisting of 300 accessions. We identified a total of 37 QTLs, 13 of which had phenotypic contributions > 10%. The novel QTLs qBL6.2/qRL6.8, qBL6.3/qRL6.9, qBL6.4/qRL6.10, and qBL6.5/qRL6.11 on chromosome 6 were stably detected across BL and RL, and a total of 31 genes were detected in these four intervals. Concerning the gene annotation information and expression profiles, LOC_Os06g17090, LOC_Os06g17120, LOC_Os06g17140, LOC_Os06g17220, and LOC_Os06g17260 were selected as possible target genes. Through the validation of a knockout transgenic experiment, LOC_Os06g17260 was identified as the causal gene for submergence tolerance in rice at the germination stage. LOC_Os06g17260 encodes UDP-glucoronosyl and a UDP-glucosyl transferase domain-containing protein and contains two major haplotypes, with the Hap1 germplasm presenting greater submergence tolerance at the germination stage. These results provide new clues for exploring the molecular mechanisms that regulate submergence tolerance in rice and provide a promising source of genes for the molecular breeding of direct-seeded rice.

Mitochondrial AOX1a and an H2O2 feed-forward signalling loop regulate flooding tolerance in rice

Flooding is a widespread natural disaster that causes tremendous yield losses of global food production. Rice is the only cereal capable of growing in aquatic environments. Direct seeding by which seedlings grow underwater is an important cultivation method for reducing rice production cost. Hypoxic germination tolerance and root growth in waterlogged soil are key traits for rice adaptability to flooded environments. Alternative oxidase (AOX) is a non-ATP-producing terminal oxidase in the plant mitochondrial electron transport chain, but its role in hypoxia tolerance had been unclear. We have discovered that AOX1a is necessary and sufficient to promote germination/coleoptile elongation and root development in rice under flooding/hypoxia. Hypoxia enhances endogenous H2O2 accumulation, and H2O2 in turn activates an ensemble of regulatory genes including AOX1a to facilitate the conversion of deleterious reactive oxygen species to H2O2 in rice under hypoxia. We show that AOX1a and H2O2 act interdependently to coordinate three key downstream events, that is, glycolysis/fermentation for minimal ATP production, root aerenchyma development and lateral root emergence under hypoxia. Moreover, we reveal that ectopic AOX1a expression promotes vigorous root and plant growth, and increases grain yield under regular irrigation conditions. Our discoveries provide new insights into a unique sensor-second messenger pair in which AOX1a acts as the sensor perceiving low oxygen tension, while H2O2 accumulation serves as the second messenger triggering downstream root development in rice against hypoxia stress. This work also reveals AOX1a genetic manipulation and H2O2 pretreatment as potential targets for improving flooding tolerance in rice and other crops.

Optimization of γ-Aminobutyric Acid Production in Brown Rice via Prolonged Seed Priming

Germinated whole seeds possess elevated levels of bioactive nutrients; however, their application is hindered by several constraints. The germination process is typically time-consuming, and germinated seeds present challenges in terms of storage and transportation compared to dry seeds. This study introduces a novel processing method for rice, termed prolonged priming (PLP), aiming to combine the benefits of germinated and dry seeds. PLP involves soaking the seeds until the embryo exposure stage, followed by redrying. At 10 h (hour) germination post PLP, the γ-aminobutyric acid (GABA) levels in Hanyou73 (HY73) and IRAT exceeded 20 mg/100 g. Additionally, there was an induction of various nutrient components, including an increase in protein content, a reduction in amylose levels, and an elevation in fatty acid content, among others. Malondialdehyde levels, indicating oxidative damage, remained stable, and PLP preserved better seed integrity compared to routine priming in the desiccation-tolerant HY73. Collectively, the PLP treatment demonstrates an optimization of the nutritional value and storage in germinated brown rice (GBR). This novel process holds potential for enhancing the nutritional profile of GBR and may be applicable to other crop species.

Hypoxia stress: plant's sensing, responses, and tolerance mechanisms

Oxygen (O2) is an inhibiting factor for plant growth and development in submerged and flooding environments. Plants experience different O2 concentrations, such as normoxia, hypoxia, and anoxia, which can change over space and time. Plants have evolved various morphological, physiological, and biochemical adaptations to withstand low O2 stress, many of which have been well investigated. This review provides a detailed analysis of how plants respond to hypoxia, a significant stress factor primarily caused by flooding. Hypoxia affects plants at various cellular, developmental, and environmental levels. This review highlights genetic, molecular, and metabolic adaptations crops employ to cope with O2 deficiency. The roles of various transcription factors (TFs) and gene regulation mechanisms in enabling plants to modulate their physiological responses under hypoxic conditions are notable. The review also identifies a significant gap in research on plant responses during reoxygenation, the phase of returning to normal O2 levels, especially under natural lighting conditions. This transition poses ROS generation and photoinhibition challenges, affecting plant recovery post-hypoxia. We discuss various strategies to enhance plant hypoxia tolerance, including traditional breeding, genetic modification, and grafting techniques. It emphasizes integrating these approaches with a comprehensive understanding of hypoxia sensing and response mechanisms. We underscore the complexity of plant adaptations to hypoxia and the need for continued research in this field, especially in the face of global climate change. This is vital for developing sustainable agricultural practices and ensuring future food security.

Exogenous metabolite application is a potential strategy for expanding the use of direct rice seeding with the aim of reducing seeding costs

Rice is a staple food for over half of the global population, necessitates efficient and cost-effective production methods to ensure food security. However, direct seeding of rice often encounters challenges due to adverse environmental conditions, resulting in increased seeding costs. In this study, we analyzed the germination and physiological data of sixty-six rice varieties under cold and submergence conditions. Our results demonstrate that selecting rice varieties with superior germination capacity in these adverse conditions can improve germination rates by 39.43%. Transcriptomic and metabolomic analyses of two contrasting varieties revealed potential regulatory mechanisms involving hormonal pathways and the glycerophospholipid metabolism pathway. Furthermore, we found that the exogenous application of specific metabolites provides a cost-effective seed enhancement strategy for varieties with poor germination capacity. These findings suggest that combining suitable variety selection with seed enhancement treatments can significantly reduce seeding costs in rice production. This research offers valuable insights for developing resilient rice varieties and cost-effective seeding strategies, potentially contributing to improved rice cultivation practices and enhanced global food security.

Identification of hub genes involved in gibberellin-regulated elongation of coleoptiles of rice seeds germinating under submerged conditions

Rapid elongation of coleoptiles from rice seeds to reach the water surface enables plants to survive submergence stress and therefore plays a crucial role in allowing direct seeding in rice cultivation. Gibberellin (GA) positively influences growth in rice, but the molecular mechanisms underlying its regulation of coleoptile elongation under submerged conditions remain unclear. In this study, we performed a weighted gene co-expression network analysis to conduct a preliminarily examination of the mechanisms. Four key modules were identified with high correlations to the GA regulation of submergence tolerance. The genes within these modules were mainly involved in the Golgi apparatus and carbohydrate metabolic pathways, suggesting their involvement in enhancing submergence tolerance. Further analysis of natural variation revealed that the specific hub genes Os03g0337900, Os03g0355600, and Os07g0638400 exhibited strong correlations with subspecies divergence of the coleoptile elongation phenotype. Consistent with this analysis, mutation of Os07g0638400 resulted in a lower germination potential and a stronger inhibition of coleoptile elongation under submerged conditions. The hub genes identified in this study provide new insights into the molecular mechanisms underlying GA-dependent tolerance to submergence stress in rice, and a potential basis for future modification of rice germplasm to allow for direct seeding.

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.

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

BACKGROUND

Rice 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.

RESULTS

In 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.

CONCLUSION

The 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.

Recycled Iron Phosphates: A New Phosphorus Fertilizer for Paddy Rice

The potential of recycled iron phosphates (FePs), e.g., vivianites (Fe3(PO4)2·8H2O) and Fe(III)-rich phosphorus (P) adsorbent materials, as phosphorus fertilizer is limited by the strong interaction between Fe and P. In this study, the efficiency of FePs as P fertilizer was explored by applying them as granules or powder in flooded strongly P-fixing soils (acid and calcareous), thereby taking advantage of increased P release induced by reductive dissolution of P-bearing Fe(III) minerals. First, no P diffusion from granular FeP fertilizers into flooded soils was detectable by the diffusive gradient in thin films (DGT) technique and microfocused X-ray fluorescence (μ-XRF) analysis of thin soil sections, in contrast to detectable P diffusion away from granules of soluble triple superphosphate (TSP) fertilizer. On the contrary, powdered FePs demonstrated an excellent increase in extractable P (1 mM CaCl2) in a 120-day incubation experiment in flooded soils. Second, a pot experiment was performed with rice (Oryza sativa) grown in flooded acid and calcareous soils. The fertilizer value of FePs was remarkable when dosed as powder, as it was even up to 3-fold higher than TSP in the acid soil and similar to TSP in the calcareous soil. The beneficial effect of FeP over TSP in the acid soil is attributed to the slow release of P from FePs, which allows to partly overcome P fixation. The promising results of FePs as P fertilizer applied as powders in flooded soils debunk the generally accepted idea that FePs are poor sources of P while demonstrating the importance of the timing of FeP fertilizer application.

Flooding Tolerance of Rice: Regulatory Pathways and Adaptive Mechanisms

Rice is a major food crop for more than half of the world's population, while its production is seriously threatened by flooding, a common environmental stress worldwide. Flooding leads to oxygen deficiency, which is a major problem for submerged plants. Over the past three decades, significant progress has been made in understanding rice adaptation and molecular regulatory mechanisms in response to flooding. At the seed germination and seedling establishment stages, the CIPK15-SnRK1A-MYBS1 signaling cascade plays a central role in determining rice submergence tolerance. However, from seedlings to mature plants for harvesting, SUB1A- and SK1/SK2-regulated pathways represent two principal and opposite regulatory mechanisms in rice. In addition, phytohormones, especially gibberellins, induce adaptive responses to flooding throughout the rice growth period. This review summarizes the significant adaptive traits observed in flooded rice varieties and updates the molecular genetics and mechanisms of submergence tolerance in rice.

Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice

In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.

Salinity inhibits seed germination and embryo growth by reducing starch mobilization efficiency in barley

Barley is one of the world's earliest domesticated crops, which is widely used for beer production, animal feeding, and health care. Barley seed germination, particularly in increasingly saline soils, is key to ensure the safety of crop production. However, the mechanism of salt-affected seed germination in barley remains elusive. Here, two different colored barley varieties were used to independently study the regulation mechanism of salt tolerance during barley seed germination. High salinity delays barley seed germination by slowing down starch mobilization efficiency in seeds. The starch plate test revealed that salinity had a significant inhibitory effect on α-amylase activity in barley seeds. Further, NaCl treatment down-regulated the expression of Amy1, Amy2 and Amy3 genes in germinated seeds, thereby inhibiting α-amylase activity. In addition, the result of embryogenic culture system in vitro showed that the shoot elongation of barley was significantly inhibited by salt stress. These findings indicate that it is a feasible idea to study the regulation mechanism of salinity on barley seed germination and embryo growth from the aspect of starch-related source-sink communication.

Flooding-adaptive root and shoot traits in rice

Wetland plants, including rice (Oryza spp.), have developed multiple functional adaptive traits to survive soil flooding, partial submergence or even complete submergence. In waterlogged soils and under water, diffusion of O2 and CO2 is extremely slow with severe impacts on photosynthesis and respiration. As a response to shallow floods or rising floodwater, several rice varieties, including deepwater rice, elongate their stems to keep their leaves above the water surface so that photosynthesis can occur unhindered during partial submergence. In stark contrast, some other varieties hardly elongate even if they become completely submerged. Instead, their metabolism is reduced to an absolute minimum so that carbohydrates are conserved enabling fast regrowth once the floodwater recedes. This review focuses on the fascinating functional adaptive traits conferring tolerance to soil flooding, partial or complete submergence. We provide a general analysis of these traits focusing on molecular, anatomical and morphological, physiological and ecological levels. Some of these key traits have already been introgressed into modern high-yielding genotypes improving flood tolerance of several cultivars used by millions of farmers in Asia. However, with the ongoing changes in climate, we propose that even more emphasis should be placed on improving flood tolerance of rice by breeding for rice that can tolerate longer periods of complete submergence or stagnant flooding. Such tolerance could be achieved via additional tissues; i.e. aquatic adventitious roots relevant during partial submergence, and leaves with higher underwater photosynthesis caused by a longer gas film retention time.

GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination

Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.

Progress in the study of functional genes related to direct seeding of rice

Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.

Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.

The Impact of Carbohydrate Management on Coleoptile Elongation in Anaerobically Germinating Seeds of Rice (Oryza sativa L.) under Light and Dark Cycles

The ability of rice to elongate coleoptiles under oxygen deprivation is a determinant of anaerobic germination tolerance, critical for successful direct seeding. Most studies on anaerobic coleoptile elongation have been performed under constant darkness or in flooded soils because a drilling method was the primary approach for direct seeding of rice. However, aerial seeding is becoming popular, in which seeds which land on flooded soils are exposed to light during the daytime. Here, we investigated physiological mechanisms underlying anaerobic elongation of coleoptiles under light and dark cycles. This study identified two novel varieties, LG and L202, enabling the development of long coleoptiles under oxygen limitation, comparable to well-characterized varieties with strong anaerobic germination tolerance. Germination experiments using these two tolerant and two intolerant varieties, including Takanari and IR64, revealed that light and dark cycles increased coleoptile length in LG, Takanari, and IR64 relative to constant darkness. Interestingly, even in intolerant lines, dramatic starch breakdown and soluble carbohydrate accumulation occurred under oxygen limitation. However, intolerant lines were more susceptible to a representative soluble sugar, glucose, than tolerant lines under oxygen deprivation, suggesting that coleoptile growth can be inhibited in intolerant lines due to hypersensitivity to soluble sugars accumulated in anaerobically germinating seeds.

Ethylene-mediated regulation of coleoptile elongation in rice seedlings

Rice is an important food crop in the world and the study of its growth and plasticity has a profound influence on sustainable development. Ethylene modulates multiple agronomic traits of rice as well as abiotic and biotic stresses during its lifecycle. It has diverse roles, depending on the organs, developmental stages and environmental conditions. Compared to Arabidopsis (Arabidopsis thaliana), rice ethylene signalling pathway has its own unique features due to its special semiaquatic living environment and distinct plant structure. Ethylene signalling and responses are part of an intricate network in crosstalk with internal and external factors. This review will summarize the current progress in the mechanisms of ethylene-regulated coleoptile growth in rice, with a special focus on ethylene signaling and interaction with other hormones. Insights into these molecular mechanisms may shed light on ethylene biology and should be beneficial for the genetic improvement of rice and other crops.

Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches

Natural and man-made ecosystems worldwide are subjected to flooding, which is a form of environmental stress. Genetic variability in the plant response to flooding involves variations in metabolism, architecture, and elongation development that are related with a low oxygen escape strategy and an opposing quiescence scheme that enables prolonged submergence endurance. Flooding is typically associated with a decrease in O₂ in the cells, which is especially severe when photosynthesis is absent or limited, leading to significant annual yield losses globally. Over the past two decades, considerable advancements have been made in understanding of mechanisms of rice adaptation and tolerance to flooding/submergence. The mapping and identification of Sub1 QTL have led to the development of marker-assisted selection (MAS) breeding approach to improve flooding-tolerant rice varieties in submergence-prone ecosystems. The Sub1 incorporated in rice varieties showed tolerance during flash flood, but not during stagnant conditions. Hence, gene pyramiding techniques can be applied to combine/stack multiple resistant genes for developing flood-resilient rice varieties for different types of flooding stresses. This review contains an update on the latest advances in understanding the molecular mechanisms, metabolic adaptions, and genetic factors governing rice flooding tolerance. A better understanding of molecular genetics and adaptation mechanisms that enhance flood-tolerant varieties under different flooding regimes was also discussed.

Regain flood adaptation in rice through a 14-3-3 protein OsGF14h

Contemporary climatic stress seriously affects rice production. Unfortunately, long-term domestication and improvement modified the phytohormones network to achieve the production needs of cultivated rice, thus leading to a decrease in adaptation. Here, we identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance. OsGF14h acts as a signal switch to balance ABA signaling and GA biosynthesis by interacting with the transcription factors OsHOX3 and OsVP1, thereby boosting the seeding rate from 13.5% to 60.5% for anaerobic sensitive variety under flooded direct-seeded conditions. Meanwhile, OsGF14h co-inheritance with the Rc (red pericarp gene) promotes divergence between temperate japonica cultivated rice and temperate japonica weedy rice through artificial and natural selection. Our study retrieves a superior allele that has been lost during modern japonica rice improvement and provides a fine-tuning tool to improve flood adaptation for elite rice varieties.

Strawberry FaSnRK1α Regulates Anaerobic Respiratory Metabolism under Waterlogging

Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) is a central integrator of plant stress and energy starvation signalling pathways. We found that the FaSnRK1α-overexpression (OE) roots had a higher respiratory rate and tolerance to waterlogging than the FaSnRK1α-RNAi roots, suggesting that FaSnRK1α plays a positive role in the regulation of anaerobic respiration under waterlogging. FaSnRK1α upregulated the activity of anaerobic respiration-related enzymes including hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH) and lactate dehydrogenase (LDH). FaSnRK1α also enhanced the ability to quench reactive oxygen species (ROS) by increasing antioxidant enzyme activities. We sequenced the transcriptomes of the roots of both wild-type (WT) and FaSnRK1α-RNAi plants, and the differentially expressed genes (DEGs) were clearly enriched in the defence response, response to biotic stimuli, and cellular carbohydrate metabolic process. In addition, 42 genes involved in glycolysis and 30 genes involved in pyruvate metabolism were significantly regulated in FaSnRK1α-RNAi roots. We analysed the transcript levels of two anoxia-related genes and three ERFVIIs, and the results showed that FaADH1, FaPDC1, FaHRE2 and FaRAP2.12 were upregulated in response to FaSnRK1α, indicating that FaSnRK1α may be involved in the ethylene signalling pathway to improve waterlogging tolerance. In conclusion, FaSnRK1α increases the expression of ERFVIIs and further activates anoxia response genes, thereby enhancing anaerobic respiration metabolism in response to low-oxygen conditions during waterlogging.

Comparison of transcriptomic adjustments to availability of sugar, cellular energy, and oxygen in germinating rice embryos

During germination, the availability of sugars, oxygen, or cellular energy fluctuates under dynamic environmental conditions, likely affecting the global RNA profile of rice genes. Most genes that exhibit sugar-regulation in rice embryos under aerobic conditions are responsive to low energy and anaerobic conditions, indicating that sugar regulation is strongly associated with energy and anaerobic signaling. The interference pattern of sugar regulation by either anaerobic or low energy conditions indicates that induction is likely the more prevalent regulatory mechanism than repression for altering the expression of sugar-regulated genes. Among the aerobically sugar-regulated genes, limited genes exhibit sugar regulation under anaerobic conditions, indicating that anaerobic conditions strongly influence sugar regulated gene expression. Anaerobically responsive genes substantially overlap with low energy responsive genes. In particular, the expression levels of anaerobically downregulated genes are consistent with those provoked by low energy conditions, suggesting that anaerobic downregulation results from the prevention of aerobic respiration due to the absence of the final electron acceptor, i.e., molecular oxygen. It has been noted that abscisic acid (ABA) responsive genes are over representative of genes upregulated under low energy conditions, in contrast to downregulated genes. This suggests that either ABA itself or upstream signaling components of the ABA signaling pathway are likely to be involved in the signaling pathways activated by low energy conditions.

Transcriptome profiling of two rice genotypes under mild field drought stress during grain-filling stage

Drought is one of the most critical abiotic stresses that threaten crop production worldwide. This stress affects the rice crop in all stages of rice development; however, the occurrence during reproductive and grain-filling stages has the most impact on grain yield. Although many global transcriptomic studies have been performed during the reproductive stage in rice, very limited information is available for the grain-filling stage. Hence, we intend to investigate how the rice plant responds to drought stress during the grain-filling stage and how the responses change over time under field conditions. Two rice genotypes were selected for RNA-seq analysis: '4610', previously reported as a moderately tolerant breeding line, and Rondo, an elite indica rice cultivar susceptible to drought conditions. Additionally, 10 agronomic traits were evaluated under normal irrigated and drought conditions. Leaf tissues were collected during grain-filling stages at two time points, 14 and 21 days after the drought treatment, from both the drought field and normal irrigated field conditions. Based on agronomic performances, '4610' was less negatively affected than Rondo under mild drought conditions, and expression profiling largely aligned with the phenotypic data. The transcriptomic data indicated that, in general, '4610' had much earlier responses than its counterpart in mitigating the impact of drought stress. Several key genes and gene families related to drought stress or stress-related conditions were found differentially expressed in this study, including transcription factors, drought tolerance genes and reactive oxygen species scavengers. Furthermore, this study identified novel differentially expressed genes (DEGs) without function annotations that may play roles in drought tolerance-related functions. Some of the important DEGs detected in this study can be targeted for future research.

Comparative multi-omics analysis of hypoxic germination tolerance in weedy rice embryos and coleoptiles

Hypoxic germination tolerance is an important trait for seedling establishment of direct-seeded rice. Our comparative metabolomics analysis revealed that weedy rice accumulated more sugar and amino acids than cultivated rice accumulated in the embryo and coleoptile tissues under hypoxic stress. At the transcriptional level, oxidative phosphorylation activity in weedy rice was higher than in cultivated rice that likely led to more efficient energy metabolism during hypoxic stress. Based on our comparative proteomics analysis, enriched proteins related to cell wall implied that the advantages in energy metabolism of weedy rice were ultimately reflected in the formation of tissue structures. In this study, we found that most of key hypoxic germination tolerance (HGT) genes shared the same genetic backgrounds with Oryza japonica, however, several of them genetically similar to other Oryza plant also play important roles. Our findings suggest weedy rice can serve as genetic resources for the improvement of direct-seeding rice.

The Molecular Regulatory Pathways and Metabolic Adaptation in the Seed Germination and Early Seedling Growth of Rice in Response to Low O2 Stress

As sessile organisms, flooding/submergence is one of the major abiotic stresses for higher plants, with deleterious effects on their growth and survival. Therefore, flooding/submergence is a large challenge for agriculture in lowland areas worldwide. Long-term flooding/submergence can cause severe hypoxia stress to crop plants and can result in substantial yield loss. Rice has evolved distinct adaptive strategies in response to low oxygen (O₂) stress caused by flooding/submergence circumstances. Recently, direct seeding practice has been increasing in popularity due to its advantages of reducing cultivation cost and labor. However, establishment and growth of the seedlings from seed germination under the submergence condition are large obstacles for rice in direct seeding practice. The physiological and molecular regulatory mechanisms underlying tolerant and sensitive phenotypes in rice have been extensively investigated. Here, this review focuses on the progress of recent advances in the studies of the molecular mechanisms and metabolic adaptions underlying anaerobic germination (AG) and coleoptile elongation. Further, we highlight the prospect of introducing quantitative trait loci (QTL) for AG into rice mega varieties to ensure the compatibility of flooding/submergence tolerance traits and yield stability, thereby advancing the direct seeding practice and facilitating future breeding improvement.

Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater

Crops with resilience to multiple climatic stresses are essential for increased yield stability. Here, we evaluate the interaction between two loci associated with flooding survival in rice (Oryza sativa L.). ANAEROBIC GERMINATION 1 (AG1), encoding trehalose 6-phosphate phosphatase 7 (TPP7), promotes mobilization of endosperm reserves to enhance the elongation of a hollow coleoptile in seeds that are seeded directly into shallow paddies. SUBMERGENCE 1 (SUB1), encoding the ethylene-responsive transcription factor SUB1A-1, confers tolerance to complete submergence by dampening carbohydrate catabolism, to enhance recovery upon desubmergence. Interactions between AG1/TPP7 and SUB1/SUB1A-1 were investigated under three flooding scenarios using four near-isogenic lines by surveying growth and survival. Pyramiding of the two loci does not negatively affect anaerobic germination or vegetative-stage submergence tolerance. However, the pyramided AG1 SUB1 genotype displays reduced survival when seeds are planted underwater and maintained under submergence for 16 d. To better understand the roles of TPP7 and SUB1A-1 and their interaction, temporal changes in carbohydrates and shoot transcriptomes were monitored in the four genotypes varying at the two loci at four developmental timeponts, from day 2 after seeding through day 14 of complete submergence. TPP7 enhances early coleoptile elongation, whereas SUB1A-1 promotes precocious photoautotrophy and then restricts underwater elongation. By contrast, pyramiding of the AG1 and SUB1 slows elongation growth, the transition to photoautotrophy, and survival. mRNA-sequencing highlights time-dependent and genotype-specific regulation of mRNAs associated with DNA repair, cell cycle, chromatin modification, plastid biogenesis, carbohydrate catabolism and transport, elongation growth, and other processes. These results suggest that interactions between AG1/TPP7 and SUB1/SUB1A-1 could impact seedling establishment if paddy depth is not effectively managed after direct seeding.

The Many Facets of Hypoxia in Plants

Plants are aerobic organisms that require oxygen for their respiration. Hypoxia arises due to the insufficient availability of oxygen, and is sensed by plants, which adapt their growth and metabolism accordingly. Plant hypoxia can occur as a result of excessive rain and soil waterlogging, thus constraining plant growth. Increasing research on hypoxia has led to the discovery of the mechanisms that enable rice to be productive even when partly submerged. The identification of Ethylene Response Factors (ERFs) as the transcription factors that enable rice to survive submergence has paved the way to the discovery of oxygen sensing in plants. This, in turn has extended the study of hypoxia to plant development and plant–microbe interaction. In this review, we highlight the many facets of plant hypoxia, encompassing stress physiology, developmental biology and plant pathology.