EARLY FLOWERING3-1 represses Grain number, plant height, and heading date7 to promote ABC1 REPRESSOR1 and regulate nitrogen uptake in rice.

The extensive use of nitrogen fertilizer boosts rice (Oryza sativa) production but also harms ecosystems. Therefore, enhancing crop nitrogen use efficiency is crucial. Here, we performed map-based cloning and identified the EARLY FLOWERING3 (ELF3) like protein-encoding gene OsELF3-1, which confers enhanced nitrogen uptake in rice. OsELF3-1 forms a ternary complex (OsEC) with OsELF4s and OsLUX, the putative orthologs of ELF4 and LUX ARRHYTHMO (LUX) in Arabidopsis (Arabidopsis thaliana), respectively. OsEC directly binds to the promoter of Grain number, plant height, and heading date7 (Ghd7) and represses its expression. Ghd7 encodes a transcription factor that has major effects on multiple agronomic traits. Ghd7 is also a transcriptional repressor and directly suppresses the expression of ABC1 REPRESSOR1 (ARE1), a negative regulator of nitrogen use efficiency. Therefore, targeting the OsEC-Ghd7-ARE1 module offers an approach to enhance nitrogen uptake, presenting promising avenues for sustainable agriculture.

Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice.

Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.

Formin protein DRT1 affects gross morphology and chloroplast relocation in rice.

Plant height and tiller number are two major factors determining plant architecture and yield. However, in rice (Oryza sativa), the regulatory mechanism of plant architecture remains to be elucidated. Here, we reported a recessive rice mutant presenting dwarf and reduced tillering phenotypes (drt1). Map-based cloning revealed that the phenotypes are caused by a single point mutation in DRT1, which encodes the Class I formin protein O. sativa formin homolog 13 (OsFH13), binds with F-actin, and promotes actin polymerization for microfilament organization. DRT1 protein localized on the plasma membrane (PM) and chloroplast (CP) outer envelope. DRT1 interacted with rice phototropin 2 (OsPHOT2), and the interaction was interrupted in drt1. Upon blue light stimulus, PM localized DRT1 and OsPHOT2 were translocated onto the CP membrane. Moreover, deficiency of DRT1 reduced OsPHOT2 internalization and OsPHOT2-mediated CP relocation. Our study suggests that rice formin protein DRT1/OsFH13 is necessary for plant morphology and CP relocation by modulating the actin-associated cytoskeleton network.

OsHRZ1 negatively regulates rice resistant to Magnaporthe oryzae infection by targeting OsVOZ2.

Rice blast disease caused by Magnaporthe oryzae significantly reduces yield production. Blast resistance is closely associated with iron (Fe) status, but the mechanistic basis linking iron status to immune function in rice remains largely unknown. Here, iron-binding haemerythrin RING ubiquitin ligases OsHRZ1 was confirmed to play key roles in iron-mediated rice blast resistance. The expression of OsHRZ1 was suppressed by M. oryzae inoculation and high iron treatment. Both mutants of OsHRZ1 enhanced rice resistance to M. oryzae. OsPR1a was up-regulated in OsHRZ1 mutants. Yeast two-hybrid, bimolecular fluorescence complementation, and Co-IP assay results indicated that OsHRZ1 interacts with Vascular Plant One Zinc Finger 2 (OsVOZ2) in the nucleus. Additionally, the vitro ubiquitination assay indicated that OsHRZ1 can ubiquitinate OsVOZ2 and mediate the degradation of OsVOZ2. The mutants of OsVOZ2 showed reduced resistance to M. oryzae and down-regulated the expression of OsPR1a. Yeast one-hybrid, EMSA, and dual-luciferase reporter assay results indicated that OsVOZ2 directly binds to the promoter of OsPR1a, activating its expression. In summary, OsHRZ1 plays an important role in rice disease resistance by mediated degradation of OsVOZ2 thus shaping PR gene expression dynamics in rice cells. This highlights an important link between iron signaling and rice pathogen defenses.

bZIP23 interacts with NAC028 to modulate rice resistance to sheath blight disease.

Rice sheath blight disease (ShB) is a serious threat to rice production, and breeding ShB-resistance varieties is the most effective strategy for ShB control. However, the molecular mechanisms of rice resistance to ShB are largely unknown. In this study, the NAC transcription factor NAC028 was shown to be sensitive to ShB infection. ShB inoculation assays revealed that NAC028 is a positive regulator of ShB resistance. To elucidate the molecular basis of NAC028-mediated ShB resistance, another transcription factor (bZIP23) was identified as a NAC028-interacting protein. Results of the transcriptome and qRT-PCR analyses demonstrated that CAD8B, a key enzyme for lignin biosynthesis and ShB resistance, is regulated by both bZIP23 and NAC028. The combination of the yeast-one hybrid, ChIP-qPCR, and transactivation assays illustrated that both bZIP23 and NAC028 directly bind the CAD8B promoter and activate its expression. The transcriptional connection between bZIP23 and NAC028 was also investigated and the results of in vitro and in vivo assays demonstrated that NAC028 was one of the target genes of bZIP23, but not vice versa. The results presented here provide new insights into the molecular basis of ShB resistance and contribute to the potential targets for the ShB resistance breeding program.

Red-light receptor phytochrome B inhibits BZR1-NAC028-CAD8B signaling to negatively regulate rice resistance to sheath blight.

Phytochrome (Phy)-regulated light signalling plays important roles in plant growth, development, and stress responses. However, its function in rice defence against sheath blight disease (ShB) remains unclear. Here, we found that PhyB mutation or shade treatment promoted rice resistance to ShB, while resistance was reduced by PhyB overexpression. Further analysis showed that PhyB interacts with phytochrome-interacting factor-like 15 (PIL15), brassinazole resistant 1 (BZR1), and vascular plant one-zinc-finger 2 (VOZ2). Plants overexpressing PIL15 were more susceptible to ShB in contrast to bzr1-D-overexpressing plants compared with the wild-type, suggesting that PhyB may inhibit BZR1 to negatively regulate rice resistance to ShB. Although BZR1 is known to regulate brassinosteroid (BR) signalling, the observation that BR signalling negatively regulated resistance to ShB indicated an independent role for BZR1 in controlling rice resistance. It was also found that the BZR1 ligand NAC028 positively regulated resistance to ShB. RNA sequencing showed that cinnamyl alcohol dehydrogenase 8B (CAD8B), involved in lignin biosynthesis was upregulated in both bzr1-D- and NAC028-overexpressing plants compared with the wild-type. Yeast-one hybrid, ChIP, and transactivation assays demonstrated that BZR1 and NAC028 activate CAD8B directly. Taken together, the analyses demonstrated that PhyB-mediated light signalling inhibits the BZR1-NAC028-CAD8B pathway to regulate rice resistance to ShB.

The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil.

BACKGROUND: Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study. RESULTS: In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice. CONCLUSIONS: Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils.

Cloning and functional analysis of the novel rice blast resistance gene Pi65 in japonica rice.

KEY MESSAGE: Pi65, a leucine-rich repeat receptor-like kinase (LRR-RLK) domain cloned from Oryza sativa japonica, is a novel rice blast disease resistance gene. Rice blast seriously threatens rice production worldwide. Utilizing the rice blast resistance gene to breed rice blast-resistant varieties is one of the best ways to control rice blast disease. Using a map-based cloning strategy, we cloned a novel rice blast resistance gene, Pi65, from the resistant variety GangYu129 (abbreviated GY129, Oryza sativa japonica). Overexpression of Pi65 in the susceptible variety LiaoXing1 (abbreviated LX1, Oryza sativa japonica) enhanced rice blast resistance, while knockout of Pi65 in GY129 resulted in susceptibility to rice blast disease. Pi65 encodes two transmembrane domains, with 15 LRR domains and one serine/threonine protein kinase catalytic domain, conferring resistance to isolates of Magnaporthe oryzae (abbreviated M. oryzae) collected from Northeast China. There were sixteen amino acid differences between the Pi65 resistance and susceptible alleles. Compared with the Pi65-resistant allele, the susceptible allele exhibited one LRR domain deletion. Pi65 was constitutively expressed in whole plants, and it could be induced in the early stage of M. oryzae infection. Transcriptome analysis revealed that numerous genes associated with disease resistance were specifically upregulated in GY129 24 h post inoculation (HPI); in contrast, photosynthesis and carbohydrate metabolism-related genes were particularly downregulated at 24 HPI, demonstrating that disease resistance-associated genes were activated in GY129 (carrying Pi65) after rice blast fungal infection and that cellular basal metabolism and energy metabolism were inhibited simultaneously. Our study provides genetic resources for improving rice blast resistance and enriches the study of rice blast resistance mechanisms.

The kinesin-13 protein BR HYPERSENSITIVE 1 is a negative brassinosteroid signaling component regulating rice growth and development.

Phytohormones performed critical roles in regulating plant architecture and thus determine grain yield in rice. However, the roles of brassinosteroids (BRs) compared to other phytohormones in shaping rice architecture are less studied. In this study, we report that BR hypersensitive1 (BHS1) plays a negative role in BR signaling and regulate rice architecture. BHS1 encodes the kinesin-13a protein and regulates grain length. We found that bhs1 was hypersensitive to BR, while BHS1-overexpression was less sensitive to BR compare to WT. BHS1 was down-regulated at RNA and protein level upon exogenous BR treatment, and proteasome inhibitor MG132 delayed the BHS1 degradation, indicating that both the transcriptional and posttranscriptional regulation machineries are involved in BHS1-mediated regulation of plant growth and development. Furthermore, we found that the BR-induced degradation of BHS1 was attenuated in Osbri1 and Osbak1 mutants, but not in Osbzr1 and Oslic mutants. Together, these results suggest that BHS1 is a novel component which is involved in negative regulation of the BR signaling downstream player of BRI1.

A coiled-coil domain mutation in the NLR receptor SbYR1 coordinates plant growth and stress tolerance in sorghum.

NLRs are a group of specific plant receptors that recognizes effectors secreted by pathogens, activates downstream immune responses, and confers resistance to pathogens. Despite variations, the functions of some NLR genes may be conserved across species, but their role in sorghum remains unclear. In this study, we investigated the stunted and yellow ripple leaf mutant sbyr1 from sorghum BTx623. Map-based cloning revealed that SbYR1 was annotated as a coiled-coil NLR with three conserved domains, namely, RX-CC, NB-ARC, and LRR, with a Thr4Met mutation in the CC domain. Inoculation experiments revealed that the sbyr1 mutation enhanced tolerance to head smut disease in sorghum. To further verify the function of SbYR1, we analysed the transcriptomes and metabolomes of the shoots of sbyr1 and BTx623. The results indicated that both the DEGs and the DAMs were enriched in secondary metabolic pathways, such as the flavonoid, JA, and ABA pathways. The increased contents of JA and ABA as a downstream effect of sbyr1 suppressed growth, whereas the application of exogenous inhibitors of JA and ABA inhibited the endogenous hormones and thus caused sbyr1 to grow productively. Overexpression and homologous gene knockout in rice confirmed that sbyr1 affects plant growth and development. In conclusion, our study revealed that a CC domain mutation in SbYR1 influences plant growth and plays a role in resistance to head smut disease and downstream secondary metabolism. KEY MESSAGE: •The Thr4Met mutation in the coiled-coil domain of the NLR receptor SbYR1 coordinates plant growth and stress tolerance in sorghum.

Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China.

As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood. Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F(2) population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes. Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indica subspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China. Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice.

Compositional Shifts and Assembly in Rhizosphere-Associated Fungal Microbiota Throughout the Life Cycle of Japonica Rice Under Increased Nitrogen Fertilization.

Soil fungal microbiomes facilitate a range of beneficial functions for their host plants, and rhizosphere fungal community composition, richness, and diversity affect plant growth and development, and crop yield. Therefore, exploring the community structure and assembly of the rhizosphere fungal microbiome and its relationship with soil biochemical properties are fundamental to elucidating how rice plants benefit from their fungal symbionts. In this study, soil samples were collected at seedling, tillering, heading, and ripening stages of rice subjected to three levels of nitrogen fertilization. Plant growth demonstrates a substantial influence on fungal community composition and diversity. From the tillering to the ripening stage, the fungal communities were governed by homogenizing dispersal and dispersal limitation. The prevalence of Glomeromycota, the beneficial fungi, was considerably higher during the heading stage compared to the three other growth stages. This increase in abundance was strongly associated with increased levels of soil nutrients and enhanced activity of nitrogen acquisition enzymes. This may be a strategy developed by rice grown in flooded soil to recruit beneficial fungi in the rhizosphere to meet high nitrogen demands. Our study findings contribute to elucidating the influence of plant development and nitrogen fertilization on the structure and composition of the fungal community as well as its relationship with soil key soil nutrient content and nitrogen-related enzyme activities. They also illustrate how a shift in the fungal community mediates and reflects the effects of nitrogen fertilization input in rice agroecosystems. These findings provide new insights into the effects of changes in nitrogen application in rice rhizosphere at different growth stages on fungal communities and soil biochemical characteristics.

The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China.

Hybridization between indica and japonica rice combined with utilization of ideal plant type has led to the development of high-yielding japonica rice in northern China. However, the contribution at the genomic level of intersubspecific hybridization to the increased yield of northern Chinese japonica rice is uncertain. In this study, we analyzed the genomic pedigree of descendants of hybridization between indica and japonica rice grown in northeastern China between 1963 and 2008. Simple sequence repeat markers indicated that since 1990 the genetic diversity among northern japonica cultivars was enriched. Genome-wide analysis with subspecies-specific indel and intron length polymorphism markers showed indica-allele frequencies were significantly increased in cultivars bred after 1990, and were significantly positively correlated with spikelet number per panicle and significantly negatively correlated with panicle number per plant. Among eight genes controlling agronomic traits, GN1a and GS3 were partially fixed in the genome of northern japonica cultivars. In contrast, Waxy and qSH1 were eliminated, whereas DEP1 and qSW5 were retained. Indica germplasm is an important contributor to the increased yield of northern japonica rice. Breeding for high yield and grain quality in combination is a complicated process and difficult to achieve when relying on only one or several functional genes, thus the selection expertise of the breeder remains critical.

Multi-omics approach reveals the contribution of OsSEH1 to rice cold tolerance.

As low environmental temperature adversely affects the growth, development and geographical distribution, plants have evolved multiple mechanisms involving changing physiological and metabolic processes to adapt to cold stress. In this study, we revealed that nucleoporin-coding gene OsSEH1 was a positive regulator of cold stress in rice. Physiological assays showed that the activity of antioxidant enzymes showed a significant difference between osseh1 knock-out lines and wild type under cold stress. Metabolome analysis revealed that the contents of large-scale flavonoids serving as ROS scavengers were lower in osseh1 mutants compared with wild type under cold stress. Transcriptome analysis indicated that the DEGs between osseh1 knock-out lines and wild type plants were enriched in defense response, regulation of hormone levels and oxidation-reduction process. Integration of transcriptomic and metabolic profiling revealed that OsSEH1 plays a role in the oxidation-reduction process by coordinately regulating genes expression and metabolite accumulation involved in phenylpropanoid and flavonoid biosynthetic pathway. In addition, Exogenous ABA application assays indicated that osseh1 lines had hypersensitive phenotypes compared with wild type plants, suggesting that OsSEH1 may mediate cold tolerance by regulating ABA levels.

Higher CO2 Assimilation in Selected Rice Recombinant Inbred Lines Is Driven by Higher CO2 Diffusion and Light Use Efficiency Related to Leaf Anatomy and Mesophyll Cell Density.

Leaf anatomy determining the light distribution within the leaf and exerting influence on CO2 diffusion is considered to have dramatic potential for photosynthesis performance increase. In this study, we observed that two rice recombinant inbred lines, H138 and H217 (RILF11 plants from Sasanishiki × IRAT10), have higher net CO2 assimilation (An) than their parent Sasanishiki due mainly to the improvement of leaf anatomy. Our results showed that An positively correlated with anatomy traits' mesophyll cell number per cross-sectional area (NO.mescell/Acros) and mesophyll area (Ames). NO.mescell/Acros exert direct and indirect effects on An. Compared to Sasanishiki flag leaves, IRAT10, H138, and H217 have higher mesophyll cell numbers. Simultaneously, higher chlorophyll content and expression of genes encoding the light-harvesting protein of PSII and PSI (Lhcb1, 2, 3 and Lhca1, 2, 3) were recorded in IRAT10, H138, and H217, which facilitates light use efficiency. Higher electron transport rate and RuBP concentration were recorded in IRAT10, H138, and H217 flag leaves. Retinoblastoma-related gene (OsRBR1), exerting effects on mesophyll cell density, can be used to modify leaf anatomy for improving leaf photosynthesis. Additionally, higher stomatal conductance and mesophyll conductance were also recorded in H138 and H217 than in Sasanishiki. Furthermore, we modeled mesophyll conductance through anatomical traits, and the results revealed that chloroplast thickness was the dominant factor restricting CO2 diffusion within mesophyll cells rather than cell wall thickness. Higher RuBP content accompanied by higher CO2 concentration within the carboxylation set in H138 and H217 flag leaves contributed to higher CO2 assimilation.

Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).

Cold stress is a major threat to the sustainability of rice yield. Brassinosteroids (BR) application can enhance cold tolerance in rice. However, the regulatory mechanism related to cold tolerance and the BR signaling pathway in rice has not been clarified. In the current study, the seedling shoot length (SSL), seedling root length (SRL), seedling dry weight (SDW), and seedling wet weight (SWW) were used as the indices for identifying cold tolerance under cold stress and BR-combined cold treatment in a backcross recombinant inbred lines (BRIL) population. According to the phenotypic characterization for cold tolerance and a high-resolution SNP genetic map obtained from the GBS technique, a total of 114 QTLs were identified, of which 27 QTLs were detected under cold stress and 87 QTLs under BR-combined cold treatment. Among them, the intervals of many QTLs were coincident under different treatments, as well as different traits. A total of 13 candidate genes associated with cold tolerance or BR pathway, such as BRASSINAZOLE RESISTANT1 (OsBZR1), OsWRKY77, AP2 domain-containing protein, zinc finger proteins, basic helix-loop-helix (bHLH) protein, and auxin-induced protein, were predicted. Among these, the expression levels of 10 candidate genes were identified under different treatments in the parents and representative BRIL individuals. These results were helpful in understanding the regulation relationship between cold tolerance and BR pathway in rice.

Mining Beneficial Genes for Salt Tolerance From a Core Collection of Rice Landraces at the Seedling Stage Through Genome-Wide Association Mapping.

Rice is a salt-sensitive plant. High concentration of salt will hinder the absorption of water and nutrients and ultimately affect the yield. In this study, eight seedling-stage salt-related traits within a core collection of rice landraces were evaluated under salinity stress (100 mM NaCl) and normal conditions in a growth chamber. Genome-wide association study (GWAS) was performed with the genotypic data including 2,487,353 single-nucleotide polymorphisms (SNPs) detected in the core collection. A total of 65 QTLs significantly associated with salt tolerance (ST) were identified by GWAS. Among them, a co-localization QTL qTL4 associated with the SKC, RN/K, and SNC on chromosome 6, which explained 14.38-17.94% of phenotypic variation, was selected for further analysis. According to haplotype analysis, qRT-PCR analysis, and sequence alignment, it was finally determined that 4 candidate genes (LOC_Os06g47720, LOC_Os06g47820, LOC_Os06g47850, LOC_Os06g47970) were related to ST. The results provide useful candidate genes for marker assisted selection for ST in the rice molecular breeding programs.

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.

Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response.

Weedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 µM ABA or 10 µM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

Rhizosphere-Associated Microbiomes of Rice (Oryza sativa L.) Under the Effect of Increased Nitrogen Fertilization.

Crops assemble and rely on rhizosphere-associated microbiomes for plant nutrition, which is crucial to their productivity. Historically, excessive nitrogen fertilization did not result in continuously increasing yields but rather caused environmental issues. A comprehensive understanding should be developed regarding the ways in which crops shape rhizosphere-associated microbiomes under conditions of increased nitrogen fertilization. In this study, we applied 16S and 18S ribosomal RNA gene profiling to characterize bacterial and fungal communities in bulk and rhizosphere soil of rice subjected to three levels of nitrogen fertilization for 5 years. Soil biochemical properties were characterized, and carbon-, nitrogen-, and phosphorus-related soil enzyme activities were investigated, by assays. Increasing nitrogen fertilization led to a decreasing trend in the variation of microbial community structures and demonstrated a more definite influence on fungal rather than bacterial community compositions and functions. Changes in the level of nitrogen fertilization significantly affected chemical properties such as soil pH, nutrient content, and microbial biomass levels in both rhizosphere and bulk soil. Soil enzyme activity levels varied substantially across nitrogen fertilization intensities and correlated more with the fungal than with the bacterial community. Our results indicated that increased nitrogen input drives alterations in the structures and functions of microbial communities, properties of soil carbon, nitrogen, and phosphorus, as well as enzyme activities. These results provide novel insights into the associations among increased nitrogen input, changes in biochemical properties, and shifts in microbial communities in the rhizosphere of agriculturally intensive ecosystems.