Field experiments were conducted in farmers' rice fields in 2001 and 2002 to study the effects of nitrogen (N) management strategies on N use efficiency in recovery (RE), agronomy (AE) and physiology (PE) and redistribution of dry matter accumulation (DMA) and nitrogen accumulation (NA) in two typical rice cultivars in Jinhua, Zhejiang Province. This study aimed mainly at identifying the possible causes of poor fertilizer N use efficiency (NUE) of rice in Zhejiang by comparing farmers' fertilizer practice (FFP) with advanced site-specific nutrient management (SSNM) and real-time N management (RTNM). The results showed that compared to FFP, SSNM and RTNM reduced DMA and NA before panicle initiation and increased DMA and NA at post-flowering. There is no significant difference between SSNM and FFP in post-flowering dry matter redistribution (post-DMR) and post-flowering nitrogen redistribution (post-NR). These results suggest that high input rate of fertilizer N and improper fertilizer N timing are the main factors causing low NUE of irrigated rice in the farmer's routine practice of Zhejiang. With SSNM, about 15% of the current total N input in direct-seeding early rice and 45% in single rice could be reduced without yield loss in Zhejiang, China.
Crops, Agricultural ; metabolism ; Fertilizers ; Nitrogen ; metabolism ; Oryza ; metabolism

Potential growth of two widely-grown hybrid rice varieties in the Jinhua district of Zhejiang Province, Shanyou63 for mid-rice and Xieyou46 for late rice, was simulated using a crop growth model of WOFOST. Parameters of the rice growth in WOFOST were calibrated through field experiments from 1999 to 2002 in Jinhua. The potential yield simulated with WOFOST was about 12 t/ha for Shanyou63 and 10 t/ha for Xieyou46, which are in good agreement with the highest recorded yield obtained in this area. Under farmers practice, current yield is about 7.5 t/ha for Shanyou63 and 6.5 t/ha for Xieyou46. There is a gap between the actual rice yield and the potential yield for these two hybrid rice varieties grown in this area. The attainable target yields were set to 70% to 75% of their potential yields for the two varieties. A recently developed software "Nutrient Decision Support System (NuDSS)" for irrigated rice was used to optimize nutrient management for these two rice varieties. According to NuDSS, the optimal fertilizer N requirement for the target yields was about 150 kg/ha for Shanyou63 and about 120 kg/ha for Xieyou46, which were only about 70% of the fertilizer N application under current farmers' practice. Comparing with farmers' practice, there is great potential to increase actual rice yields and to reduce fertilizer N use rates by improving rice crop management practice in Jinhua.
Agriculture ; China ; Fertilizers ; Oryza ; growth & development ; metabolism ; Soil ; analysis

The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
Arabidopsis/metabolism* ; Oryza/metabolism* ; RNA, Circular/metabolism* ; RNA, Plant/metabolism* ; Sequence Analysis, RNA/methods*

Recently, returning straw to the fields has been proved as a direct and effective method to tackle soil nutrient loss and agricultural pollution. Meanwhile, the slow decomposition of straw may harm the growth of the next crop. This study aimed to determine the effects of rumen microorganisms (RMs) on straw decomposition, bacterial microbial community structure, soil properties, and soil enzyme activity. The results showed that RMs significantly enhanced the degradation rate of straw in the soil, reaching 39.52%, which was 41.37% higher than that of the control on the 30th day after straw return. After 30 d, straw degradation showed a significant slower trend in both the control and the experimental groups. According to the soil physicochemical parameters, the application of rumen fluid expedited soil matter transformation and nutrient buildup, and increased the urease, sucrase, and cellulase activity by 10%‒20%. The qualitative analysis of straw showed that the hydroxyl functional group structure of cellulose in straw was greatly damaged after the application of rumen fluid. The analysis of soil microbial community structure revealed that the addition of rumen fluid led to the proliferation of Actinobacteria with strong cellulose degradation ability, which was the main reason for the accelerated straw decomposition. Our study highlights that returning rice straw to the fields with rumen fluid inoculation can be used as an effective measure to enhance the biological value of recycled rice straw, proposing a viable solution to the problem of sluggish straw decomposition.
Animals ; Rumen/metabolism* ; Agriculture/methods* ; Soil/chemistry* ; Microbiota ; Bacteria/metabolism* ; Oryza/metabolism* ; Soil Microbiology ; Cellulose

Ferulic acid esterase (FAE) was used to hydrolyze feruloyl ester linkages between hemicellulose and lignin in natural lignocellulose, and the possibility of FAE accelerating cellulase to hydrolyze steam-exploded rice straw by breaking covalent linkages was studied. When the dosage of FAE was 240 mu/g substrate, the cellulose conversion rate and the weight-loss rate of insoluble substrate at 72 h were respectively 32.00% and 32.77%, more than without using FAE; Cellulose conversion rate and the weight-loss rate of insoluble substrate were respectively 29.85% and 32.48% with FAE (300 mu/g substrate) processing time of 120 min. By comparison of the accessibility and FT-IR spectra of lignocellulosic material treated by different enzyme methods, it indicated that FAE hydrolyzed some ester bonds within it, and improved the accessibility by over 50%. It is concluded that FAE and cellulase have great synergistic effect, and FAE can help cellulase hydrolyze natural lignocellulose and enhance hydrolytic efficiency.
Carboxylic Ester Hydrolases ; metabolism ; Cellulase ; metabolism ; Cellulose ; metabolism ; Oryza ; enzymology ; Plant Stems ; enzymology ; Steam

To efficiently use both cellulose and hemicellulose for lipid production, rice straw was hydrolyzed by a two-step process including dilute acid pretreatment and then enzymatic hydrolysis, and the hydrolysate was used as carbon source for lipid fermentation by Trichosporon fermentans HWZ004. After a simple overliming, the concentrations of acetic acid, furfural and 5-hydroxymethyl-furfural were 0.4 g/L, 0.1 g/L and 0.05 g/L, respectively. The hydrolysate could be used for lipid fermentation with T. fermentans HWZ004 without adding other nutrients except for a small amount of nitrogen source and trace CuSO4.5H2O. The optimum inoculum size, initial pH and temperature were 5.0%, 7.0 and 25 degrees C, respectively. A total biomass of 26.4 g/L with a lipid content of 52.2% (corresponding to a lipid yield of 13.8 g/L) was achieved after cultivation of T. fermentans HWZ004 under the above-mentioned conditions for 7 days. The lipid coefficient (lipid yield on substrate consumed) is 17.0, which is much higher than the corresponding one (11.9) obtained on detoxified rice straw hemicullulose hydrolysate by original yeast T. fermentans CICC 1368. The fatty acid composition of the lipid was found to be similar to that of vegetable oil and its unsaturated fatty acid content was over 70%, thus the lipid is a promising material for biodiesel production.
Fermentation ; Lignin ; metabolism ; Oils ; metabolism ; Oryza ; Plant Stems ; chemistry ; Trichosporon ; metabolism

Ethyl carbamate (EC) as a potential carcinogen commonly exists in traditional fermented foods. It is important eliminate urea that is the precursors of EC in many fermented foods, including Chinese Rice wine. On the basis of achieving high-level overexpression of food-grade ethanol-resistant acid urease, we studied the hydrolysis of urea and EC with the recombinant acid urease. Recombinant acid urease showed degraded urea in both the simulated system with ethanol and Chinese Rice wine (60 mg/L of urea was completely degraded within 25 h), indicating that the recombinant enzyme is suitable for the elimination of urea in Chinese Rice wine. Although recombinant acid urease also has degradation catalytic activity on EC, no obvious degradation of EC was observed. Further investigation results showed that the Km value for urea and EC of the recombinant acid urease was 0.7147 mmol/L and 41.32 mmol/L, respectively. The results provided theoretical foundation for realizing simultaneous degradation of urea and EC.
Oryza ; Recombinant Proteins ; metabolism ; Urea ; chemistry ; Urease ; metabolism ; Urethane ; chemistry ; Wine ; analysis

Disparity in the root morphology of six rice (Oryza sativa L.) genotypes varying in potassium (K) efficiency was studied with three K levels: 5 mg/L (low), 10 mg/L (moderate) and 40 mg/L (adequate) in hydroponic culture. Morphological parameters included root length, surface area, volume and count of lateral roots, as well as fine (diameter<0.2 mm) and thick (diameter>0.2 mm) roots. The results indicate that the root growth of all genotypes was reduced under low K, but moderate K deficiency increased the root length of the efficient genotypes. At deficient and moderate K levels, all the efficient rice genotypes developed more fine roots (diameter<0.2 mm) than the inefficient ones. Both fine root count and root surface area were found to be the best parameters to portray K stress in rice. In accordance with the root morphology, higher K concentrations were noted in shoots of the efficient genotypes when grown at moderate and deficient K levels, indicating that root morphology parameters are involved in root uptake for K and in the translocation of K up to shoots. K deficiency affected not only the root morphology, but also the root ultra-structure. The roots of high-efficient genotypes had stronger tolerance to K deficient stress for root membrane damage, and could maintain the developed root architecture to adapt to the low K growth medium.
Genotype ; Oryza ; growth & development ; metabolism ; ultrastructure ; Plant Roots ; growth & development ; ultrastructure ; Potassium ; metabolism

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.
Acetylation ; Lysine/metabolism* ; Oryza/metabolism* ; Plant Proteins/metabolism* ; Protein Interaction Maps ; Protein Processing, Post-Translational ; Proteome/metabolism* ; Ubiquitin/metabolism* ; Ubiquitination

We characterized yield-relevant characters and their variations over genotypes and environments (locations and years) by examining two rice varieties (9746 and Jinfeng) with high yield potential. 9746 and Jinfeng were planted in two locations of Shanghai, China, during 2005 and 2006. The results show that there was a large variation in grain yield between locations and years. The realization of high yield potential for the two types of rice was closely related to the improved sink size, such as more panicles per square meter or grains per panicle. Stem and leaf biomasses were mainly accumulated from tillering stage to heading stage, and showed slow decline during grain filling. Meanwhile, some photosynthetic characters including net photosynthesis rate (Pn), leaf area index (LAI), specific leaf area (SLA), fluorescence parameter (maximum quantum yield of PSII, Fv/Fm), chlorophyll content (expressed as SPAD value), as well as nutrient (N, P, K) uptake were also measured to determine their variations over genotypes and environments and their relationships with grain yield. Although there were significant differences between years or locations for most measurements, SLA at tillering and heading stages, Fv/Fm and LAI at heading stage, stem biomass at heading and maturity stages, and leaf nitrogen concentration at tillering and heading stages remained little changed, indicating their possible applications as selectable characters in breeding programs. It was also found that stem nitrogen accumulation at tillering stage is one of the most important and stable traits for high yield formation.
Biomass ; Environment ; Genotype ; Nitrogen ; metabolism ; Oryza ; genetics ; growth & development ; Phosphorus ; metabolism ; Photosynthesis ; Plant Leaves ; metabolism ; Potassium ; metabolism