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Production and distribution are critical components of the furniture supply chain, and achieving optimal performance through their integration has become a vital focus for both the academic and business communities. Moreover, as economic globalization progresses, distributed manufacturing has become a pioneering production technique. Via leveraging a distributed flexible manufacturing system, mass flexible production at lower costs can be achieved. To this end, this study presents an integrated distributed flexible job shop and distribution problem to minimize makespan and total tardiness. In our research, a set of custom furniture orders from different customers are processed among flexible job shops and then delivered by vehicles to customers as the due date. To distinctly show the presented problem, a mixed integer mathematical programming model is created, and a multi-objective brain storm optimization method is introduced considering the problem's features. In comparison to the other three advanced methods, the superiority of the algorithm created is showcased. The findings of the experiments demonstrate that the constructed model and the introduced algorithm have remarkable competitiveness in addressing the problem being examined., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Multi-layered structure of reconstituted meat-based products from minced fish was formed by physical extrusion, followed by an investigation into the impact of extrusion strength on structural and physicochemical properties before and after frying. Under an appropriate pressure (3-9 kPa), the air within minced fish underwent enrichment and rearrangement to form a stratified phase, promoting the formation of multi-layered structure during frying. Conversely, the lower pressure (≤1.5 kPa) was insufficient for phase separation and directional rearrangement, while the higher pressure (≥15 kPa) would cause the stratified phase to flow out of food system. Moreover, by directly increasing water mobility and meat compactness, physical extrusion indirectly caused more water loss and stronger ionic bonds during frying, which was positively correlated with multi-layered structure. However, an excessive pressure caused an increase in random coil and hydrophobic interactions during frying, which was negatively correlated with multi-layered structure. In conclusion, appropriate physical extrusion strength promoted the formation of multi-layered structure., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Introduction: Weeds are one of the main factors affecting crop growth, making weed control a pressing global problem. In recent years, interest in intelligent mechanical weed-control equipment has been growing., Methods: We propose a semantic segmentation network, RDS_Unet, based on corn seedling fields built upon an improved U-net network. This network accurately recognizes weeds even under complex environmental conditions, facilitating the use of mechanical weeding equipment for reducing weed density. Our research utilized field-grown maize seedlings and accompanying weeds in expansive fields. We integrated the U-net semantic segmentation network, employing ResNeXt-50 for feature extraction in the encoder stage. In the decoder phase, Layer 1 uses deformable convolution with adaptive offsets, replacing traditional convolution. Furthermore, concurrent spatial and channel squeeze and excitation is incorporated after ordinary convolutional layers in Layers 2, 3, and 4., Results: Compared with existing classical semantic segmentation models such as U-net, Pspnet, and DeeplabV3, our model demonstrated superior performance on our specially constructed seedling grass semantic segmentation dataset, CGSSD, during the maize seedling stage. The Q6mean intersection over union (MIoU), precision, and recall of this network are 82.36%, 91.36%, and 89.45%, respectively. Compared to those of the original network, the proposed network achieves improvements of 5.91, 3.50, and 5.49 percentage points in the MIoU, precision, and recall, respectively. The detection speed is 12.6 frames per second. In addition, ablation experiments further confirmed the impactful contribution of each improvement component on the overall semantic segmentation performance., Discussion: This study provides theoretical and technical support for the automated operation of intelligent mechanical weeding devices., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Cui, Tan, Bai and Fu.)

With improved quality of life, types of waste have become increasingly complex, and waste classification has become a global issue. As a result, the world is facing a waste-classified collection problem. However, the existing research on waste collection has paid little attention to waste classification. In this paper, we consider the pretreatment and classification of waste transfer stations. In recent years, global warming caused by carbon emissions has become a serious problem. Therefore, this work proposes the first dual-objective multi-depot two-echelon green vehicle routing system with various pickups to optimize waste-classified collection based on a mixed-integer programming model. To ensure the efficiency of our developed model, we designed a multiobjective brainstorming optimization algorithm with a novel clustering strategy based on the rank-clustering method and differential mutation. Compared with two classical multiobjective optimization algorithms in various generated test instances and a real-world case, the experimental results showed that the proposed model can help sanitation departments improve the economic and environmental benefits of waste-classified collection, and the proposed algorithm is an excellent optimizer for solving associated problems., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Inspired by Nature's ingenuity, considerable progress has been made in recent years to develop chemoenzymatic processes by the integration of environmentally friendly feature of biocatalysis with versatile reactivity of chemocatalysis. However, the current types of chemoenzymatic processes are relatively few and mostly rely on metal catalysts. Here, we report a previously unexplored cooperative chemoenzymatic system for the synthesis of N-heterocycles. Starting from alcohols and amines, benzimidazole, pyrazine, quinazoline, indole, and quinoline can be obtained in excellent yields in water with O 2 as the terminal oxidant. Synthetic bridged flavin analog is served as a bifunctional organocatalyst for the regeneration of cofactor nicotinamide adenine dinucleotide in the bioprocess and oxidative cyclodehydrogenation in the chemoprocess. Compared to the classical acceptorless dehydrogenative coupling strategy, being metal and base free, requiring only water as solvent, and not needing atmosphere protection were observed for the present method, exhibiting a favorable green and sustainable alternative.

The global pandemic of COVID-19 has caused severe damage to the supply chain such that manufacturers may face long-term supply disruptions. In this paper, a disruption recovery strategy of a supply chain system is investigated from the perspective of product change, in which the life cycle and design change time of a new product are both considered in order to minimize the losses of manufacturer after disruptions. A mixed-integer linear programming (MILP) model is presented to address the disruption recovery problem for this multi-period, multi-supplier, and multi-stage supply chain system. A two-stage heuristic algorithm is designed to solve the problem. Experimental results show that the proposed disruption mitigation strategy can effectively reduce the profit loss of manufacturer due to supply disruption, and demonstrate the impact of product life cycle in the selection of new product design planning. A sensitivity analysis is performed to ensure the applicability of the model in the actual environment, which illustrates the effect of different parameter changes on the results. This work can help manufacturers establish an optimal recovery strategy whenever the supply chain system experiences supply disruptions., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Nowadays, the reverse supply chain management receives much attention because of its critical role in environmental protection and economic development. Disassembly is very important in the reverse supply chain. It aims at dismantling valuable components from end-of-life products which are then remanufactured into like-new ones after reprocessing and reassembly operations. To efficiently organize and manage the remanufacturing process from the perspective of sustainable development, this work proposes a stochastic disassembly sequence planning problem with consideration of noise pollution and energy consumption to achieve disassembly profit maximization. A chance-constrained programming model is formulated to describe it mathematically. Then, a discrete marine predators algorithm combined with a stochastic simulation approach is specially designed. By conducting simulation experiments on some real-life instances and comparing the designed approach with two popularly known methods in literature, we mainly find that the proposed model and approach can make better disassembly plan for the investigated problem with maximal profit subject to the given noise pollution and energy consumption constraints. The results demonstrate that the proposed method can efficiently and effectively handle the considered problem, which contributes to reaching the highly reliable and environmentally sustainable disassembly process.

Small fructans improve plant tolerance for cold stress. However, the underlying molecular mechanisms are poorly understood. Here, we have demonstrated that the small fructan tetrasaccharide nystose improves the cold stress tolerance of primary rice roots. Roots developed from seeds soaked in nystose showed lower browning rate, higher root activity, and faster growth compared to seeds soaked in water under chilling stress. Comparative proteomics analysis of nystose-treated and control roots identified a total of 497 differentially expressed proteins. GO classification and KEGG pathway analysis documented that some of the upregulated differentially expressed proteins were implicated in the regulation of serine/threonine protein phosphatase activity, abscisic acid-activated signaling, removal of superoxide radicals, and the response to oxidative stress and defense responses. Western blot analysis indicated that nystose promotes the growth of primary rice roots by increasing the level of RSOsPR10, and the cold stress-induced change in RSOsPR10levelis regulated by jasmonate, salicylic acid, and abscisic acid signaling pathways in rice roots. Furthermore, OsMKK4-dependentmitogen-activated protein kinase signaling cascades may be involved in the nystose-induced cold tolerance of primary rice roots. Together, these results indicate that nystose acts as an immunostimulator of the response to cold stress by multiple signaling pathways., Competing Interests: The authors have declared that no competing interests exist.

ING3 (inhibitor of growth gene 3) is a member of the ING gene family, and is considered as a candidate tumor suppressor gene. In order to explore the roles of ING3 in tumorigenesis and cancer progression of head and neck squamous cell carcinoma (HNSCC), ING3 expression was assessed in 173 cases of HNSCC by immunohistochemistry. The expression of ING3 was also compared to clinicopathological variables, and the expression of several tumorigenic markers. Nuclear expression of ING3 in HNSCC was significantly lower than that in dysplasia and normal epithelium, and was negatively correlated with a poor-differentiated status, T staging and TNM staging. In contrast, cytoplasmic expression of ING3 was significantly increased in HNSCC, and was statistically associated with lymph node metastasis and 14-3-3η expression. In addition, nuclear expression of ING3 was positively correlated with the expression of p300, p21 and acetylated p53. In conclusion, decreases in nuclear ING3 may play important roles in tumorigenesis, progression and tumor differentiation in HNSCC. Increases in cytoplasmic ING3 may be due to 14-3-3η binding and may also be involved in malignant progression. Nuclear ING3 may modulate the transactivation of target genes, promoting apoptosis through interactions with p300 and p21. Moreover, ING3 may interact with p300 to upregulate the level of acetylation of p53, and promote p53-mediated cell cycle arrest, senescence and/or apoptosis. Therefore, ING3 may be a potential tumor suppressor and a possible therapeutic target in HNSCC.

Experimental design focuses on describing or explaining the multifactorial interactions that are hypothesized to reflect the variation. The design introduces conditions that may directly affect the variation, where particular conditions are purposely selected for observation. Combinatorial design theory deals with the existence, construction and properties of systems of finite sets whose arrangements satisfy generalized concepts of balance and/or symmetry. In this work, borrowing the concept of "balance" in combinatorial design theory, a novel method for multifactorial bio-chemical experiments design is proposed, where balanced templates in combinational design are used to select the conditions for observation. Balanced experimental data that covers all the influencing factors of experiments can be obtianed for further processing, such as training set for machine learning models. Finally, a software based on the proposed method is developed for designing experiments with covering influencing factors a certain number of times.

Because of the long and unpredictable flowering period in bamboo, the molecular mechanism of bamboo flowering is unclear. Recent study showed that Arabidopsis PIN1-type parvulin 1 (Pin1At) is an important floral activator and regulates floral transition by facilitating the cis/trans isomerization of the phosphorylated Ser/Thr residues preceding proline motifs in suppressor of overexpression of CO 1 (SOC1) and agamous-like 24 (AGL24). Whether bamboo has a Pin1 homolog and whether it works in bamboo flowering are still unknown. In this study, we cloned PvPin1 , a homolog of Pin1At , from Phyllostachys violascens (Bambusoideae). Bioinformatics analysis showed that PvPin1 is closely related to Pin1-like proteins in monocots. PvPin1 was widely expressed in all tested bamboo tissues, with the highest expression in young leaf and lowest in floral bud. Moreover, PvPin1 expression was high in leaves before bamboo flowering then declined during flower development. Overexpression of PvPin1 significantly delayed flowering time by downregulating SOC1 and AGL24 expression in Arabidopsis under greenhouse conditions and conferred a significantly late flowering phenotype by upregulating OsMADS56 in rice under field conditions. PvPin1 showed subcellular localization in both the nucleus and cytolemma. The 1500-bp sequence of the PvPin1 promoter was cloned, and cis -acting element prediction showed that ABRE and TGACG-motif elements, which responded to abscisic acid (ABA) and methyl jasmonate (MeJA), respectively, were characteristic of P. violascens in comparison with Arabidopsis . On promoter activity analysis, exogenous ABA and MeJA could significantly inhibit PvPin1 expression. These findings suggested that PvPin1 may be a repressor in flowering, and its delay of flowering time could be regulated by ABA and MeJA in bamboo.

Flowering time is an important agronomic trait that coordinates the plant life cycle with regional adaptability and thereby impacts yield potentials for cereal crops. The CONSTANS (CO)-like gene family plays vital roles in the regulation of flowering time. CO-like proteins are typically divided into four phylogenetic groups in rice. Several genes from groups I, III, and IV have been functionally characterized, though little is known about the genes of group II in rice. We report the functional characterization in rice of a constitutive floral inhibitor, OsCOL16, encoding a group-II CO-like protein that delays flowering time and increases plant height and grain yield. Overexpression of OsCOL16 resulted in late heading under both long-day and short-day conditions. OsCOL16 expression exhibits a diurnal oscillation and serves as a transcription factor with transcriptional activation activity. We determined that OsCOL16 up-regulates the expression of the floral repressor Ghd7, leading to down-regulation of the expression of Ehd1, Hd3a, and RFT1. Moreover, genetic diversity and evolutionary analyses suggest that remarkable differences in flowering times correlate with two major alleles of OsCOL16. Our combined molecular biology and phylogeographic analyses revealed that OsCOL16 plays an important role in regulating rice photoperiodic flowering, allowing for environmental adaptation of rice., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Homogalacturonan (HG) is the main component of pectins. HG methylesterification has recently emerged as a key determinant controlling cell attachment, organ formation, and phyllotaxy. However, whether and how HG methylesterification affects intercellular metabolite transport has rarely been reported. Here, we identified and characterized knockout mutants of the rice ( Oryza sativa ) OsQUA2 gene encoding a putative pectin methyltransferase. Osqua2 mutants exhibit a remarkable decrease in the degree of methylesterification of HG in the culm-sieve element cell wall and a markedly reduced grain yield. The culm of Osqua2 mutant plants contains excessive sucrose (Suc), and a 13 CO 2 feeding experiment showed that the Suc overaccumulation in the culm was caused by blocked Suc translocation. These and other findings demonstrate that OsQUA2 is essential for maintaining a high degree of methylesterification of HG in the rice culm-sieve element cell wall, which may be critical for efficient Suc partitioning and grain filling. In addition, our results suggest that the apoplastic pathway is involved in long-distance Suc transport in rice. The identification and characterization of the OsQUA2 gene and its functionality revealed a previously unknown contribution of HG methylesterification and provided insight into how modification of the cell wall regulates intercellular transport in plants., (© 2017 American Society of Plant Biologists. All Rights Reserved.)

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease 9 (CRISPR/Cas9) system has emerged as a promising technology for specific genome editing in many species. Here we constructed one vector targeting eight agronomic genes in rice using the CRISPR/Cas9 multiplex genome editing system. By subsequent genetic transformation and DNA sequencing, we found that the eight target genes have high mutation efficiencies in the T 0 generation. Both heterozygous and homozygous mutations of all editing genes were obtained in T 0 plants. In addition, homozygous sextuple, septuple, and octuple mutants were identified. As the abundant genotypes in T 0 transgenic plants, various phenotypes related to the editing genes were observed. The findings demonstrate the potential of the CRISPR/Cas9 system for rapid introduction of genetic diversity during crop breeding.

A rice mutant with light-green leaves was discovered from a transgenic line of Oryza sativa. The mutant has reduced chlorophyll content and abnormal chloroplast morphology throughout its life cycle. Genetic analysis revealed that a single nuclear-encoded recessive gene is responsible for the mutation, here designated as lgl1. To isolate the lgl1 gene, a high-resolution physical map of the chromosomal region around the lgl1 gene was made using a mapping population consisting of 1984 mutant individuals. The lgl1 gene was mapped in the 76.5kb region between marker YG4 and marker YG5 on chromosome 12. Sequence analysis revealed that there was a 39bp deletion within the fourth exon of the candidate gene Os12g0420200 (TIGR locus Os12g23180) encoding a chloroplast stem-loop-binding protein of 41kDa b (CSP41b). The lgl1 mutation was rescued by transformation with the wild type CSP41b gene. Accordingly, the CSP41b gene is identified as the LGL1 gene. CSP41b was transcribed in various tissues and was mainly expressed in leaves. Expression of CSP41b-GFP fusion protein indicated that CSP41b is localized in chloroplasts. The expression levels of some key genes involved in chlorophyll biosynthesis and photosynthesis, such as ChlD, ChlI, Hema1, Ygl1, POR, Cab1R, Cab2R, PsaA, and rbcL, was significantly changed in the lgl1 mutant. Our results demonstrate that CSP41b is a novel gene required for normal leaf color and chloroplast morphology in rice., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)

Key Message: Moderate overexpression of CYP734A4 improves grain number per main panicle and seed setting rate. Brassinosteroid (BR) homeostasis and signaling are crucial for plant growth and development. CYP734A genes encode cytochrome P450 monooxygenases that control the level of bioactive BRs by degrading BRs. However, fertile plants overexpressing CYP734As have not been reported in rice. Here, we isolated a novel semi-dominant mutant brd3-D, in which T-DNA was inserted approximately 4 kb upstream of the CYP734A4 gene (GenBank Accession AB488667), causing its overexpression. The mutant is characterized by dwarfism, small grains, and erect leaves and is less sensitive to brassinolide-induced lamina joint inclination and primary root elongation. However, increased grain number per main panicle and improved seed setting rate were also found in heterozygous brd3-D. To our knowledge, these traits have not been reported in other BR deficient mutants. Quantitative real-time PCR analysis indicated that phenotypic severity of the brd3-D mutant is positively correlated with the CYP734A4 transcription level. In accordance with the increased expression of CYP734A4, a lower castasterone (a rice BR) content was detected in the brd3-D mutants. Knockout of brd3-D by using the CRISPR/Cas9 system rescued the mutation. In addition, transgenic plants overexpressing CYP734A4 with the 35S enhancer mimicked the brd3-D phenotypes, confirming that moderate overexpression of the CYP734A4 gene can improve grain number per main panicle and the seed setting rate in rice. Further studies showed that overexpression of CYP734A4 influences the expressions of multiple genes involved in the BR pathway, and the expression of CYP734A4 is induced by exogenous brassinolide, confirming the negative regulatory role of CYP734A4 in the BR pathway. CYP734A4 might provide a useful gene resource for developing new high-yielding rice varieties.

Background: Polyploidy has pivotal influences on rice (Oryza sativa L.) morphology and physiology, and is very important for understanding rice domestication and improving agricultural traits. Diploid (DP) and triploid (TP) rice shows differences in morphological parameters, such as plant height, leaf length, leaf width and the physiological index of chlorophyll content. However, the underlying mechanisms determining these morphological differences are remain to be defined. To better understand the proteomic changes between DP and TP, tandem mass tags (TMT) mass spectrometry (MS)/MS was used to detect the significant changes to protein expression between DP and TP., Results: Results indicated that both photosynthesis and metabolic pathways were highly significantly associated with proteomic alteration between DP and TP based on biological process and pathway enrichment analysis, and 13 higher abundance chloroplast proteins involving in these two pathways were identified in TP. Quantitative real-time PCR analysis demonstrated that 5 of the 13 chloroplast proteins ATPF, PSAA, PSAB, PSBB and RBL in TP were higher abundance compared with those in DP., Conclusions: This study integrates morphology, physiology and proteomic profiling alteration of DP and TP to address their underlying different molecular mechanisms. Our finding revealed that ATPF, PSAA, PSAB, PSBB and RBL can induce considerable expression changes in TP and may affect the development and growth of rice through photosynthesis and metabolic pathways.

Rice hull, the outer cover of the rice grain, determines grain shape and size. Changes in the rice hull proteome in different growth stages may reflect the underlying mechanisms involved in grain development. To better understand these changes, isobaric tags for relative and absolute quantitative (iTRAQ) MS/MS was used to detect statistically significant changes in the rice hull proteome in the booting, flowering, and milk-ripe growth stages. Differentially expressed proteins were analyzed to predict their potential functions during development. Gene ontology (GO) terms and pathways were used to evaluate the biological mechanisms involved in rice hull at the three growth stages. In total, 5,268 proteins were detected and characterized, of which 563 were differentially expressed across the development stages. The results showed that the flowering and milk-ripe stage proteomes were more similar to each other (r=0.61) than either was to the booting stage proteome. A GO enrichment analysis of the differentially expressed proteins was used to predict their roles during rice hull development. The potential functions of 25 significantly differentially expressed proteins were used to evaluate their possible roles at various growth stages. Among these proteins, an unannotated protein (Q7X8A1) was found to be overexpressed especially in the flowering stage, while a putative uncharacterized protein (B8BF94) and an aldehyde dehydrogenase (Q9FPK6) were overexpressed only in the milk-ripe stage. Pathways regulated by differentially expressed proteins were also analyzed. Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), and two magnesium-chelatase subunits, ChlD (Q6ATS0), and ChlI (Q53RM0), were associated with chlorophyll biosynthesis at different developmental stages. The expression of Q9SDJ2 in the flowering and milk-ripe stages was validated by qRT-PCR. The 25 candidate proteins may be pivotal markers for controlling rice hull development at various growth stages and chlorophyll biosynthesis pathway related proteins, especially magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase (Q9SDJ2), may provide new insights into the molecular mechanisms of rice hull development and chlorophyll associated regulation.

A narrow leaf mutant was isolated from transgenic rice (Oryza sativa L.) lines carrying a T-DNA insertion. The mutant is characterized by narrow leaves during its whole growth period, and was named nal9 (narrow leaf 9). The mutant also has other phenotypes, such as light green leaves at the seedling stage, reduced plant height, a small panicle and increased tillering. Genetic analysis revealed that the mutation is controlled by a single recessive gene. A hygromycin resistance assay showed that the mutation was not caused by T-DNA insertion, so a map-based cloning strategy was employed to isolate the nal9 gene. The mutant individuals from the F₂ generations of a cross between the nal9 mutant and Longtepu were used for mapping. With 24 F₂ mutants, the nal9 gene was preliminarily mapped near the marker RM156 on the chromosome 3. New INDEL markers were then designed based on the sequence differences between japonica and indica at the region near RM156. The nal9 gene was finally located in a 69.3 kb region between the markers V239B and V239G within BAC OJ1212_C05 by chromosome walking. Sequence and expression analysis showed that an ATP-dependent Clp protease proteolytic subunit gene (ClpP) was most likely to be the nal9 gene. Furthermore, the nal9 mutation was rescued by transformation of the ClpP cDNA driven by the 35S promoter. Accordingly, the ClpP gene was identified as the NAL9 gene. Our results provide a basis for functional studies of NAL9 in future work., (© 2013 Institute of Botany, Chinese Academy of Sciences.)

The BURP-domain protein family comprises a diverse group of plant-specific proteins that share a conserved BURP domain at the C terminus. However, there have been only limited studies on the functions and subcellular localization of these proteins. Members of the RD22-like subfamily are postulated to associate with stress responses due to the stress-inducible nature of some RD22-like genes. In this report, we used different transgenic systems (cells and in planta) to show that the expression of a stress-inducible RD22-like protein from soybean (GmRD22) can alleviate salinity and osmotic stress. We also performed detailed microscopic studies using both fusion proteins and immuno-electron microscopic techniques to demonstrate the apoplast localization of GmRD22, for which the BURP domain is a critical determinant of the subcellular localization. The apoplastic GmRD22 interacts with a cell wall peroxidase and the ectopic expression of GmRD22 in both transgenic Arabidopsis thaliana and transgenic rice resulted in increased lignin production when subjected to salinity stress. It is possible that GmRD22 regulates cell wall peroxidases and hence strengthens cell wall integrity under such stress conditions., (© 2012 Blackwell Publishing Ltd.)

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. Using map-based strategy and in silico approach we isolated a new rice (Oryza sativa L.) blast resistance allele of Pid3, designated Pi25, from a stable blast resistance cultivar Gumei2. Over-expression analysis and complementation test showed that Pi25 conferred blast resistance to M. oryzae isolate js001-20. Sequence analysis showed that Pi25 was an intronless gene of 2,772 nucleotides with single nucleotide substitution in comparison to Pid3 at the nucleotide position 459 and predicatively encoded a typical coiled coil--nucleotide binding site--leucine rich repeat (CC--NBS--LRR) protein of 924 amino acid residuals with 100% identity to Pid3 putative protein. The susceptible allele pi25 in Nipponbare contained a nonsense mutation at the nucleotide position 2,209 resulting in a truncated protein with 736 amino acid residuals. In addition, 14 nucleotide substitutions resulting in 10 amino acid substitutions were identified between Pi25 and pi25 upstream the premature stop codon in the susceptible allele. Although the mechanism of Pi25/Pid3-mediated resistance needs to be further investigated, the isolation of the allele would facilitate the utilization of Pi25/Pid3 in rice blast resistance breeding program via transgenic approach and marker assisted selection., (Copyright © 2011. Published by Elsevier Ltd.)

Small silencing RNAs (sRNAs) are non-coding RNA regulators that negatively regulate gene expression by guiding mRNA degradation, translation repression or chromatin modification. Plant sRNAs play crucial roles in various developmental processes, hormone signaling, immune responses and adaptation to a variety of abiotic stresses. miR441 and miR446 were previously annotated as microRNAs (miRNAs) because their precursors can form typical stem-loop structures, but are not considered as real miRNAs because of inconsistency with some ancillary criteria of the recent guidelines for annotation of plant miRNAs. We tentatively rename them small interfering (si)R441 and siR446, respectively, in this study. It has recently been shown that the precursors of siR441 and siR446 might originate from the miniature inverted-repeat transposable element (MITE) Stowaway1. In this report, we show that, in contrast with Dicer-like (DCL)3- and RNA-dependent RNA polymerase (RDR)2-dependent MITE-derived ra-siRNAs, siR441 and siR446 are processed by OsDCL3a but independent of OsRDR2, indicating that siR441 and siR446 are generated from single-stranded stem-loop precursors. We also show that abscisic acid (ABA) and abiotic stresses downregulate the expression of siR441 and siR446 but, surprisingly, increase the accumulation of their precursors in rice plants, implying that processing of siRNA precursors is inhibited. We provide evidence to show that this defective processing is due to increased precursor accumulation per se, possibly by intermolecular self-pairing of the processing intermediate sequences, thus hindering their normal processing. Functional examinations indicate that siR441 and siR446 are positive regulators of rice ABA signaling and tolerance to abiotic stress, possibly by regulating MAIF1 expression., (© 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.)

Background: In plants, HIR (Hypersensitive Induced Reaction) proteins, members of the PID (Proliferation, Ion and Death) superfamily, have been shown to play a part in the development of spontaneous hypersensitive response lesions in leaves, in reaction to pathogen attacks. The levels of HIR proteins were shown to correlate with localized host cell deaths and defense responses in maize and barley. However, not much was known about the HIR proteins in rice. Since rice is an important cereal crop consumed by more than 50% of the populations in Asia and Africa, it is crucial to understand the mechanisms of disease responses in this plant. We previously identified the rice HIR1 (OsHIR1) as an interacting partner of the OsLRR1 (rice Leucine-Rich Repeat protein 1). Here we show that OsHIR1 triggers hypersensitive cell death and its localization to the plasma membrane is enhanced by OsLRR1., Result: Through electron microscopy studies using wild type rice plants, OsHIR1 was found to mainly localize to the plasma membrane, with a minor portion localized to the tonoplast. Moreover, the plasma membrane localization of OsHIR1 was enhanced in transgenic rice plants overexpressing its interacting protein partner, OsLRR1. Co-localization of OsHIR1 and OsLRR1 to the plasma membrane was confirmed by double-labeling electron microscopy. Pathogen inoculation studies using transgenic Arabidopsis thaliana expressing either OsHIR1 or OsLRR1 showed that both transgenic lines exhibited increased resistance toward the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. However, OsHIR1 transgenic plants produced more extensive spontaneous hypersensitive response lesions and contained lower titers of the invading pathogen, when compared to OsLRR1 transgenic plants., Conclusion: The OsHIR1 protein is mainly localized to the plasma membrane, and its subcellular localization in that compartment is enhanced by OsLRR1. The expression of OsHIR1 may sensitize the plant so that it is more prone to HR and hence can react more promptly to limit the invading pathogens' spread from the infection sites.

Appropriate leaf shape has proved to be useful in improving photosynthesis and increasing grain yield. To understand the molecular mechanism of leaf morphogenesis, we identified a rice mutant nrl1, which was characterized by a phenotype of narrow and rolled leaves. Microscopic observation showed that the mutation significantly decreased the number of vascular bundles of leaf and stem. Genetic analysis revealed that the mutation was controlled by a single nuclear-encoded recessive gene. To isolate the nrl1 gene, 756 F(2) and F(3) mutant individuals from a cross of the nrl1 mutant with Longtepu were used and a high-resolution physical map of the chromosomal region around the nrl1 gene was made. Finally, the gene was mapped in 16.5 kb region between marker RL21 and marker RL36 within the BAC clone OSJNBa0027H05. Cloning and sequencing of the target region from the mutant showed that there was a 58 bp deletion within the second exon of the cellulose synthase-like D4 gene (TIGR locus Os12g36890). The nrl1 mutation was rescued by transformation with the wild-type cellulose synthase-like D4 gene. Accordingly, the cellulose synthase-like D4 gene was identified as the NRL1 gene. NRL1 was transcribed in various tissues and was mainly expressed in panicles and internodes. NAL7 and SLL1 were found to be upregulated, whereas OsAGO7 were downregulated in the nrl1 mutant. These findings suggested that there might be a functional association between these genes in regulating leaf development.

The preliminary role of calcineurin B-like protein-interacting protein kinases (CIPKs) in stress response is defined but the exact function of OsCIPK10 gene in rice stress response and its expression pattern yet unclear. In this study we explored the possible functions of OsCIPK10 gene by reverse genetics approaches and also revealed its expression pattern by GUS staining. From the preliminary study of this gene we presumed its function to assist plant to resist stress but over-expressed OsCIPK10 rice transgenic lines showed no significant phenotypic differences from the wild type either under high salt or low potassium conditions, however the gene knockdown plants using inverted repeat strategy presented meaningful healthy plants compared to wild type under the stress of salt. Further we checked the expression profile under high salt and low potassium conditions in wild type and found that OsCIPK10 decreases under high salt and increases on low potassium conditions. So we speculate that OsCIPK10 is actually going to function in response to high salt and low potassium stress. We also explored the expression pattern of this gene using Gus staining and found that gene expresses in all plant tissues, the only exception observed was its higher expression in the vascular tissues.

Tiller number is highly regulated by controlling the formation of tiller bud and its subsequent outgrowth in response to endogenous and environmental signals. Here, we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines, which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not affect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud. To isolate the htd2 gene, a map-based cloning strategy was employed and 17 new insertions-deletions (InDels) markers were developed. A high-resolution physical map of the chromosomal region around the htd2 gene was made using the F(2) and F(3) population. Finally, the gene was mapped in 12.8 kb region between marker HT41 and marker HT52 within the BAC clone OSJNBa0009J13. Cloning and sequencing of the target region from the mutant showed that the T-DNA insertion caused a 463 bp deletion between the promoter and first exon of an esterase/lipase/thioesterase family gene in the 12.8 kb region. Furthermore, transgenic rice with reduced expression level of the gene exhibited an enhanced tillering and dwarf phenotype. Accordingly, the esterase/lipase/thioesterase family gene (TIGR locus Os03g10620) was identified as the HTD2 gene. HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a significantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway. The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway.

Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.

Gene expression in rice roots under nutritional stress was studied using micro array techniques. The results showed that when re-supplied with sufficient amounts of nutrition after nutrition stress, the expression of OsPra2 (a small G protein which is homologous with Pea Pra2 protein) decreased in the plants root tissue. The cDNA sequence of the OsPra2 gene and its promoter, which is about 1 kb upstream of the translation origin point, was obtained using RT-PCR and PCR approaches. The OsPra2 protein contains four conserved GTP/GDP binding domains and specific domain of Rab small G protein family. The expression of OsPra2 and GST fusion protein in onion epidermal cells showed that OsPra2 protein was localized in the membrane and nucleus of the cell. The fusion expression of OsPra2 promoter and GUS reporter gene in transgenic rice suggested that the OsPra2 promoter allowed GUS expression in coleoptiles and roots. Compared with wild type rice, OsPra2 over expressed transgenic rice showed an obvious dwarf phenotype which resembles the BR deficient rice.

G-proteins (guanine nucleotide-binding proteins that usually exhibit GTPase activities) and related signal transduction processes play important roles in mediating plant defense responses; here, a rice (Oryza sativa) cDNA clone, OsGAP1, encoding a GTPase-activating protein (GAP) that also contains a protein kinase C conserved region 2 (C2) domain is reported. An interacting G-protein partner for the OsGAP1 protein was identified by yeast two-hybrid library screening and confirmed by co-immunoprecipitation; the GTPase-activation activity of OsGAP1 on this interacting G-protein was demonstrated using in vitro assays. OsGAP1 was induced by wounding in rice and the presence of the R locus Xa14 enhances such induction. Gain-of-function tests in transgenic rice and Arabidopsis thaliana showed that constitutive expression of OsGAP1 led to increased resistance to bacterial pathogens in both monocots and dicots.

Phospholipase Ds (PLDs) exist in many plants. PLDs catalyse the hydrolysis of phospholipids (e.g. phosphatidylcholine) in cell membrane into phosphatidic acid (PA) and polar free heads (e.g. choline). Two PLD members from rice, OsPLD3 and OsPLD4, were studied by reverse genetics approaches. The results showed that the promoters of OsPLD3 and OsPLD4 could drive the expression of the reporter gene in various tissues of the rice flower organs at different levels. The expression of both genes was induced by wounding and methyl jasmonate (MeJA), but with different intensity at different time intervals. No prominent phenotypes were observed by RNA interference with the gene-specific artificial miRNAs or over-expression of the target genes in rice plants, implying the functional redundancy among different members of the rice PLD family.

A thermo-sensitive chlorophyll deficient mutant was isolated from more than 15,000 transgenic rice lines. The mutant displayed normal phenotype at 23 degrees C or lower temperature (permissive temperature). However, when grown at 26 degrees C or higher (nonpermissive temperature) the plant exhibited an abnormal phenotype characterized by yellow green leaves. Genetic analysis revealed that a single nuclear-encoded recessive gene is responsible for the mutation, which is tentatively designed as cde1(t) (chlorophyll deficient 1, temporally). PCR analysis and hygromycin resistance assay indicated the mutation was not caused by T-DNA insertion. To isolate the cde1(t) gene, a map-based cloning strategy was employed and 15 new markers (five SSR and ten InDels markers) were developed. A high-resolution physical map of the chromosomal region around the cde1(t) gene was made using F(2) and F(3) population consisting of 1,858 mutant individuals. Finally, the cde1(t) gene was mapped in 7.5 kb region between marker ID10 and marker ID11 on chromosome 2. Sequence analysis revealed only one candidate gene, OsGluRS, in the 7.5 kb region. Cloning and sequencing of the target region from the cde1(t) mutant showed that a missense mutation occurred in the mutant. So the OsGluRS gene (TIGR locus Os02 g02860) which encode glutamyl-tRNA synthetase was identified as the Cde1(t) gene.

Auxin response factors (ARFs) are transcription factors that bind with specificity to TGTCTC-containing auxin response elements (AuxREs) found in promoters of primary/early auxin response genes and mediate responses to the plant hormone auxin. The ARF genes are represented by a large multigene family in plants. A comprehensive genome-wide analysis was carried out in this study to find all ARFs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa subsp. japonica), 23 and 25 ARF genes, named as AtARFs and OsARFs, were identified, respectively. Chromosomal locations of all OsARFs were presented and it was found that the duplication of OsARFs was associated with only the chromosomal block duplications but not local tandem duplications. A phylogenetic tree was generated from alignments of the full-length protein sequences of 25 OsARFs and 23 AtARFs to examine the phylogenetic relationships of rice and Arabidopsis ARF proteins. All 48 members of ARF gene families fell into three major classes, a total of 13 sister pairs, including 9 OsARF-OsARF, 2 AtARF-AtARF and 2 AtARF-OsARF sister pairs were formed, showing different orthologous relationships between AtARFs and OsARFs. EST analysis and RT-PCR assays demonstrated that 24 of all 25 OsARF genes were active and the transcript abundance of some OsARF genes was affected by auxin treatment or light- and dark-grown conditions. The outcome of the present study provides basic genomic information for the rice ARF gene family and will pave the way for elucidating the precise role of OsARFs in plant growth and development in the future.

A rice mutant, designated pse(t) (premature senescence, tentatively), was isolated from a T-DNA-inserted transgenic population. Senescence advanced more markedly in pse(t) than in wild-type ('Zhonghua 11', japonica) plants. Genetic analysis of pse(t) revealed that the premature senescence mutation was controlled by a single recessive nuclear gene, but that it was not induced by T-DNA insertion. In an effort to understand the genetic and molecular basis underlying premature senescence in rice, a map-based cloning strategy was used to localize Pse(t). High-resolution mapping of the Pse(t) locus was carried out using simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers. An F2 population, comprising 1691 pse(t) individuals derived from a cross of the pse(t) mutant with 'Longtepu' (indica), was constructed. Several new polymorphism markers were developed in this study. Genetic linkage analysis showed that the Pse(t) gene was located on the long arm of chromosome 7. It was found that the Pse(t) gene cosegregated with 3 markers and was flanked by markers SS22 and PP21. Thus, the Pse(t) gene is located within a genetic distance of 0.15 cM, corresponding to a physical distance of 220 kb. These findings provide the basic information that can be used for the final isolation of this gene in the rice premature-senescence pathway.