Molecular mechanism of tillering response to nitrogen in rice.

Nitrogen (N) fertilizer acts as the main driving force for agricultural productivity improvement. However, overuse of N fertilizer has caused severe effects to environment and ecosystem. Thus, it is pivotal to improve nitrogen use efficiency (NUE) for future sustainable agriculture. Agronomic traits response to N are significant indices for NUE phenotyping. For example, tiller number, grain number per panicle, and grain weight are three major components for cereal yields. Although regulatory mechanisms regarding to these three traits have been largely reported, few is known about how N affects them. Tiller number is one of the most sensitive traits response to N and also plays a key role for N-promoted yield improvement. It is thereby of great significance to dissect the genetic basis underlying tillering response to N. In this review, we summarize the factors contributing to NUE as well as the regulatory mechanisms over rice tillering and emphasize how N affects rice tillering, future research directions are also discussed for further improving NUE.

Analysis of rice root bacterial microbiota of Nipponbare and IR24.

The root-associated bacterial microbiota is closely related to life activities of land plants, and its composition is affected by geographic locations and plant genotypes. However, the influence of plant genotypes on root microbiota in rice grown in northern China remains to be explained. In this study, we performed 16S rRNA gene amplicon sequencing to generate bacterial community profiles of two representative rice cultivars, Nipponbare and IR24. They are planted in Changping and Shangzhuang farms in Beijing and have reached the reproductive stage. We compared their root microbiota in details by Random Forest machine learning algorithm and network analysis. We found that the diversity of rice root microbiota was significantly affected by geographic locations and rice genotypes. Nipponbare and IR24 showed distinct taxonomic composition of the root microbiota and the interactions between different bacteria. Moreover, the root bacteria could be used as biomarkers to distinguish Nipponbare from IR24 across regions. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota in Northern China and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.

Sweet Sorghum Originated through Selection of Dry, a Plant-Specific NAC Transcription Factor Gene.

Sorghum (Sorghum bicolor) is the fifth most popular crop worldwide and a C4 model plant. Domesticated sorghum comes in many forms, including sweet cultivars with juicy stems and grain sorghum with dry, pithy stems at maturity. The Dry locus, which controls the pithy/juicy stem trait, was discovered over a century ago. Here, we found that Dry gene encodes a plant-specific NAC transcription factor. Dry was either deleted or acquired loss-of-function mutations in sweet sorghum, resulting in cell collapse and altered secondary cell wall composition in the stem. Twenty-three Dry ancestral haplotypes, all with dry, pithy stems, were found among wild sorghum and wild sorghum relatives. Two of the haplotypes were detected in domesticated landraces, with four additional dry haplotypes with juicy stems detected in improved lines. These results imply that selection for Dry gene mutations was a major step leading to the origin of sweet sorghum. The Dry gene is conserved in major cereals; fine-tuning its regulatory network could provide a molecular tool to control crop stem texture.

Cold stress tolerance in rice: physiological changes, molecular mechanism, and future prospects.

Low temperature is a major factor affecting rice geographical distribution growth, development, and productivity. Cold stress mediates a series of physiological and metabolite changes, such as alterations in chlorophyll fluorescence, electrolyte leakage, reactive oxygen species (ROS), malondialdehyde (MAD), sucrose, lipid peroxides, proline, and other metabolites, plant endogenous hormones abscisic acid (ABA) and gibberellin (GA) also changes. In this review, we summarize the recent research progress on physiological and metabolic changes under low temperature, cold stress related loci and QTL reported by map-based cloning and genome-wide association analysis (GWAS), and some molecular mechanisms in response to low temperature in rice. We also discuss the future prospects on breeding cold tolerance varieties of rice.

Nitric oxide ameliorates zinc oxide nanoparticles-induced phytotoxicity in rice seedlings.

Nitric oxide (NO) has been found to function in enhancing plant tolerance to various environmental stresses. However, role of NO in relieving zinc oxide nanoparticles (ZnO NPs)-induced phytotoxicity remains unknown. Here, sodium nitroprusside (SNP, a NO donor) was used to investigate the possible roles and the regulatory mechanisms of NO in counteracting ZnO NPs toxicity in rice seedlings. Our results showed that 10 µM SNP significantly inhibited the appearance of ZnO NP toxicity symptoms. SNP addition significantly reduced Zn accumulation, reactive oxygen species production and lipid peroxidation caused by ZnO NPs. The protective role of SNP in reducing ZnO NPs-induced oxidative damage is closely related to NO-mediated antioxidant system. A decrease in superoxide dismutase activity, as well as an increase in reduced glutathione content and peroxidase, catalase and ascorbate peroxidase activity was observed under SNP and ZnO NPs combined treatments, compared to ZnO NPs treatment alone. The relative transcript abundance of corresponding antioxidant genes exhibited a similar change. The role of NO in enhancing ZnO NPs tolerance was further confirmed by genetic analysis using a NO excess mutant (noe1) and an OsNOA1-silenced plant (noa1) of rice. Together, this study provides the first evidence indicating that NO functions in ameliorating ZnO NPs-induced phytotoxicity.

Ethylene responses in rice roots and coleoptiles are differentially regulated by a carotenoid isomerase-mediated abscisic acid pathway.

Ethylene and abscisic acid (ABA) act synergistically or antagonistically to regulate plant growth and development. ABA is derived from the carotenoid biosynthesis pathway. Here, we analyzed the interplay among ethylene, carotenoid biogenesis, and ABA in rice (Oryza sativa) using the rice ethylene response mutant mhz5, which displays a reduced ethylene response in roots but an enhanced ethylene response in coleoptiles. We found that MHZ5 encodes a carotenoid isomerase and that the mutation in mhz5 blocks carotenoid biosynthesis, reduces ABA accumulation, and promotes ethylene production in etiolated seedlings. ABA can largely rescue the ethylene response of the mhz5 mutant. Ethylene induces MHZ5 expression, the production of neoxanthin, an ABA biosynthesis precursor, and ABA accumulation in roots. MHZ5 overexpression results in enhanced ethylene sensitivity in roots and reduced ethylene sensitivity in coleoptiles. Mutation or overexpression of MHZ5 also alters the expression of ethylene-responsive genes. Genetic studies revealed that the MHZ5-mediated ABA pathway acts downstream of ethylene signaling to inhibit root growth. The MHZ5-mediated ABA pathway likely acts upstream but negatively regulates ethylene signaling to control coleoptile growth. Our study reveals novel interactions among ethylene, carotenogenesis, and ABA and provides insight into improvements in agronomic traits and adaptive growth through the manipulation of these pathways in rice.

[Major domestication traits in Asian rice].

Rice (Oryza sativa L.) is an excellent model plant in elucidation of cereal domestication. Loss of seed shattering, weakened dormancy, and changes in plant architecture were thought to be three key events in the rice domestication and creating the high-yield, uniform-germinating, and densely-planting modern rice. Loss of shattering is considered to be the direct morphological evidence for identifying domesticated rice. Two major shattering QTLs, Sh4 and qSH1, have displayed different domestication histories. Weakened seed dormancy is essential for synchronous germination in agricultural production. Genes Sdr4, qSD7-1, and qSD12 impose a global and complementary adaptation strategies in controlling seed dormancy. The prostate growth habit of wild rice is an adaptation to disturbed habitats, while the erect growth habit of rice cultivars meet the needs of compact planting, and such a plant architecture is mainly controlled by PROG1. The outcrossing habit of wild rice promotes propagation of domestication genes among different populations, while the self-pollinating habit of cultivated rice facilitates fixation of domestication genes. Currently, the researches on rice domestication mainly focus on individual genes or multiple neutral markers, and much less attention has been paid to the evolution of network controlling domestication traits. With the progress in functional genomics research, the molecular mechanism of domestication traits is emerging. Rice domestication researches based on network will be more comprehensive and better reflect rice domestica-tion process. Here, we reviewed most progresses in molecular mechanisms of rice domestication traits, in order to provide the new insights for rice domestication and molecular breeding.

[Characterisation of a rice dwarf and twist leaf 1 (dtl1) mutant and fine mapping of DTL1 gene].

Plant height is one of the most important agronomic traits, which determines grain yield. By a largescale screening of our mutant population, we identified a dwarf with twisty leaf mutant (dwarf and twist leaf 1, dtl1). Besides dwarf with twisty leaf, dtl1 also showed reduced tiller number and sterile phenotypes. Based on the internode length of dtl1, this mutant belongs to the nl type of dwarfing phenotype. Physiological assay with two phytohormones, gibberellin (GA), and brassinosteroid (BR), suggested that dtl1 was neither deficient nor insensitive to GA and BR. Genetic analysis showed that the phenotype of dtl1 was controlled by a single recessive gene. Using F2 population derived from a cross between dtl1 and an indica cultivar Taichung Native 1, the DTL1 gene was narrowed down to a 70.4 kb between two SSR markers, RM25923 and RM6673, on the long arm of chromosome 10, and co-segregated with InDel marker Z10-29, where thirteen open reading frames were predicted without known gene involved in controlling plant height. Thus, the DTL1 gene might be a novel gene which is related to plant height in rice.

Arsenic biotransformation and volatilization in transgenic rice.

• Biotransformation of arsenic includes oxidation, reduction, methylation, and conversion to more complex organic arsenicals. Members of the class of arsenite (As(III)) S-adenosylmethyltransferase enzymes catalyze As(III) methylation to a variety of mono-, di-, and trimethylated species, some of which are less toxic than As(III) itself. However, no methyltransferase gene has been identified in plants. • Here, an arsM gene from the soil bacterium Rhodopseudomonas palustris was expressed in Japonica rice (Oryza sativa) cv Nipponbare, and the transgenic rice produced methylated arsenic species, which were measured by inductively coupled plasma mass spectrometry (ICP-MS) and high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS). • Both monomethylarsenate (MAs(V)) and dimethylarsenate (DMAs(V)) were detected in the roots and shoots of transgenic rice. After 12 d exposure to As(III), the transgenic rice gave off 10-fold greater volatile arsenicals. • The present study demonstrates that expression of an arsM gene in rice induces arsenic methylation and volatilization, theoretically providing a potential stratagem for phytoremediation.

[Plant SNAREs and their biological functions].

The signal communication between various organelles is essential for cells of eukaryotic organisms. Vesicle trafficking is an important pathway for this kind of communication. Most of the membrane fusion is mediated by SNAREs (Soluble N-ethyl-maleimide-sensitive fusion protein attachment protein receptors), which are highly conserved from various species. Compared with genomes of other eukaryotes, plant genome encodes an even higher number of SNAREs. Accumulating evidences support that plant SNAREs is a multifunctional protein family, which is involved in variety of biological processes. We review the recent advances on molecular mechanism and biological functions of plant SNAREs.

S-nitrosylation of AtSABP3 antagonizes the expression of plant immunity.

Changes in cellular redox status are a well established response across phyla following pathogen challenge. In this context, the synthesis of nitric oxide (NO) is a conspicuous feature of plants responding to attempted microbial infection and this redox-based regulator underpins the development of plant immunity. However, the associated molecular mechanism(s) have not been defined. Here we show that NO accretion during the nitrosative burst promotes increasing S-nitrosylation of the Arabidopsis thaliana salicylic acid-binding protein 3 (AtSABP3) at cysteine (Cys) 280, suppressing both binding of the immune activator, salicylic acid (SA), and the carbonic anhydrase (CA) activity of this protein. The CA function of AtSABP3 is required for the expression of resistance in the host against attempted pathogen infection. Therefore, inhibition of AtSBAP3 CA function by S-nitrosylation could contribute to a negative feedback loop that modulates the plant defense response. Thus, AtSABP3 is one of the first targets for S-nitrosylation in plants for which the biological function of this redox-based post-translational modification has been uncovered. These data provide a molecular connection between the changes in NO levels triggered by attempted pathogen infection and the expression of disease resistance.

[Plant non-host resistance: current progress and future prospect].

Plant non-host resistance is the most common form of disease resistance exhibited by plant against the majority of potentially pathogenic microorganisms. The broad spectrum and durable resistance of non-host resistance suggests that plant non-host resistance has a significantly agricultural application, however, it's molecular mechanism is still poorly understood. Here we summarized the recent progress on the molecular mechanism of the non-host resistance, plant-pathogen interaction systems, PEN1 encoding SNARE protein mediated non-host disease resistance, and its future prospect.

Arabidopsis SDIR1 enhances drought tolerance in crop plants.

Arabidopsis E3 ligase salt- and drought-induced RING-finger 1 (SDIR1) has been found to be involved in abscisic acid (ABA)-related stress signaling. SDIR1-overexpressing Arabidopsis plants exhibit improved tolerance to drought. Tobacco (Nicotiana tabacum) and rice (Oryza sativa) are two important agronomic crop plants. To determine whether SDIR1 enhances drought resistance in crop plants, SDIR1 transgenic tobacco and rice plants were generated. Ectopic expression of SDIR1 in both plants conferred improved drought tolerance ability. These results suggest that SDIR1 can function as a drought-tolerance gene in both dicotyledons and monocotyledons, and that it can serve as a drought-tolerance engineering candidate gene in crop plants.

[An overview of flowering transition in higher plants].

In higher plant, flowering transition represents a crucial transition from the vegetative stage to the reproductive stage in life cycle. This process is controlled by both endogenous and environmental factors. In Arabidopsis thaliana, four pathways, photoperiod pathway, vernalization pathway, autonomous pathway, and GA pathway were involved in flowering control. These flowering transition pathways are shown to be highly conserved in Arabidopsis and other higher plants including rice (Oryza sativa L.). This review summarizes recent progresses on flowering time control.

[Expression of TMV coat protein gene RNAi in transgenic tobacco plants confer immunity to tobacco mosaic virus infection].

RNAi technique has been proved as a powerful tool for plant breeding. In this paper, the coat protein of tobacco mosaic virus (TMV) was used for constructing the RNAi interference vector. The tobacco varieties K326 and Longjiang 911 were transformed via Agrobacterium tumefaciens-mediated transformation, and transgenic plants were generated. The expression analysis with real-time PCR indicated that TMV RNA had been degraded varied in different transgenic lines. Field assay revealed that 83% and 90 % transgenic plants showed immunity resistance to TMV in K326 and Longjiang 911 respectively.

[Expression of rabbit neutrophile peptide-1 in nitrate reductase-deficient mutant of Chlorella ellipsoidea].

Application of transgenic Cholrella as bioreactor to express rabbit neutrophile pepetide-1 (NP-1) shows great practical value. In this paper, an NP-1 expression vector containing two selective marker genes NPTII and nitrate reductase gene was constructed. The NP-1 gene was transformed into the nitrate reductase-deficient mutant nrm-4 of Chlorella ellipsoidea via electroporation, and the transgenic alga expressed the active NP-1 were obtained.

Leafy head2, which encodes a putative RNA-binding protein, regulates shoot development of rice.

During vegetative development, higher plants continuously form new leaves in regular spatial and temporal patterns. Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatory mechanism of plant architecture, but also enrich the ways to its modification by which crop yield could be improved. Here, we reported the characterization of the rice leafy-head2 (lhd2) mutant that exhibits shortened plastochron, dwarfism, reduced tiller number, and failure of phase transition from vegetative to reproductive growth. Anatomical and histological study revealed that the rapid emergence of leaves in lhd2 was resulted from the rapid initiation of leaf primordia whereas the reduced tiller number was a consequence of the suppression of the tiller bud outgrowth. The molecular and genetic analysis showed that LHD2 encodes a putative RNA binding protein with 67% similarity to maize TE1. Comparison of genome-scale expression profiles between wild-type and lhd2 plants suggested that LHD2 may regulate rice shoot development through KNOX and hormone-related genes. The similar phenotypes caused by LHD2 mutation and the conserved expression pattern of LHD2 indicated a conserved mechanism in controlling the temporal leaf initiation in grass.

OsGLU1, a putative membrane-bound endo-1,4-beta-D-glucanase from rice, affects plant internode elongation.

A dwarf mutant glu was identified from screening of T-DNA tagged rice population. Genetic analysis of the T1 generation of glu revealed that a segregation ratio of wild-type:dwarf phenotype was 3:1, suggesting that the mutated phenotype was controlled by a single recessive nuclear locus. The mutated gene OsGLU1, identified by Tail-PCR, encodes a putative membrane-bound endo-1,4-beta-D-glucanase, which is highly conserved between mono- and dicotyledonous plants. Mutation of OsGLU1 resulted in a reduction in cell elongation, and a decrease in cellulose content but an increase in pectin content, suggesting that OsGLU1 affects the internode elongation and cell wall components of rice plants. Transgenic glu mutants harboring the OsGLU1 gene complemented the mutation and displayed the wild-type phenotype. In addition, OsGLU1 RNAi plants showed similar phenotype as the glu mutant has. These results indicate that OsGLU1 plays important roles in plant cell growth. Gibberellins and brassinosteroids induced OsGLU1 expression. In rice genome, endo-1,4-beta-D-glucanases form a multiple gene family with 15 members, and each may have a distinct expression pattern in different organs. These results indicate that endo-1,4-beta-D-glucanases may play diverse roles in growth and developmental process of rice plants.

OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1.

WRKY family proteins are a class of plant specific transcription factors that involve in many stress response pathways. It has been shown that one Arabidopsis WRKY protein, AtWRKY29/22, is activated by MAP kinase signaling cascade and confers resistance to both bacterial and fungal pathogens. However, little is known about the biological roles of WRKY proteins in rice. In this study, we investigated the expression patterns of rice AtWRKY29/22 homolog, OsWRKY03, under different conditions, and also its possible role involved in plant defense. Our results showed that OsWRKY03 was up-regulated by several defense signaling molecules or different treatments. Further analysis revealed that the expression of OsWRKY03 was light dependent. Transcriptional activation activity of OsWRKY03 was also demonstrated by yeast functional assay. Transient expression of OsWRKY03-GFP fusion protein in onion epidermis cells showed that OsWRKY03 was a nuclear localized protein. OsNPR1 as well as several other pathogenesis-related genes, such as OsPR1b, phenylalanine ammonia-lyase (ZB8) and peroxidase (POX22.3), were induced in OsWRKY03-overexpressing transgenic plants. These results indicated that OsWRKY03 is located upstream of OsNPR1 as a transcriptional activator in salicylic acid (SA)-dependent or jasmonic acid (JA)-dependent defense signaling cascades.

[PCR detection of transgenic elements in feed raw material].

Based on the heterogeneous genes usually used in transgenic crops, the PCR technique was performed with primers derived from CaMV 35S promoter (35S-promoter,originated from cauliflower mosaic virus), NOS terminator (nopaline synthase-terminator,derived from Agrobacterium tumefaciens), EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene, and CryIA(b) (delta-endotoxin,evolved from Bacillus thuringiensis subsp. kurstaki) gene to detect transgenic agents from feed raw materials of soybean dregs and corn gluten meal, respectively. Endogenous corn Zein (a protein extracted from corn gluten) gene, soybean Lectin (chitin-binding protein) gene and negative, positive control were applied for avoiding false results. The method established here has been successfully applied in detecting transgenic elements in imported feed raw material.