Methane Emission from Rice Fields:Necessity for Molecular Approach for Mitigation

Anthropogenic methane emissions are a leading cause of the increase in global averagetemperatures,often referred to as global warming.Flooded soils play a significant role in methaneproduction,where the anaerobic conditions promote the production of methane by methanogenicmicroorganisms.Rice fields contribute a considerable portion of agricultural methane emissions,as riceplants provide both factors that enhance and limit methane production.Rice plants harbor both methaneproducingand methane-oxidizing microorganisms.Exudates from rice roots provide source for methaneproduction,while oxygen delivered from the root aerenchyma enhances methane oxidation.Studies haveshown that the diversity of these microorganisms depends on rice cultivars with some genes characterizedas harboring specific groups of microorganisms related to methane emissions.However,there is still aneed for research to determine the balance between methane production and oxidation,as rice plantspossess the ability to regulate net methane production.Various agronomical practices,such as fertilizerand water management,have been employed to mitigate methane emissions.Nevertheless,studiescorrelating agronomic and chemical management of methane with productivity are limited.Moreover,evidences for breeding low-methane-emitting rice varieties are scattered largely due to the absence ofcoordinated breeding programs.Research has indicated that phenotypic characteristics,such as rootbiomass,shoot architecture,and aerenchyma,are highly correlated with methane emissions.This reviewdiscusses available studies that involve the correlation between plant characteristics and methaneemissions.It emphasizes the necessity and importance of breeding low-methane-emitting rice varieties inaddition to existing agronomic,biological,and chemical practices.The review also delves into the idealphenotypic and physiological characteristics of low-methane-emitting rice and potential breeding techniques,drawing from studies conducted with diverse varieties,mutants,and transgenic plants.

Natural sources, biosynthesis, biological functions, and molecular mechanisms of shikimic acid and its derivatives

Shikimic acid is a hydroaromatic compound possessing critical biological properties,such as antibacterial and antiviral activity.This review mainly focused on shikimic acid and its derivatives.We first briefly introduced the sources of shikimic acid and its derivatives and discussed their biosynthesis.Several in vitro and in vivo studies indicate that shikimic acid and its derivatives exhibit diverse bioactivities,such as antioxidant,antiviral,anti-inflammatory,antibacterial,hypolipidemic,bone protective,skin protective,neuroprotective,and antidiabetic activities.We mainly focused on the related molecular mechanisms.Overall,the wide range of bioactivities of shikimic acid and its derivatives indicate that a more detailed exploration of their potential for the prevention and treatment of certain diseases is warranted.

Ubiquitination-mediated protein degradation and modification:an emerging theme in plant-microbe interactions

translational 以后修正对蛋白质稳定性并且到蛋白质活动的调整中央。蛋白质修正的各种各样的类型例如 phosphorylation， methylation， acetylation， myristoylation， glycosylation，和 ubiquitination，被报导了。在他们之中， ubiquitination 把自己与其它区分开来因为大多数 ubiquitinated 蛋白质为降级被指向到 26S proteasome。ubiquitin/26S proteasome 系统在房间组成主要蛋白质降级小径。在最近的年里，在众多的真核细胞的细胞的函数的控制的 ubiquitination 机械的重要性逐渐地被欣赏了。增加 E3 ubiquitin ligases 和他们的底层的数字，包括许多必要细胞的管理者被识别了。过去的几年里的研究表明了 ubiquitination 系统为大量植物是重要的发展过程和回答到不能生活、关於生命的压力。这评论从在植物微生物相互作用起重要作用的植物和病原体在联系 ubiquitination 的蛋白质的功能的分析讨论最近的进展。

Current Status of Conventional and Molecular Interventions for Blast Resistance in Rice

Pyricularia oryzae anamorph of Magnaporthe oryzae is one of the most notorious fungal pathogens causing severe economic loss in rice production worldwide. Various methods, viz. cultural, biological and molecular approaches, are utilized to counteract this pathogen. Moreover, some tolerant or resistant rice varieties have been developed with the help of breeding programmes. Isolation and molecular characterization of different blast resistance genes now open the gate for new possibilities to elucidate the actual allelic variants of these genes via various molecular breeding and transgenic approaches. However, the behavioral pattern of this fungus breakups the resistance barriers in the resistant or tolerant rice varieties. This host-pathogen barrier will be possibly countered in future research by comparative genomics data from available genome sequence data of rice and M. oryzae for durable resistance. Present review emphasized fascinating recent updates, new molecular breeding approaches, transgenic and genomics approaches(i.e. mi RNA and genome editing) for the management of blast disease in rice. The updated information will be helpful for the durable, resistance breeding programme in rice against blast pathogen.

Molecular mechanisms of salinity tolerance in rice

Salinity is one of the major abiotic stresses which impose constraints to plant growth and production.Rice(Oryza sativa L.)is one of the most important staple food crops and a model monocot plant.Its production is expanding into regions that are affected by soil salinity,requiring cultivars more tolerant to saline conditions.Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice.In spite of extensive studies exploring the mechanism of salt tolerance,there has been limited progress in breeding for increased salinity tolerance.In this review,we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance.We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity,prompting a need for a comprehensive functional analysis.We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue-and/or cell-specific gene expression.More details of salt-responsive channel and transporter activities at tissue-and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm.Thus,future studies should focus on diversity of available genetic resources and,particular,wild rice relatives,to reincorporate salinity tolerance traits lost during domestication.

Plant Ionomics: A Platform for Identifying Novel Gene Regulating Plant Mineral Nutrition

In the present era of genomics, ionomics is one of the major pillars for the structural and functional genomic study. The complete set of ions present in an organism is referred to as the ionome of the organism. Hence, the ionomics is defined as the, “study of quantitative complement of low molecular weight molecules present in cells in a particular physiological and developmental state of the plant” [1]. The complete ionomic profiling of the plants are done by using a number of analytical tools like ICP-MS, ICP-OES, X-Ray crystallography, Neutron Activation Analysis (NAA) etc. All these analytical tools gave complete profile of the ions present in the plants. These data are stored in a database called PiiMS (Purdue Ionomics Information Management System) [2]. The huge data available in the database helps in the forward and reverse genetic approach for studying the structural and functional genomics of the particular organism. This review describes the role of the ionomic study in crop plants like arabidopsis, rice and maize.

Somatic Embryogenesis in Iberian Grapevine (Vitis vinifera) Cultivars Using Carpels as Initial Explants: Protocol Establishment and Histological Evaluation

Trincadeira and Aragonez are two important grapevine cultivars in the Iberian Peninsula, used for high quality red wines production. Both cultivars are strongly affected by fungal diseases, with consequent high loses on plant productivity and fruit quality. A successful protocol for plant regeneration via somatic embryogenesis (SE) was established for both cultivars allowing further plant improvement based on gene transfer technology. Several factors were evaluated during the three different phases which characterize an SE plant regeneration protocol. The culture room temperature during the induction phase, a parameter usually accepted as standard by most researchers, proved in these trials to significantly affect the embryo induction rates. Concerning embryo conversion, it was specially affected by the embryo developmental stage, by the intensity and duration of the chilling treatment and by the supplementation of conversion culture medium with activated charcoal. The responses obtained, both for induction and conversion, proved to be highly genotype dependent. Calli structure, as well as embryo integrity, was histologically observed, allowing to characterize embryonic and non-embryonic masses and to identify abnormalities on embryo development.

Role of Pathogen-Related Protein 10 (PR 10) under Abiotic and Biotic Stresses in Plants

Members of the Pathogenesis Related(PR)10 protein family have been identified in a variety of plant species and a wide range of functions ranging from defense to growth and development has been attributed to them.PR10 protein possesses ribonuclease(RNase)activity,interacts with phytohormones,involved in hormone-mediated signalling,afforded protection against various phytopathogenic fungi,bacteria,and viruses particularly in response to biotic and abiotic stresses.The resistance mechanism of PR10 protein may include activation of defense signalling pathways through possible interacting proteins involved in mediating responses to pathogens,degradation of RNA of the invading pathogens.Moreover,several morphological changes have been shown to accompany the enhanced abiotic stress tolerance.In this review,the possible mechanism of action of PR10 protein against biotic and abiotic stress has been discussed.Furthermore,our findings also confirmed that the in vivo Nitric oxide(NO)is essential for most of environmental abiotic stresses and disease resistance against pathogen infection.The proper level of NO may be necessary and beneficial,not only in plant response to the environmental abiotic stress,but also to biotic stress.The updated information on this interesting group of proteins will be useful in future research to develop multiple stress tolerance in plants.

Impeded Carbohydrate Metabolism in Rice Plants under Submergence Stress

The detrimental effects of submergence on physiological performances of some rice varieties with special references to carbohydrate metabolisms and their allied enzymes during post-flowering stages have been documented and clarified in the present investigation. It was found that photosynthetic rate and concomitant translocation of sugars into the panicles were both related to the yield. The detrimental effects of the complete submergence were recorded in generation of sucrose, starch, sucrose phosphate synthase and phosphorylase activity in the developing panicles of the plants as compared to those under normal or control （i.e. non-submerged） condition. The accumulation of starch was significantly lower in plants under submergence and that was correlated with ADP-glucose pyrophosphorylase activity. Photosynthetic rate was most affected under submergence in varying days of post-flowering and was also related to the down regulation of Ribulose bisphosphate carboxylase activity. However, under normal or control condition, there recorded a steady maintenance of photosynthetic rate at the post-flowering stages and significantly higher values of Ribulose bisphosphate carboxylase activity. Still, photosynthetic rate of the plants under both control and submerged conditions had hardly any significant correlation with sugar accumulation and other enzymes of carbohydrate metabolism like invertase with grain yield. Finally, plants under submergence suffered significant loss of yield by poor grain filling which was related to impeded carbohydrate metabolism in the tissues. It is evident that loss of yield under submergence is attributed both by lower sink size or sink capacity （number of panicles, in this case） as well as subdued carbohydrate metabolism in plants and its subsequent partitioning into the grains.

Molecular cloning and characterization of fruit specific promoter from <i>Cucumis sativus</i>L.

The isolation and characterization of fruit specific promoters are critical for the manipulation of nutritional value and agronomic quality of fruits by genetic engineering and also opened a new era in edible vaccine technology. Expansins are proteins that induce loosening of individual plant cells by disrupting the non-covalent interactions between cellulose and hemicellulose microfibrils and hence have role in growth programs including fruit ripening. We report the identification of an expansin gene (CsExp) from Cucumis sativus that exhibits high levels of mRNA abundance and is specifically expressed in ripened fruit. The promoter region of CsExp also contains elements responsible for its fruit specific expression. Transient expression studies of the CsExp promoter were conducted with particle bombardment, followed by GUS histochemical assay and real time PCR. CaMV35S promoter was used as the positive control in all these experiments. Clear fruit specificity was observed for CsExp promoter in all the experiments. Thus CsExp promoter from Cucumber is a good candidate to target expression of the foreign genes to engineer fruit specific traits.

Tagging of Brown Planthopper Resistance Genes in F_2s of IR50 × Ptb33 of Rice by Using Bulked Segregant Analysis

Brown planthopper （Nilaparvata lugens Stal） is one of the most damaging pests causing hopper burn in rice, and thereby reducing the productivity and also the quality of the product. The effective management strategy to control this pest is the identification and transfer of desirable genes to local rice cultivars. The most important approach for developing resistant cultivars is the identification of markers, which can help in marker-assisted selection of more durable resistant genotype. The susceptible parent IR50 and the resistant parent Ptb33, and their F2 populations were used in bulked segregant analysis for identification of resistant genes with random amplified polymorphic DNA marker （RAPD） primers. The primers OPC7 and OPAG14 showed both dominant and susceptible specific banding pattern so called co-dominant markers. Moreover, OPC7697 and OPAG14680 showed resistant specific bands and thus being in coupling phase, whereas OPC7846 and OPAG14650 showed susceptible specific genotypic bands in bulked segregant analysis. Therefore, the coupling phase markers, OPC7697 and OPAG14680, are considered to be more useful in marker-assisted selection of rice genotypes in crop improvement.

Evaluation of antifungal plant extracts against cereal and legume seed-borne pathogens for effective management

Sri Lanka as an agricultural country needs to manage the seed-borne fungal pathogens that have caused infections and diseases that result in significant crop losses and a decline in yield and productivity.Therefore,it is imperative to apply pathogen management strategies that are environmentally friendly,and economically feasible such as plant extractions,to reduce seed-borne fungi and increase the quality of the seed.This study was aimed at identifying the antifungal efficacy of Allium sativum,Aloe vera,Azadirachta indica,and Zingiber officinale extracts and their effective concentrations to control the seed-borne fungal pathogens;Aspergillus flavus,A.niger,Orbilia foliicola,Rhizopus oryzae,and Talaromyces oumae-annae isolated from Arachis hypogea,Oryza sativa,Vigna radiata,and V.sinensis respectively.Antifungal efficacy was determined by the agar well diffusion method and poisoned food technique.Plant extracts’effectiveness for seed germination and seed quality was evaluated by pot experiments.Zingiber officinale crude extract exhibited the highest antifungal activity against the tested pathogens which was as effective as Captan 50%(WP),a positive control.Further analysis of the results from the pot experiment revealed that O.sativa,and V.radiata seeds treated with A.indica,and Z.officinale aqueous extracts showed 100%germination percentage.Azadirachta indica,and Z.officinale aqueous extracts are the most effective in promoting seed germination and seedling vigor while A.vera extract is the least effective extract.Comparing the two different extracts,aqueous extracts significantly promote seed germination and increase seedling vigor.

The proposed role of MSL-lncRNAs in causing sex lability of female poplars

Labile sex expression is frequently observed in dioecious plants,but the underlying genetic mechanism remains largely unknown.Sex plasticity is also observed in many Populus species.Here we carried out a systematic study on a maleness-promoting gene,MSL,detected in the Populus deltoides genome.Our results showed that both strands of MSL contained multiple cis-activating elements,which generated long non-coding RNAs(lncRNAs)promoting maleness.Although female P.deltoides did not have the male-specific MSL gene,a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome.Based on sequence alignment,the MSL sequence could be divided into three partial sequences,and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness.Since activation of the MSL sequences can only result in female sex lability,we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.

Sex effect on growth performance and marker-aided sex discrimination of seedlings of Populus deltoides

Sex has a significant effect on various traits among dioecious plants.In this analysis of the sex effect on the radial growth and wood density of numerous 20-yearold trees of Populus deltoides growing in a common garden,male trees performed better than the females in radial growth,but sex did not significantly affect wood density.Growth rate and wood density were weakly negatively correlated.Sex selection is also critical for controlling seed-hair pollution from P.deltoides plantations.However,because the juvenile period of P.deltoides lasts for years,a reliable technique to determine the sex of juveniles has been needed.Here we developed a marker-aided technique to discriminate the sexes of P.deltoides seedlings.This study provides essential information on target traits and a highly desirable genetic toolkit for accelerate breeding programs for this important tree species.

In-Silico Identification and Differential Analysis of Mitochondrial RNA Editing Events in Helianthus Genotypes/Species and Powdery Mildew Infected Variants

Sunflower is one of the most used commercial oilseed crops and suffers due to Powdery mildew. RNA sequence alteration occurs due to RNA editing which is a post transcriptional modification. It causes a deviation from the genomic DNA sequence resulting in RNA-DNA differences. Accurate study of RNA editing events in diverse species is possible by NGS based methods. Here, we performed RNA sequencing of 12 leaf transcriptomes, which include three genotypes of Helianthus annuus (2023B, TX16R and ID25), H. debilis, H. niveus, and H. praecox along with their respective powdery mildew pathogen infected variants and systematically analysed the mitochondrial RNA editing events using computational reference-based mapping approach. We discovered 687 editing sites, 220 editing events in the protein-coding regions, among all species and genotypes considered in this study. These included “C to U” and “U to C” RNA editing events. On further analysis, we observed that these editing events include 14 different types of amino acid changes that involve the creation of two stop codon events. The conserved editing sites identified were 247 accounting for ~36% of all the editing sites identified. This study provides a detailed picture of the Helianthus species’ mitochondrial RNA editing status. We have identified and characterized for the first time, genotype-specific, species-specific, and stress-specific RNA editing events which may be useful as a potential source for stress-responsive studies in the future.

Anti-inflammatory natural products modulate interleukins and their related signaling markers in inflammatory bowel disease:A systematic review

This review aims to identify in vivo studies investigating the potential of plant substances and their natural molecules in managing inflammatory bowel disease(IBD).Specifically,the objective is to examine the impact of these substances on interleukins and other key inflammatory signaling markers.Relevant articles published up to December 2022 were identified through a search of the PubMed,Scopus,Web of Science,and Embase databases.The search used keywords including“inflammatory bowel disease”,“medicinal plants”,“natural molecules”,“anti-inflammatory”,and“ulcerative colitis”,and identified 1,878 potentially relevant articles,of which 89 were included in this review after completion of the selection process.This study provides preclinical data on natural products(NPs)that can potentially treat IBD,including ulcerative colitis.The main actions of these NPs relate to their effects on nuclear factor kappa B(NF-κβ),the Janus kinase(JAK)/signal transducer and activator of transcription(STAT)signaling pathway,the regulation of T helper 17/regulatory T cells balance,and oxidative stress.The ability of these NPs to inhibit intestinal inflammation appears to be dependent on lowering levels of the pro-inflammatory cytokines tumor necrosis factor-alpha(TNF-α),interleukin(IL)-1β,and IL-17,via the Jun N-terminal kinase(JNK)1,NF-κβ-p65,and STAT3 pathways.In addition,NPs were shown to reduce oxidative stress and the severity of ulcerative colitis,as well as increase the activity of antioxidant enzymes.These actions suggest that NPs represent a promising treatment for IBD,and potentially have greater efficacy and safety than current treatments.

Chloroplast immunity: A cornerstone of plant defense

Increasing evidence supports the notion that pattern-recognition-receptor-mediated immunity goes beyond plasma membrane-to-nucleus signaling.With the findings of the pathways linking plasma membrane and chloroplasts and the functions of stromules and perinuclear chloroplast clustering(PCC)in plant defense,chloroplast immunity has emerged as a cornerstone of plant defense and a target of plant pathogens.

A new oxidative pathway of nitric oxide production from oximes in plants

Nitric oxide(NO)is an essential reactive oxygen species and a signal molecule in plants.Although several studies have proposed the occurrence of oxidative NO production,only reductive routes for NO production,such as the nitrate(NO_(3)^(-))-upper-reductase pathway,have been evidenced to date in land plants.However,plants grown axenically with ammonium as the sole source of nitrogen exhibit contents of nitrite and NO3−,evidencing the existence of a metabolic pathway for oxidative production of NO.We hypothesized that oximes,such as indole-3-acetaldoxime(IAOx),a precursor to indole-3-acetic acid,are intermediate oxidation products in NO synthesis.We detected the production of NO from IAOx and other oximes catalyzed by peroxidase(POD)enzyme using both 4-amino-5-methylamino-2′,7′-difluorescein fluorescence and chemiluminescence.Flavins stimulated the reaction,while superoxide dismutase inhibited it.Interestingly,mouse NO synthase can also use IAOx to produce NO at a lower rate than POD.We provided a full mechanism for POD-dependent NO production from IAOx consistent with the experimental data and supported by density functional theory calculations.We showed that the addition of IAOx to extracts from Medicago truncatula increased the in vitro production of NO,while in vivo supplementation of IAOx and other oximes increased the number of lateral roots,as shown for NO donors,and a more than 10-fold increase in IAOx dehydratase expression.Furthermore,we found that in vivo supplementation of IAOx increased NO production in Arabidopsis thaliana wild-type plants,while prx33-34 mutant plants,defective in POD33-34,had reduced production.Our data show that the release of NO by IAOx,as well as its auxinic effect,explain the superroot phenotype.Collectively,our study reveals that plants produce NO utilizing diverse molecules such as oximes,POD,and flavins,which are widely distributed in the plant kingdom,thus introducing a long-awaited oxidative pathway to NO production in plants.This knowledge has essential implications for understanding signaling in biological systems.

用不同蛋白质分析方法鉴定玉米分泌蛋白组的比较研究

玉米根系在生长过程中向根际分泌蛋白质类大分子物质。采用双向聚丙烯酰胺凝胶电泳-质谱技术,一维液相色谱-质谱联用(LC/MS)和Shotgun三种不同鉴定方法对无菌条件收集的玉米根系分泌蛋白进行了分离、分析与鉴定,对3种鉴定方法在分泌蛋白分析中的应用做了详细阐述和比较。结果表明,双向电泳通过银染可以看到200个蛋白质点,但由于蛋白量少,通过质谱无法对玉米根系分泌蛋白进行鉴定;用LC/MS鉴定得到了152个蛋白;用Shotgun技术鉴定得到了2 848个蛋白。LC/MS鉴定得到的蛋白全部出现在用Shotgun技术鉴定得到的2 848个蛋白中,后2种方法的结果可以互相验证。Shotgun技术具有更高的灵敏性,更适合对蛋白质浓度低、干扰物多的植物根分泌蛋白组进行鉴定,能够获得完整可靠的信息。

Overexpression of PGA37/MYB118 and MYB115 promotes vegetative-to-embryonic transition in Arabidopsis

从 non-germline 房间的体的胚胎的形成对更高的植物唯一并且能被操作在许多种类。以前的研究表明包括 WUSCHEL (WUS )/PLANT 生长 ACTIVATOR6 (PGA6 ) ，几 Arabidopsis 基因的 overexpression 纵容繁荣，叶状的 COTYLEDON1 (LEC1 ) ，和 LEC2，能引起 vegetative-to-embryonic 转变或体的胚胎的形成。这里，我们报导那在 Arabidopsis PGA37 基因的一个 gain-of-function 变化，编码 MYB118 抄写因素，导致的 vegetative-to-embryonic 转变，从根将生物的活组织移植于培养基中培养的体的胚胎的形成，和提高的 LEC1 表示水平。两倍变异的分析证明 WUS 没被 PGA37/MYB118 为体的胚胎的正式就职要求。另外， MYB115 的 overexpression， PGA37/MYB118 的一个相当或相同的事物，引起了象 pga37 一样显型。两倍异种没显示出的 myb118 myb115 明显的发展畸形。一起，这些结果建议 PGA37/MYB118 和 MYB115 支持 vegetative-to-embryonic 转变，通过 WUS 的一个发信号的小径独立人士。