A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE

The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE - CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly available, to improve the research and development of cassava by making a wealth of genetics and genomics data available through open, common, and worldwide forum for all individuals interested in the field. AVAILABILITY: The database is available for free at http://www.tnaugenomics.com/biogenbase/casava.php.     

Progress and challenges for abiotic stress proteomics of crop plants

Plants are continually challenged to recognize and respond to adverse changes in their environment to avoid detrimental effects on growth and development. Understanding the mechanisms that crop plants employ to resist and tolerate abiotic stress is of considerable interest for designing agriculture breeding strategies to ensure sustainable productivity. The application of proteomics technologies to advance our knowledge in crop plant abiotic stress tolerance has increased dramatically in the past few years as evidenced by the large amount of publications in this area. This is attributed to advances in various technology platforms associated with MS‐based techniques as well as the accessibility of proteomics units to a wider plant research community. This review summarizes the work which has been reported for major crop plants and evaluates the findings in context of the approaches that are widely employed with the aim to encourage broadening the strategies used to increase coverage of the proteome     

植物microRNA的生物信息学预测与分析

microRNAs(miRNAs)是一类广泛存在于真核生物中调控基因转录后表达的非编码小分子RNA。大量研究表明,miRNA在调节多种生物途径中起着重要的作用,采用生物信息学方法预测与分析miRNA是当前发现和鉴定植物miRNA的重要策略之一。研究内容总结了生物信息学预测植物miRNA及其靶基因的方法策略,阐述了生物信息学在植物miRNA研究中的重要作用,为今后的研究奠定了基础。     

植物法呢基焦磷酸合成酶的生物信息学分析

采用生物信息学的方法和工具对已在GenBank上注册的番茄(Lycopersicon esculentum)、橡胶(Hevea brasiliensis)、香蕉(Musa acuminata)、苹果(Malus×domestica)、向日葵(Helianthus annuus)、葡萄(Vitis vinifera)等的法呢基焦磷酸合成酶的核苷酸及氨基酸序列进行分析,并对其组成成分、转运肽、跨膜拓朴结构域、疏水性/亲水性、蛋白质二级及三级结构、分子系统进化关系等进行预测和推断。结果表明:该酶基因的全长包括5’、3’非翻译区和一个开放阅读框;其编码的蛋白是一个无跨膜结构域、不具转运肽的亲水性蛋白,包括5个保守的结构motif,其中两个是富含天冬氨酸(Asp)的motif,α-螺旋和不规则盘绕是蛋白质二级结构最大量的结构元件,β-转角和延伸链散布于整个蛋白质中,蛋白质的功能域在空间布局上是由α-螺旋围绕形成的中间具一个“大空穴”的立体结构,“大空穴”的表面藏有五个功能保守motif,其中两个Asp-motif位于“空穴”的内壁。     

Modification of flavonoid biosynthesis in crop plants

Flavonoids comprise the most common group of polyphenolic plant secondary metabolites. In plants, flavonoids play an important role in biological processes. Beside their function as pigments in flowers and fruits, to attract pollinators and seed dispersers, flavonoids are involved in UV-scavenging, fertility and disease resistance. Since they are present in a wide range of fruits and vegetables, flavonoids form an integral part of the human diet. Currently there is broad interest in the effects of dietary polyphenols on human health. In addition to the potent antioxidant activity of many of these compounds in vitro, an inverse correlation between the intake of certain polyphenols and the risk of cardiovascular disease, cancer and other age related diseases has been observed in epidemiological studies. The potential nutritional effects of these molecules make them an attractive target for genetic engineering strategies aimed at producing plants with increased nutritional value. This review describes the current knowledge of the molecular regulation of the flavonoid pathway and the state of the art with respect to metabolic engineering of this pathway in crop plants.     

Cross-fertilizing weed science and plant invasion science to improve efficient management: A European challenge

Both weed science and plant invasion science deal with noxious plants. Yet, they have historically developed as two distinct research areas in Europe, with different target species, approaches and management aims, as well as with diverging institutions and researchers involved. We argue that the strengths of these two disciplines can be highly complementary in implementing management strategies and outline how synergies were created in an international, multidisciplinary project to develop efficient and sustainable management of common ragweed, Ambrosia artemisiifolia. Because this species has severe impacts on human health and is also a crop weed in large parts of Europe, common ragweed is one of the economically most important plant invaders in Europe. Our multidisciplinary approach combining expertise from weed science and plant invasion science allowed us (i) to develop a comprehensive plant demographic model to evaluate and compare management tools, such as optimal cutting regimes and biological control for different regions and habitat types, and (ii) to assess benefits and risks of biological control. It further (iii) showed ways to reconcile different stakeholder interests and management objectives (health versus crop yield), and (iv) led to an economic model to assess invader impact across actors and domains, and effectiveness of control measures. (v) It also led to design and implement management strategies in collaboration with the various stakeholder groups affected by noxious weeds, created training opportunities for early stage researchers in the sustainable management of noxious plants, and actively promoted improved decision making regarding the use of exotic biocontrol agents at the national and European level. We critically discuss our achievements and limitations, and list and discuss other potential Old World (Afro-Eurasian) target species that could benefit from applying such an integrative approach, as typical invasive alien plants are increasingly reported from crop fields and native crop weeds are invading adjacent non-crop land, thereby forming new source populations for further spread.     

Genomics,Proteomics & Bioinformatics

正Aims and Scope The goals of Genomics,ProteomicsBioinformatics(GPB)are to disseminate new frontiers of its focused research fields,to publish high-quality discoveries in a fast-pace,and to promote open access and prompt online publication for efficient publishing.     

Genomics,Proteomics & Bioinformatics

正Aims and Scope The goals of Genomics,ProteomicsBioinformwtics(GPB)are to disseminate new frontiers of its focused research fields,to publish high-quality discoveries in a fast-pace,and to promote open access and prompt online publication for efficient publishing.     

Genomics,Proteomics & Bioinformatics

正Aims and Scope The goals of Genomics,ProteomicsBioinformatics(GPB)are to disseminate new frontiers of its focused research fields,to publish high-quality discoveries in a fast-pace,and to promote open access and prompt online publication for efficient publishing.     

Interactions between plant nutrients,water and carbon dioxide as factors limiting crop yields

Biomass production of annual crops is often directly proportional to the amounts of radiation intercepted, water transpired and nutrients taken up. In many places the amount of rainfall during the period of rapid crop growth is less than the potential rate of evaporation, so that depletion of stored soil water is commonplace. The rate of mineralization of nitrogen (N) from organic matter and the processes of nutrient loss are closely related to the availability of soil water. Results from Kenya indicate the rapid changes in nitrate availability following rain.<br>Nutrient supply has a large effect on the quantity of radiation intercepted and hence, biomass production. There is considerable scope for encouraging canopy expansion to conserve water by reducing evaporation from the soil surface in environments where it is frequently rewetted, and where the unsaturated hydraulic conductivity of the soil is sufficient to supply water at the energy limited rate (e.g. northern Syria). In regions with high evaporative demand and coarse-textured soils (e.g. Niger), transpiration may be increased by management techniques that reduce drainage.<br>Increases in atmospheric [CO₂] are likely to have only a small impact on crop yields when allowance is made for the interacting effects of temperature, and water and nutrient supply. <br>     

Opinion piece: genomics and crop plant science in Europe

Recent report reviews and funding initiatives in the field of plant genomic research are considered in the context of their translation into practical and economic value via plant breeding. It is concluded that there is a deficit in investment and that a change in working styles towards knowledge sharing and connectivity is required.     

A new mechanism in plant engineering: The potential roles of microRNAs in molecular breeding for crop improvement

MicroRNAs (miRNAs) are small, endogenous, noncoding RNAs that negatively modulate the expression of genes by inhibiting translation or by promoting the degradation of target mRNAs. miRNAs are now known to have greatly expanded roles in a variety of plant developmental processes, in signal transduction, and in the response to environmental stress and pathogen invasion. Because of their ability to inactivate either specific genes or entire gene families, artificial miRNAs function as dominant suppressors of gene activity when brought into a plant. Consequently, miRNA-based manipulations have emerged as promising new approaches for the improvement of crops. This includes the development of breeding strategies and the genetic modification of agronomic traits. Herein, we highlight new findings regarding the roles of miRNAs in plant traits, and describe the current miRNA-based plant engineering approaches. Finally, we consider the feasibility of modulating current approaches to address future challenges such as breeding programs to increase crop yield.     

Transgenic Plant Monitor (TPM): a relational database for the management and analysis of information in plant tissue culture and transformation laboratories

Increased public concern and strict statutory regulations relating tothe generation and exploitation of genetically modified organisms, make itimperative to track accurately individual plants through DNA transformationprogrammes. The ability to rapidly retrieve information associated withspecifictransgenic events and to provide accurate reports on demand is an increasinglyimportant feature for public research laboratories. Transgenic Plant Monitor(TPM) has been developed as a database structured to allow efficient recording,monitoring and analysis of the extensive and complex data generated in planttissue culture and transformation experiments. TPM is built upon the widelyavailable Microsoft Access database engine and can be readily adoptedand/or adapted by other users. The key features and the utility of TPM as aresearch tool are discussed in this article.     

Genomics,Proteomics & Bioinformatics Volume 12 2014 CONTENTS

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Arabidopsis cryptochrome and Quantum Biology: new insights for plant science and crop improvement

Journal of Plant Biochemistry and Biotechnology - Arabidopsis is the plant species in which Cryptochrome, the first known flavin-type blue light receptor, was identified after over...