Plant genetic reseources: effective utilization

Characterizing better understanding the genome organization and differentiating identity of genotypes based on their morphology and genome characteristics are vital determinants in their commercialization, management of germplasm repositories, and genetic conservation. Morphoagronomic characterization of plants is not always feasible or sometimes labor intensive. Employing chloroplast, mitochondrial, and nuclear genome diversity using molecular biology tools will enhance the effectiveness and efficiency of revealing identity differences between genotypes. Using organelle and nuclear genome diversity can also answer a broad range of genetic, evolutionary relationships, and ecological questions

Virus-Induced Gene Silencing, a Post Transcriptional Gene Silencing Method

Virus-induced gene silencing (VIGS) is one of the reverse genetics tools for analysis of gene function that uses viral vectors carrying a target gene fragment to produce dsRNA which trigger RNA-mediated gene silencing. There are a number of viruses which have been modified to silence the gene of interest effectively with a sequence-specific manner. Therefore, different types of methodologies have been advanced and modified for VIGS approach. Virus-derived inoculations are performed on host plants using different methods such as agro-infiltration and in vitro transcriptions. VIGS has many advantages compared to other loss-of-gene function approaches. The approach provides the generation of rapid phenotype and no need for plant transformation. The cost of VIGS experiment is relatively low, and large-scale analysis of screening studies can be achieved by the VIGS. However, there are still limitations of VIGS to be overcome. Nowadays, many virus-derived vectors are optimized to silence more than one host plant such as TRV-derived viral vectors which are used for Arabidopsis and Nicothiana benthamiana. By development of viral silencing systems monocot plants can also be targeted as silencing host in addition to dicotyledonous plants. For instance, Barley stripe mosaic virus (BSMV)-mediated VIGS allows silencing of barley and wheat genes. Here we summarize current protocols and recent modified viral systems to lead silencing of genes in different host species

Turfgrass species response exposed to increasing rates of glyphosate application

To investigate the response of nine turfgrass species exposed to increasing rates of glyphosate application, the dry matter production, visual leaf injury symptoms (e.g., chlorosis and necrosis) and the concentrations of shikimate and mineral nutrients were determined in shoots. The rates of foliar glyphosate application were 0%, 5% (1.58 mM), and 20% (6.32mM) of the recommended application rate for weed control. In general, there was a negative and weak correlation between the intensity of visual injury and relative decreases in shoot dry matter production caused by glyphosate application. The decreases in shoot dry matter production and the severity of leaf damage pronounced by increasing glyphosate rate showed a substantial variation among the turfgrass species. Of the turfgrass species tested, Festuca arundinacea ‘Falcon’ and Buchloe dactyloides ‘Bowie’were selected as the most tolerant and sensitive species to applied sublethal rates of glyphosate as judged from visual injury ratings, respectively. At the highest glyphosate rate, shoot dryweightwas decreased by 4-fold in Bowie and only 1.6-fold in Falcon. When glyphosatewas not applied, shoot shikimate concentration of all species was very low and below 2.8mol g−1 FW (fresh weight). Glyphosate applications resulted in increases in shoot shikimate concentration with substantial variations among species. At 6.32mM glyphosate treatment, shikimate concentration ranged between 156.1mol g−1 (F. rubra, Ambrose) and 16.5mol g−1 FW (F. rubra, Cindy Lou). However, the highly sensitive and the tolerant genotypes were not different in shoot shikimate concentrations. Even, in the case of some genotypes, high glyphosate tolerance is accompanied by higher shoot concentrations of shikimate. Depending on the turfgrass species and mineral nutrients tested, increasing glyphosate application either did not affect or reduced mineral nutrient concentrations. In the case of decreases in shoot concentration of mineral nutrients, the decreases in Ca, Mg, Mn and Fe were most distinct. The results obtained indicate existence of a large genetic variation in tolerance to glyphosate toxicity among the turfgrass species. This differential variation in tolerance to glyphosate could not be explained by the changes in shoot concentrations of shikimate and mineral nutrients

Techniques to Study Autophagy in Plants

Autophagy (or self eating), a cellular recycling mechanism, became the center of interest and subject of intensive research in recent years. Development of new molecular techniques allowed the study of this biological phenomenon in various model organisms ranging from yeast to plants and mammals. Accumulating data provide evidence that autophagy is involved in a spectrum of biological mechanisms including plant growth, development, response to stress, and defense against pathogens. In this review, we briefly summarize general and plant-related autophagy studies, and explain techniques commonly used to study autophagy. We also try to extrapolate how autophagy techniques used in other organisms may be adapted to plant studies

Bioconjugated nanomaterials for monitoring food contamination

Maintaining food safety and hygiene standards is top priority and challenge for farmers, food industries, governments and food technologists working in the food supply chain. Pesticides, toxins, veterinary drug residues, foodborne pathogens and many other harmful chemicals that may be present in a vast array of food products, due to various stages of their production like packaging and transport, constitute a global health problem that requires powerful and innovative technologies allowing constant and accurate detection of food products from production to consumption. Recent progress in generation of specific synthetic oligonucleotides against food contaminants has provided a new insight into the current sensor technologies, where these functional synthetic oligonucleotides, so-called aptamers, have been successfully combined with nanomaterials for rapid and cost-effective detection of several substances related to the food contamination, such as antibiotics, mycotoxins, heavy metals, carcinogenic dyes, pesticides, pathogens and other plastic products used for food packaging. Unique characteristics of aptamers over antibodies, such as in vitro selection, chemical and thermal stability, small size and ease of labeling have laid the solid foundation for exploring aptamers further in multiplexed food monitoring systems. In this chapter, we reviewed the application of aptamer-conjugated nanomaterials in food safety surveillance as well as the conventional techniques used for food safety monitoring in order to provide a comprehensive and comparative approach

A short overview on the latest updates on cereal crop plant genome sequencing with an emphasis on cereal crops and their wild relatives

The advent of next generation sequencing has brought a revolution in the sequencing and availability of whole genome data for numerous plant species. However the genome sequencing of major staple food crops has been noticeably obscure and till relatively recently majorly unaccomplished. The obstacles for sequencing of genomes of the Poaceae grasses including sugarcane and the Triticeae wheat, barley and rye has been largely ascribed to the complex polyploid nature of their genomes, having undergone numerous evolutionary changes duplications and additions resulting in their huge modern genomes of today. Undertaking their sequencing has been a daunting task however due to the sequencing of wild grass relatives such as Brachypodium and Aegilops has been an encouraging step providing an essential framework and reference for deciphering the complex genomes particularly Triticum aestivum. This paper discusses the major challenges involved, the approaches taken and the up to date accomplished tasks for sequencing a few of the major large grass crop genome

Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue) species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate

Review of Current Methodological Approaches for Characterizing MicroRNAs in Plants

Advances in molecular biology have led to some surprising discoveries. One of these includes the complexities of RNA and its role in gene expression. One particular class of RNA called microRNA (miRNA) is the focus of this paper. We will first briefly look at some of the characteristics and biogenesis of miRNA in plant systems. The remainder of the paper will go into details of three different approaches used to identify and study miRNA. These include two reverse genetics approaches: computation (bioinformatics) and experimental, and one rare forward genetics approach. We also will summarize how to measure and quantify miRNAs, and how to detect their possible targets in plants. Strengths and weaknesses of each methodological approach are discussed

Plant Small Non-coding RNAs and Their Roles in Biotic Stresses

Non-coding RNAs (ncRNAs) have emerged as critical components of gene regulatory networks across a plethora of plant species. In particular, the 20–30 nucleotide small ncRNAs (sRNAs) play important roles in mediating both developmental processes and responses to biotic stresses. Based on variation in their biogenesis pathways, a number of different sRNA classes have been identified, and their specific functions have begun to be characterized. Here, we review the current knowledge of the biogenesis of the primary sRNA classes, microRNA (miRNA) and small nuclear RNA (snRNA), and their respective secondary classes, and discuss the roles of sRNAs in plant–pathogen interactions. sRNA mobility between species is also discussed along with potential applications of sRNA–plant–pathogen interactions in crop improvement technologies