Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue

<p>Abstract</p> <p>Background</p> <p>Micro- and macroarray technologies help acquire thousands of gene expression patterns covering important biological processes during plant ontogeny. Particularly, faithful visualization methods are beneficial for revealing interesting gene expression patterns and functional relationships of coexpressed genes. Such screening helps to gain deeper insights into regulatory behavior and cellular responses, as will be discussed for expression data of developing barley endosperm tissue. For that purpose, high-throughput multidimensional scaling (HiT-MDS), a recent method for similarity-preserving data embedding, is substantially refined and used for (a) assessing the quality and reliability of centroid gene expression patterns, and for (b) derivation of functional relationships of coexpressed genes of endosperm tissue during barley grain development (0–26 days after flowering).</p> <p>Results</p> <p>Temporal expression profiles of 4824 genes at 14 time points are faithfully embedded into two-dimensional displays. Thereby, similar shapes of coexpressed genes get closely grouped by a correlation-based similarity measure. As a main result, by using power transformation of correlation terms, a characteristic cloud of points with bipolar sandglass shape is obtained that is inherently connected to expression patterns of pre-storage, intermediate and storage phase of endosperm development.</p> <p>Conclusion</p> <p>The new HiT-MDS-2 method helps to create global views of expression patterns and to validate centroids obtained from clustering programs. Furthermore, functional gene annotation for developing endosperm barley tissue is successfully mapped to the visualization, making easy localization of major centroids of enriched functional categories possible.</p

Barley Genomics: An Overview

Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge

Cereal Genomics II

During the last decades, major advances have been made in the field of cereal genomics. For instance, high-density genetic maps, physical maps, QTL maps and even draft genome sequence have become available for several cereal species. This has been facilitated by the development of next generation sequencing (NGS) technologies, so that, it is now possible to sequence genomes of hundreds or thousands of accessions of an individual cereal crop. Significant amounts of data generated using these latest NGS technologies created a demand for computational tools to analyse this massive data. These developments related to technology and the tools, along with their applications not only to plant and genome biology but also to breeding have been documented in this volume. The volume, entitled “Cereal Genomics II”, therefore supplements the earlier edited volume “Cereal Genomics” published in 2004. The new volume has updated chapters, from the leading authorities in their fields, on molecular markers, next generation sequencing platform and their use for QTL analysis, domestication studies, functional genomics and molecular breeding. In addition, there are also chapters on computational genomics, whole genome sequencing and comparative genomics of cereals. The book should prove useful to students, teachers and young research workers as a ready reference to the latest information on cereal genomics

Advances in Wheat Genetics: From Genome to Field: Proceedings of the 12th International Wheat Genetics Symposium

plant genetics; plant genomics; agricultur

Mutation breeding, genetic diversity and crop adaptation to climate change

This book presents reviews on the application of the technology for crop improvement towards food and nutrition security, and research status on mutation breeding and associated biotechnologies in both seed crops and vegetatively propagated crops. It also presents perspectives on the significance of next-generation sequencing and bioinformatics in determining the molecular variants underlying mutations and on emerging biotechnologies such as gene editing. Reviews and articles are organized into five sections in the publication: (1) Contribution of Crop Mutant Varieties to Food Security; (2) Mutation Breeding in Crop Improvement and Climate-Change Adaptation; (3) Mutation Induction Techniques for Enhanced Genetic Variation; (4) Mutation Breeding in Vegetatively Propagated and Ornamental Crops; and (5) Induced Genetic Variation for Crop Improvement in the Genomic Era. The contents of this volume present excellent reference material for researchers, students and policy makers involved in the application of induced genetic variation in plants for the maintenance of biodiversity and the acceleration of crop adaptation to climate change to feed a growing global population in the coming years and decades.illustrato

Plant breeding and farmer participation

This book complements the traditional approach to plant breeding by addressing a number of issue specifically related to the participation of farmers in a plant breeding programme, and provides a comprehensive description and assessment of the use of participatory plant breeding in developing countries. It is aimed at plant breeders, social scientists, students and practitioners interested in learning more about its use, with the hope that they all will find a common ground to discuss ways in which plant breeding can be beneficial to all and can contribute to alleviate poverty

InterDrought-V

Drought is weather-related natural disaster, which affects vast regions for months or years and has impact on food production. Drought is related to a deficiency of precipitation over a season or an extended period of time. The most immediate consequence is a fall in crop production, due to inadequate and poorly distributed rainfall. Given the severity of drought, a central challenge for researchers and policy makers is to device technologies that lend greater resilience to agricultural production under this stress. InterDrought conferences, in view of above, serve as a platform for presenting and debating key issues and strategies relevant for improving drought and other stress tolerance in crops. The main mission of the conference is to explore the possibilities of scientific and technological applications in crop improvement. In continuation of earlier InterDrought Conferences held in France (ID-I, 1995), Italy (ID-II, 2005), China (ID-III, 2009) and Australia (ID-IV, 2013), the next InterDrought Conference, InterDrought-V, is being organized in India..

Plant Biodiversity and Genetic Resources

The papers included in this Special Issue address a variety of important aspects of plant biodiversity and genetic resources, including definitions, descriptions, and illustrations of different components and their value for food and nutrition security, breeding, and environmental services. Furthermore, comprehensive information is provided regarding conservation approaches and techniques for plant genetic resources, policy aspects, and results of biological, genetic, morphological, economic, social, and breeding-related research activities. The complexity and vulnerability of (plant) biodiversity and its inherent genetic resources, as an integral part of the contextual ecosystem and the human web of life, are clearly demonstrated in this Special Issue, and for several encountered problems and constraints, possible approaches or solutions are presented to overcome these

Durch umfassende Expressionsstudien zu einem tieferen Verstaendniss einer Pseudomonas aeruginosa Infektion: Von Modellen und realen Infektionsbedingungen zu moeglichen Behandlungsstrategien

Pseudomonas aeruginosa is a threatening opportunistic pathogen that causes severe acute and chronic infections in immunocompromised patients. Global transcriptomic analysis of P. aeruginosa infecting various hosts was carried out. In vivo gene expression was successfully performed by developing accurate, specific technical procedures. The transcriptomic analysis suggested that the main factors expressed by P. aeruginosa upon infection of burn wounds are iron and zinc acquisition as well as alginate production. The bacterial state during burn wound infection was not fully acute, with bacterial cells undergoing serious iron limitation and having a slower metabolism. Iron acquisition and alginate production were shown to be important mechanisms common among the infection conditions studied, namely burn wound, CF patient and mouse tumour model. Two models for P. aeruginosa infection were tested. The tumour mouse model is a promising mammalian infection model whereby P. aeruginosa exhibits anaerobic growth, biofilm formation and expresses the type III secretion system. This model is being further tested in order to assess if it can be used as a chronic infection model. The plant infection model using lettuce leaves may be useful for the study of certain factors such as QS systems, but yielded different results as compared to the real mammalian infections and cannot therefore be used as a reliable infection model. The analysis of the gene expression data from the work presented here thus provided a wealth of new insights and established a foundation for future work directed at the understanding of P. aeruginosa infection and at finding new prevention and treatment strategies.Pseudomonas aeruginosa ist ein bedrohlicher opportunistischer Krankheitserreger, der bei immunsupprimierten Patienten schwerwiegende akute und chronische Infektionen hervorrufen kann. Eine umfassende Transkriptomanalyse von P. aeruginosa bei der Infektion verschiedener Wirte wurde durchgeführt. Die Messungen erfolgten unter in vivo Bedingungen, was die Entwicklung von präzisen und spezifischen technischen Verfahren voraussetzte. Die Transkriptomanalyse deutete darauf hin, dass die Eisen- und Zinkaufnahme und die Alginatproduktion die Hauptfaktoren sind, die von P. aeruginosa während Brandwundeninfektion exprimiert werden. Der bakterielle Zustand während einer Brandwundeninfektion war nicht ganz akut; die Bakterienzellen wurden einem erheblichen Mangel an Eisen ausgesetzt und weisen einen varlangsamten Stoffwechsel auf. Eisenaufnahme und Alginatproduktion erwiesen sich als wichtige Mechanismen, die unter den untersuchten Infektionsbedingungen, nämlich im Fall von Brandwunden, CF-Patienten und Maustumormodellen, verbreitet sind. Es wurden zwei Modelle für die P. aeruginosa Infektion untersucht. Das Tumor-Mausmodell ist ein vielversprechendes Säugetierinfektionsmodell, wobei P. aeruginosa anaerobes Wachstum und Biofilmbildung aufweist und das Typ III-Sekretionssystem exprimiert. Dieses Modell wird weiterhin untersucht, um herauszufinden, ob es als Modell für chronische Infektionen dienen kann. Das Pflanzeninfektionsmodell, wobei Salatblätter eingesetzt werden, könnte von Nutzen sein, um bestimmte Faktoren, wie das QS-System, zu untersuchen, führte jedoch zu anderen Ergebnissen als bei den Säugetierinfektionen und kann daher nicht als verlässliches Infektionsmodell eingesetzt werden. Die Analyse der Genexpressionsdaten aus der hier vorgestellten Arbeit hat eine Fülle neuer Kenntnisse ergeben und Grundlagen für zukünftige Forschungsarbeiten geschaffen, die darauf abzielen, P. aeruginosa-Infektionen zu verstehen und neue Präventions- und Behandlungsstrategien zu finden