Wheat Improvement

This open-access textbook provides a comprehensive, up-to-date guide for students and practitioners wishing to access in a single volume the key disciplines and principles of wheat breeding. Wheat is a cornerstone of food security: it is the most widely grown of any crop and provides 20% of all human calories and protein. The authorship of this book includes world class researchers and breeders whose expertise spans cutting-edge academic science all the way to impacts in farmers’ fields. The book’s themes and authors were selected to provide a didactic work that considers the background to wheat improvement, current mainstream breeding approaches, and translational research and avant garde technologies that enable new breakthroughs in science to impact productivity. While the volume provides an overview for professionals interested in wheat, many of the ideas and methods presented are equally relevant to small grain cereals and crop improvement in general. The book is affordable, and because it is open access, can be readily shared and translated -- in whole or in part -- to university classes, members of breeding teams (from directors to technicians), conference participants, extension agents and farmers. Given the challenges currently faced by academia, industry and national wheat programs to produce higher crop yields --- often with less inputs and under increasingly harsher climates -- this volume is a timely addition to their toolkit

Plant Phenotyping and Phenomics for Plant Breeding

As a consequence of the global climate change, both the reduction on yield potential and the available surface area of cultivated species will compromise the production of food needed for a constant growing population. There is consensus about the significant gap between world food consumption projected for the coming decades and the expected crop yield-improvements, which are estimated to be insufficient to meet the demand. The complexity of this scenario will challenge breeders to develop cultivars that are better adapted to adverse environmental conditions, therefore incorporating a new set of morpho-physiological and physico-chemical traits; a large number of these traits have been found to be linked to heat and drought tolerance. Currently, the only reasonable way to satisfy all these demands is through acquisition of high-dimensional phenotypic data (high-throughput phenotyping), allowing researchers with a holistic comprehension of plant responses, or ‘Phenomics’. Phenomics is still under development. This Research Topic aims to be a contribution to the progress of methodologies and analysis to help understand the performance of a genotype in a given environment

Proteomic study on the starch synthesis and regulation in developing hybrid rice seeds.

Long Xiaohang.Thesis (M.Phil.)--Chinese University of Hong Kong, 2006.Includes bibliographical references (leaves 132-155).Abstracts in English and Chinese.Thesis/Assessment Committee --- p.IStatement from Author --- p.IIAcknowledgements --- p.IIIAbstract --- p.V摘要 --- p.VIITable of Contents --- p.IXList of Tables --- p.XVList of Figures --- p.XVIList of Abbreviations --- p.XVIIIChapter Chapter 1 --- General Introduction and Literature Review --- p.1Chapter 1.1 --- General introduction --- p.1Chapter 1.2 --- Literature review --- p.5Chapter 1.2.1 --- Rice --- p.5Chapter 1.2.1.1 --- Classification of rice --- p.5Chapter 1.2.1.2 --- Rice grain quality --- p.5Chapter 1.2.2 --- Overview of current information on the starch biosynthesis and regulation during seed development --- p.7Chapter 1.2.2.1 --- Starch property --- p.7Chapter 1.2.2.1.1 --- Structure of rice starch granules --- p.7Chapter 1.2.2.1.2 --- Properties of rice starch --- p.7Chapter 1.2.2.2 --- Starch synthesis related proteins --- p.8Chapter 1.2.2.2.1 --- The formation of ADP-glucose through AGPase --- p.10Chapter 1.2.2.2.2 --- The synthesis of starch by starch synthases --- p.10Chapter 1.2.2.2.2.1 --- Amylose biosynthesis --- p.10Chapter 1.2.2.2.2.2 --- Amylopectin biosynthesis --- p.11Chapter 1.2.2.2.3 --- Branching of the glucan chain by starch branching enzymes --- p.12Chapter 1.2.2.2.4 --- The role of debranching enzymes in polymer synthesis --- p.13Chapter 1.2.2.2.5 --- Starch degradation in plastids --- p.13Chapter 1.2.2.2.6 --- Other enzymes involved in starch synthesis pathway --- p.13Chapter 1.2.2.3 --- Starch biosynthesis regulation --- p.14Chapter 1.2.2.3.1 --- Developmental regulation --- p.14Chapter 1.2.2.3.2. --- Diurnal regulation --- p.15Chapter 1.2.2.3.3 --- 3-PGA/Pi regulation --- p.16Chapter 1.2.2.3.4. --- Sugar signaling --- p.17Chapter 1.2.2.3.5. --- Hormonal signaling --- p.18Chapter 1.2.2.3.6 --- Post translational modification regulation --- p.18Chapter 1.2.2.3.6.1 --- Post translational redox modulation --- p.18Chapter 1.2.2.3.6.2 --- Protein phosphorylation --- p.19Chapter 1.2.2.4 --- Rice grain quality improvement by genetic engineering --- p.20Chapter 1.2.2.4.1 --- Cooking and eating quality improvement --- p.20Chapter 1.2.2.4.1.1 --- Manipulation of starch content --- p.20Chapter 1.2.2.4.1.2 --- Manipulation of amylose/ amylopectin ratio --- p.20Chapter 1.2.2.4.2 --- Other targets for manipulating starch quality and quantity --- p.21Chapter 1.2.3 --- Proteomics --- p.23Chapter 1.2.3.1 --- General introduction --- p.23Chapter 1.2.3.2 --- Current technologies of proteomics --- p.25Chapter 1.2.3.2.1 --- Protein separation by 2D or non-2D method --- p.25Chapter 1.2.3.2.2 --- Protein visualization --- p.26Chapter 1.2.3.2.3 --- Computer-assisted image analysis --- p.27Chapter 1.2.3.2.4 --- Protein identification by mass spectrometry --- p.28Chapter 1.2.3.2.5 --- Database search --- p.28Chapter 1.2.3.2.5.1 --- Database searching software --- p.29Chapter 1.2.3.2.5.2 --- Protein sequence database --- p.29Chapter 1.2.3.2.5.3 --- Evaluating database hits --- p.30Chapter 1.2.3.2.6 --- Bioinformatics involved in proteomics --- p.31Chapter 1.2.3.2.7 --- Post translational modification --- p.32Chapter 1.2.3.2.7.1 --- Glycosylation --- p.32Chapter 1.2.3.2.7.1.1 --- N-linked glycosylation --- p.33Chapter 1.2.3.2.7.1.2 --- O-linked glycosylation --- p.33Chapter 1.2.3.2.7.2 --- Phosphorylation --- p.33Chapter 1.2.3.2.7.3 --- Strategies for studying PTMs --- p.34Chapter 1.2.3.2.8 --- Other aspects of proteomics --- p.36Chapter 1.2.3.2.8.1 --- 2D DIGE --- p.36Chapter 1.2.3.2.8.2 --- LC/LC-MS/MS --- p.36Chapter 1.2.3.2.8.2.1 --- MudPIT --- p.36Chapter 1.2.3.2.8.2.2 --- ICAT --- p.37Chapter 1.2.3.3 --- Plant proteomics --- p.37Chapter 1.2.3.3.1 --- Proteome analysis of plant tissues and organs --- p.38Chapter 1.2.3.3.2 --- Plant organelle proteomics --- p.39Chapter 1.2.3.3.3 --- Post translational modifications in plant --- p.41Chapter 1.2.3.4 --- Recent progress in rice proteomics --- p.42Chapter 1.2.3.4.1 --- General introduction of rice proteomics --- p.42Chapter 1.2.3.4.2 --- Rice proteome database construction --- p.43Chapter 1.2.3.4.3 --- Comparative proteomics --- p.43Chapter 1.2.3.4.4 --- Post translational modification study of rice proteome --- p.44Chapter Chapter 2 --- Materials and methods --- p.45Chapter 2.1 --- Materials --- p.45Chapter 2.1.1 --- Plant materials --- p.45Chapter 2.1.2 --- Chemical reagents and commercial kits --- p.46Chapter 2.1.3 --- Instruments --- p.46Chapter 2.1.4 --- Software --- p.46Chapter 2.2 --- Methods --- p.47Chapter 2.2.1 --- Fractionation of amyloplast and amyloplast membrane proteins --- p.47Chapter 2.2.2 --- Marker enzyme assays --- p.47Chapter 2.2.3 --- 2D gel electrophoresis --- p.48Chapter 2.2.4 --- Silver staining of 2D gel --- p.49Chapter 2.2.5 --- In-gel digestion of protein spots --- p.49Chapter 2.2.6 --- Desalination of the digested sample with ZipTip --- p.49Chapter 2.2.7 --- Protein identification by mass spectrometry and database searching --- p.50Chapter 2.2.8 --- Image and data analysis --- p.50Chapter 2.2.9 --- Extraction of starch granule associated proteins --- p.51Chapter 2.2.10 --- Western blot analysis --- p.51Chapter 2.2.11 --- Sample preparation for N terminal sequencing --- p.51Chapter 2.2.12 --- Phosphorylation and glycosylation assays --- p.52Chapter Chapter 3 --- Results --- p.53Chapter 3.1 --- Protein identification by ID and 2D PAGE --- p.53Chapter 3.1.1 --- Isolation and purification of amyloplasts from rice seeds --- p.53Chapter 3.1.2 --- Identification of amyloplast and amyloplast membrane proteins by MS/MS --- p.54Chapter 3.1.2.1 --- Sample preparation --- p.54Chapter 3.1.2.2 --- 2D and ID gel electrophoresis --- p.55Chapter 3.1.2.3 --- Protein identification by MS and MS/MS --- p.56Chapter 3.1.3 --- Functional classification of identified proteins --- p.69Chapter 3.1.3.1 --- Metabolism proteins --- p.71Chapter 3.1.3.2 --- Non starch synthesis metabolism proteins --- p.73Chapter 3.1.3.3 --- Protein destination --- p.73Chapter 3.1.3.4 --- Proteins with other functions --- p.74Chapter 3.1.4 --- Cross-correlation of experimental and calculated Mw of proteins --- p.74Chapter 3.1.5 --- Granule bound starch synthase (GBSS) --- p.75Chapter 3.1.5 --- N-terminal sequencing --- p.77Chapter 3.2 --- Protein profiling --- p.80Chapter 3.2.1 --- Seed collection and stages chosen --- p.80Chapter 3.2.2 --- The proteomic profiles of rice amyloplasts at different developing stages --- p.81Chapter 3.2.4 --- Comparing the proteome of three rice lines --- p.85Chapter 3.2.4.1 --- Spot number analysis --- p.85Chapter 3.2.4.2 --- Functional distribution analysis --- p.86Chapter 3.2.4.3 --- Protein amount analysis --- p.87Chapter 3.2.5 --- Comparison of expression pattern: cluster analysis (SOM) --- p.88Chapter 3.2.5.1 --- Cluster analysis of rice amyloplast proteome --- p.88Chapter 3.2.5.2 --- Three major categories of rice amyloplast proteome expression patterns --- p.91Chapter 3.2.6 --- Scatter plots analysis --- p.94Chapter 3.2.7 --- Comparison of changes in proteins related to starch synthesis --- p.96Chapter 3.2.7.1 --- GBSS --- p.96Chapter 3.2.7.2 --- AGPase --- p.98Chapter 3.2.7.3 --- SSS --- p.98Chapter 3.2.7.4 --- SBE --- p.98Chapter 3.2.7.5 --- SP --- p.98Chapter 3.3 --- Study on protein post translational modifications --- p.102Chapter 3.3.1 --- Post translational modifications that potentially regulate starch synthesis --- p.102Chapter 3.3.2 --- Post translational modifications at different developing stages --- p.104Chapter 3.3.2.1 --- Profiling of post translational modifications of rice amyloplast proteome --- p.104Chapter 3.3.2.2 --- Starch synthesis related proteins --- p.106Chapter 3.3.2.2.1 --- GBSS --- p.106Chapter 3.3.2.2.2 --- SSS --- p.108Chapter Chapter 4 --- Discussion --- p.111Chapter 4.1 --- Methodology --- p.111Chapter 4.1.1 --- Amyloplast isolation --- p.111Chapter 4.1.2 --- Protein extraction from amyloplasts --- p.111Chapter 4.1.3 --- Protein identification by PMF and MS/MS --- p.112Chapter 4.1.4 --- Methods used to study protein expression patterns --- p.113Chapter 4.1.5 --- New methods introduced to study post translational modifications --- p.114Chapter 4.2 --- Characteristics of rice amyloplast proteins --- p.115Chapter 4.2.1 --- Amyloplast proteins associated with starch granules --- p.116Chapter 4.2.2 --- Most proteins in amyloplast proteome contain the transit peptide --- p.116Chapter 4.2.3 --- Multiple isoforms of starch synthesis related proteins --- p.117Chapter 4.2.3.1 --- Multiple spots of GBSS --- p.118Chapter 4.2.4 --- Expression patterns of amyloplast proteome --- p.120Chapter 4.2.5 --- Post translational modifications potentially regulate starch synthesis --- p.122Chapter 4.3 --- Other characteristic aspects of amyloplast proteome --- p.123Chapter 4.3.1 --- Comparison between the rice and wheat amyloplast proteomes --- p.123Chapter 4.3.2 --- Proteomic comparisons among the three rice lines --- p.124Chapter 4.3.3 --- Comparison of starch synthesis enzymes at protein and transcript levels --- p.124Chapter 4.3.4 --- Comparison of the starch synthesis related proteins among the three rice lines --- p.126Chapter 4.4 --- Limitations of proteomic approach in directly answering the question on how to improve eating and cooling quality --- p.126Chapter Chapter 5 --- Conclusion --- p.128Chapter Chapter 6 --- Future perspectives --- p.130References --- p.13

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

Abstract Book: Scales of Social, Environmental & Cultural Change in Past Societies

The interplay of environment, social relations, material culture, population dynamics, and human perception are the key factors of socio-environmental changes. The exploration of processes and parameters of societal change enable further exploration of transformations of human-environmental interactions. These processes and parameters are detectable in the development of, for example, settlement systems, material culture, or ritual sites, which link different socio-environmental components. Humans and environments deeply shaped each other, creating diverse social, environmental, and cultural constellations. On the one hand, examining the roots of social, environmental, and cultural phenomena and processes, which substantially marked past human development, can lead to a deeper understanding of the development of societies. On the other hand, a focus on transformation patterns within momentous developments of past societies opens up the possibility of identifying substantial and enduring re-organisation of socio-environmental interaction patterns