Seeds are central to crop production, human nutrition, and food security. A key component of the performance of crop seeds is the complex trait of seed vigour. Crop yield and resource use efficiency depend on successful plant establishment in the field, and it is the vigour of seeds that defines their ability to germinate and establish seedlings rapidly, uniformly, and robustly across diverse environmental conditions. Improving vigour to enhance the critical and yield-defining stage of crop establishment remains a primary objective of the agricultural industry and the seed/breeding companies that support it. Our knowledge of the regulation of seed germination has developed greatly in recent times, yet understanding of the basis of variation in vigour and therefore seed performance during the establishment of crops remains limited. Here we consider seed vigour at an ecophysiological, molecular, and biomechanical level. We discuss how some seed characteristics that serve as adaptive responses to the natural environment are not suitable for agriculture. Past domestication has provided incremental improvements, but further actively directed change is required to produce seeds with the characteristics required both now and in the future. We discuss ways in which basic plant science could be applied to enhance seed performance in crop production.

Seed vigour and crop establishment: extending performance beyond adaptation

Seed dormancy has played a significant role in adaptation and evolution of seed plants. While its biological significance is clear, molecular mechanisms underlying seed dormancy induction, maintenance and alleviation still remain elusive. Intensive efforts have been made to investigate gibberellin and abscisic acid metabolism in seeds, which greatly contributed to the current understanding of seed dormancy mechanisms. Other mechanisms, which might be independent of hormones, or specific to the seed dormancy pathway, are also emerging from genetic analysis of “seed dormancy mutants”. These studies suggest that chromatin remodeling through histone ubiquitination, methylation and acetylation, which could lead to transcription elongation or gene silencing, may play a significant role in seed dormancy regulation. Small interfering RNA and/or long non-coding RNA might be a trigger of epigenetic changes at the seed dormancy or germination loci, such as DELAY OF GERMINATION1. While new mechanisms are emerging from genetic studies of seed dormancy, novel hypotheses are also generated from seed germination study with high throughput gene expression analysis. Recent studies on tissue-specific gene expression in tomato and Arabidopsis seeds, which suggested possible “mechanosensing” in the regulatory mechanisms, advanced our understanding of embryo-endosperm interaction and have potential to re-draw the traditional hypotheses or integrate them into a comprehensive scheme. The progress in basic seed science will enable knowledge translation, another frontier of research to be expanded for food and fuel production.

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Seed dormancy and germination-emerging mechanisms and new hypotheses.

How Do Sugars Regulate Plant Growth and Development? New Insight into the Role of Trehalose-6-Phosphate

Seed germination is a key developmental process that has to be tightly controlled to avoid germination under unfavourable conditions Abscisic acid (ABA) is an essential repressor of seed germination In Arabidopsis, it has been shown that the endosperm, a single cell layer surrounding the embryo, synthesizes and continuously releases ABA towards the embryo The mechanism of ABA transport from the endosperm to the embryo was hitherto unknown Here we show that four AtABCG transporters act in concert to deliver ABA from the endosperm to the embryo: AtABCG25 and AtABCG31 export ABA from the endosperm, whereas AtABCG30 and AtABCG40 import ABA into the embryo Thus, this work establishes that radicle extension and subsequent embryonic growth are suppressed by the coordinated activity of multiple ABA transporters expressed in different tissues

/pdf/abscisic-acid-transporters-cooperate-to-control-seed-t5lhcdjjrd.pdf

Abscisic acid transporters cooperate to control seed germination

Many molecular mechanisms that regulate dormancy have been identified individually in controlled laboratory studies. However, little is known about how the seed employs this complex suite of mechanisms during dormancy cycling in the variable environment of the soil seed bank. Nevertheless, this behaviour is essential to ensure germination takes place in a favourable habitat and climate space, and in the correct season for the resulting plant to complete its life cycle. During their time in the soil seed bank, seeds continually adjust their dormancy status by sensing a range of environmental signals. Those related to slow seasonal change (e.g. temperature) are used for temporal sensing to determine the time of year and depth of dormancy. This alters their sensitivity to signals related to their spatial environment (e.g. light, nitrate, and water potential) that indicate that conditions are suitable for germination, and so trigger the termination of dormancy. We review work on the physiological, molecular, and ecological aspects of seed dormancy in Arabidopsis and interpret it in the context of dormancy cycling in the soil seed bank. This approach has provided new insight into the co-ordination of mechanisms and signalling networks, and the multidimensional sensing that regulates dormancy cycling in a variable environment.

/pdf/seed-dormancy-cycling-and-the-regulation-of-dormancy-efutx70elc.pdf

Seed dormancy cycling and the regulation of dormancy mechanisms to time germination in variable field environments.

Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high-resolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.

/pdf/transcriptional-dynamics-of-two-seed-compartments-with-4w2l3dv1dx.pdf

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination

Protein interactions are fundamental to the molecular processes occurring within an organism and can be utilized in network biology to help organize, simplify, and understand biological complexity. Currently, there are more than 10 publicly available Arabidopsis (Arabidopsis thaliana) protein interaction databases. However, there are limitations with these databases, including different types of interaction evidence, a lack of defined standards for protein identifiers, differing levels of information, and, critically, a lack of integration between them. In this paper, we present an interactive bioinformatics Web tool, ANAP (Arabidopsis Network Analysis Pipeline), which serves to effectively integrate the different data sets and maximize access to available data. ANAP has been developed for Arabidopsis protein interaction integration and network-based study to facilitate functional protein network analysis. ANAP integrates 11 Arabidopsis protein interaction databases, comprising 201,699 unique protein interaction pairs, 15,208 identifiers (including 11,931 The Arabidopsis Information Resource Arabidopsis Genome Initiative codes), 89 interaction detection methods, 73 species that interact with Arabidopsis, and 6,161 references. ANAP can be used as a knowledge base for constructing protein interaction networks based on user input and supports both direct and indirect interaction analysis. It has an intuitive graphical interface allowing easy network visualization and provides extensive detailed evidence for each interaction. In addition, ANAP displays the gene and protein annotation in the generated interactive network with links to The Arabidopsis Information Resource, the AtGenExpress Visualization Tool, the Arabidopsis 1,001 Genomes GBrowse, the Protein Knowledgebase, the Kyoto Encyclopedia of Genes and Genomes, and the Ensembl Genome Browser to significantly aid functional network analysis. The tool is available open access at http://gmdd.shgmo.org/Computational-Biology/ANAP.

Alex Marshall

Papers

Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination

ANAP: an integrated knowledge base for Arabidopsis protein interaction network analysis