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Seeds are the prime source of food in the world, not only from a nutritional point of view but also as the basis of crop production. A key requirement for farmers is vigorous and fast-germinating seed to guarantee a uniform crop of high yield. This is quite opposite to the natural behaviour of seeds which employ dormancy to spread the risk of premature death over time. This chapter addresses the genetic and molecular mechanisms of dormancy and germination. It highlights some of the most important regulatory principles, particularly in relation to the inherent complexity of the seed as a biological system, entailing numerous layers of organisation and regulation, from cells to the environment.

Seeds show incredible variation in their attributes, such as dormancy, longevity and, hence, quality. It is of eminent importance to study this variation across and within species and higher taxa in order to ensure successful agricultural production and preservation of biodiversity, not least in times of a changing climate.

The temporal control or timing of the life cycle of annual plants is presumed to provide adaptive strategies to escape harsh environments for survival and reproduction. This is mainly determined by the timing of germination, which is controlled by the level of seed dormancy, and of flowering initiation. However, the environmental factors driving the evolution of plant life cycles remain largely unknown. To address this question we have analysed nine quantitative life history traits, in a native regional collection of 300 wild accessions of Arabidopsis thaliana. Seed dormancy and flowering time were negatively correlated, indicating that these traits have coevolved. In addition, environmental–phenotypic analyses detected strong altitudinal and climatic clines for most life history traits. Overall, accessions showing life cycles with early flowering, small seeds, high seed dormancy and slow germination rate were associated with locations exposed to high temperature, low summer precipitation and high radiation. Furthermore, we analysed the expression level of the positive regulator of seed dormancy DELAY OF GERMINATION 1 (DOG1), finding similar but weaker altitudinal and climatic patterns than seed dormancy. Therefore, DOG1 regulatory mutations are likely to provide a quantitative molecular mechanism for the adaptation of A. thaliana life cycle to altitude and climate.

The temporal control or timing of the life cycle of annual plants is presumed to provide adaptive strategies to escape harsh environments for survival and reproduction. This is mainly determined by the timing of germination, which is controlled by the level of seed dormancy, and of flowering initiation. However, the environmental factors driving the evolution of plant life cycles remain largely unknown. To address this question we have analysed nine quantitative life history traits, in a native regional collection of 300 wild accessions of Arabidopsis thaliana. Seed dormancy and flowering time were negatively correlated, indicating that these traits have coevolved. In addition, environmental-phenotypic analyses detected strong altitudinal and climatic clines for most life history traits. Overall, accessions showing life cycles with early flowering, small seeds, high seed dormancy and slow germination rate were associated with locations exposed to high temperature, low summer precipitation and high radiation. Furthermore, we analysed the expression level of the positive regulator of seed dormancy DELAY OF GERMINATION 1 (DOG1), finding similar but weaker altitudinal and climatic patterns than seed dormancy. Therefore, DOG1 regulatory mutations are likely to provide a quantitative molecular mechanism for the adaptation of A. thaliana life cycle to altitude and climate.

Seed desiccation tolerance (DT) and longevity are necessary for better dissemination of plant species and establishment of soil seed bank. They are acquired by orthodox seeds during the maturation phase of development and lost upon germination. DT can be re-induced in germinated seeds by an osmotic and/or abscisic acid treatment. However, there is no information on how these treatments affect seed longevity. Germinated Sesbania virgata seeds were used as a model system to investigate the effects of an osmotic treatment to re-establish DT on seed longevity. Longevity of germinated S. virgata seeds treated and non-treated by an osmoticum was analysed after storage or artificial ageing. The radicle is the most sensitive organ, the cotyledons are the most resistant, and the ability to produce lateral roots is the key for whole seed survival. Germinated S. virgata seeds with 1mm protruded radicle tolerate desiccation and storage for up to three months without significant losses in viability. An osmotic treatment can improve DT in these seeds, but not longevity. Germinated S. virgata seeds are a good model to study DT uncoupled from longevity. Further studies are necessary to unveil the molecular mechanisms involved in both DT and longevity.

A complex phenotype such as seed germination is the result of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with "omics" analysis can help to disentangle the genetic basis of such quantitative traits. This so-called genetical genomics approach can effectively capture both genetic and epistatic interactions. However, to understand how the environment interacts with genomic-encoded information, a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup, this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated quantitative trait loci mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. In addition, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis (Arabidopsis thaliana) seeds. In the metabolome, many changes were observed that were under both environmental and genetic controls and their interaction. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics, which requires a broad understanding of both plasticity and dynamic regulation.