Seed quality is a complex trait that is the result of a large variety of developmental processes. The molecular-genetic dissection of these seed processes and their relationship with seed and seedling phenotypes will allow the identification of the regulatory genes and signalling pathways involved and, thus, provide the means to predict and enhance seed quality. Natural variation for seed-quality aspects found in recombinant inbred line (RIL) populations is a great resource to help unravel the complex networks involved in the acquisition of seed quality. Besides extensive phenotyping, RILs can also be profiled by -omics technologies, such as transcriptomics, proteomics and metabolomics in a sophisticated so-called generalized genetical genomics approach. This combined use of physiology, genetics and several -omics technologies, followed by advanced data analysis, allows the construction of regulatory networks involved in the various attributes of seed and seedling quality. This type of analysis of the genetic variation in RIL populations in combination with genome-wide association (GWA) studies will allow a relatively rapid identification of genes that are responsible for quality-related traits of seeds and seedlings. New developments in several -omics technologies, especially the fast-evolving next-generation sequencing techniques, will make a similar system-wide approach more applicable to non-model species in the near future and this will be a huge boost for the potential to breed for seed quality.

Seed dormancy and germination involve the concerted operation of molecular and biochemical programmes. It has become feasible to study these processes in great detail, using the current methods for transcriptome, proteome and metabolome analysis. Yet, the large amounts of data generated by these methods are often dazzling and demand efficient tools for data visualization. We have used the freely available PageMan/MapMan package (http://MapMan.gabipd.org) to visualize transcriptome and metabolome changes in Arabidopsis thaliana seeds during dormancy and germination. Using this package we developed two seed-specific MapMan pathways, which efficiently capture the most important molecular processes in seeds. The results demonstrated the usefulness of the PageMan/MapMan package for seed research.

The performance of cucumber (Cucumis sativus L.) seeds in relation to ovary and ovule position was monitored during seed production. Seeds from three (first, seventh and tenth nodes) fruit positions and three (stylar, intermediate and peduncular) ovule positions were harvested serially during development and characterized with physiological and cellular markers. Seed moisture contents declined to 30%approx. 35 d after pollination (DAP) and remained constant thereafter. At 42 DAP the maximum dry weight was acquired in seeds except those from peduncular segments, whose dry weight accumulation lagged behind. The onset of germinability and desiccation tolerance occurred before the attainment of maximum dry weight, whereas seed performance, as shown by laboratory germination and greenhouse emergence, was largely improved after the completion of seed development. Cell cycle activities (DNA per nucleus and β-tubulin content) ceased by 28 DAP, whereas the degradation of seed chlorophyll continued during the entire maturation period. Seeds from the top fruit and from the peduncular fruit segments were delayed in reaching maximum quality compared with seeds from other positions, and this was correlated with a slower decline of chlorophyll fluorescence.

The desiccation sensitivity of seeds of Inga vera Willd. subsp. affinis, a recalcitrant-seeded tree from Brazil, was analysed, focusing on water relations and cell-cycle aspects, including DNA content and the microtubular cytoskeleton. Seeds were collected at four developmental stages, dried to different moisture contents (MCs), assessed regarding water activity and set to germinate. Samples of fresh (non-dried) developing and mature seeds were used for assessment of DNA content by flow cytometry. Immunohistochemical detection of microtubules (MTs) was done in mature seeds at different MCs. Slight desiccation of immature seeds increased germination, but further drying resulted in a quick decline of germinability. During seed development the desiccation sensitivity decreased slightly, but DNA content of the embryonic axis cells remained constant, suggesting no relation between those two parameters. Embryonic axis cells of mature seeds showed abundant cortical microtubule arrays, which were not affected by mild desiccation, but broken down by further drying. It appeared that, upon rehydration, damaged cells were not able to reconstitute the microtubular cytoskeleton. The failure of germination of Inga vera seeds after drying could not be attributed to cellular damage to DNA synthesis and mitosis, since the radicle protruded by means of cell elongation, without a need for cell division. However, the breakdown of MTs during desiccation, and their subsequent inability to reassemble upon rehydration, may be related to the decreased germination, since MTs are required for cell elongation.

Cell cycle activities are initiated following imbibition of non-dormant seeds. However, it is not known whether cell cycle related events other than DNA replication also remain suppressed in imbibed dormant seeds. The objective of this study was to demonstrate that the transitions between the non-dormant and dormant (both primary and secondary) states are reflected in cell cycle events, such as DNA replication and the changing patterns of the microtubular cytoskeleton involved in the processes of growth and development. The present studies were conducted on seeds from tomato (Lycopersicon esculentum cv. Moneymaker) that possessed primary dormancy or were manipulated to attain secondary dormancy. In addition, a non-dormant abscisic acid (ABA)-deficient mutant, sitw, was used. DNA replication, as measured by flow cytometry, and β-tubulin accumulation, analysed by immunoblotting, were compared with immunocytological studies of active DNA synthesis and microtubular cytoskeleton formation. It is shown that the depth of dormancy, which distinguishes primary and secondary dormancy, may depend on the progression of the cell cycle prior to the induction of dormancy.

The distribution of ATP in tomato seeds was visualized by monitoring the luminescence of frozen sections on top of a gel containing all the components of the luciferase reaction, but excluding ATP. ATP was imaged in germinating tomato seeds at intervals of 3, 6, 17, 24 and 48 h and in seeds with primary or secondary dormancy. ATP was present mainly in the embryo and concentrated in the radicle tip towards the completion of germination. In contrast to germinating seeds, ATP was distributed more evenly in dormant seeds. For germination, the ratio of ATP concentration in the radicle tip versus cotyledons was decisive, rather than the absolute concentration.