Genetic variation for seed dormancy in nature is a typical quantitative trait controlled by multiple loci on which environmental factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a major scientific challenge, which also has relevance for agriculture and ecology. In this study we describe the identification of the DELAY OF GERMINATION 1 (DOG1) gene previously identified as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated by a combination of positional cloning and mutant analysis and is absolutely required for the induction of seed dormancy. DOG1 is a member of a small gene family of unknown molecular function, with five members in Arabidopsis. The functional natural allelic variation present in Arabidopsis is caused by polymorphisms in the cis-regulatory region of the DOG1 gene and results in considerable expression differences between the DOG1 alleles of the accessions analyzed.natural variation ͉ seed germination ͉ abscisic acid ͉ gibberellin ͉ cis variation

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Sugar-induced anthocyanin accumulation has been observed in many plant species. We observed that sucrose (Suc) is the most effective inducer of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana) seedlings. Other sugars and osmotic controls are either less effective or ineffective. Analysis of Suc-induced anthocyanin accumulation in 43 Arabidopsis accessions shows that considerable natural variation exists for this trait. The Cape Verde Islands (Cvi) accession essentially does not respond to Suc, whereas Landsberg erecta is an intermediate responder. The existing Landsberg erecta/Cvi recombinant inbred line population was used in a quantitative trait loci analysis for Suc-induced anthocyanin accumulation (SIAA). A total of four quantitative trait loci for SIAA were identified in this way. The locus with the largest contribution to the trait, SIAA1, was fine mapped and using a candidate gene approach, it was shown that the MYB75/PAP1 gene encodes SIAA1. Genetic complementation studies and analysis of a laboratory-generated knockout mutation in this gene confirmed this conclusion. Suc, in a concentration-dependent way, induces MYB75/PAP1 mRNA accumulation. Moreover, MYB75/PAP1 is essential for the Suc-mediated expression of the dihydroflavonol reductase gene. The SIAA1 locus in Cvi probably is a weak or loss-of-function MYB75/PAP1 allele. The C24 accession similarly shows a very weak response to Suc-induced anthocyanin accumulation encoded by the same locus. Sequence analysis showed that the Cvi and C24 accessions harbor mutations both inside and downstream of the DNA-binding domain of the MYB75/PAP1 protein, which most likely result in loss of activity.

Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available.

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways. recombinant inbred lines | quantitative trait loci analyses | near isogenic lines | transcriptome analyses S eed dormancy is an important adaptive trait that together with flowering time is a primary component of the different life history strategies of plants (1). Seasonal timing of germination might well be a stronger factor conditioning the flowering time of Arabidopsis in the field than variation in the genetic basis for flowering time itself (2). Seed dormancy controls the timing of germination by arresting growth and development, despite the presence of favorable environmental conditions to complete germination. Specific environmental and developmental triggers can overcome this arrest. Environmental factors can act during seed development on the mother plant, during seed storage (i.e., after-ripening; AR) and in mature imbibed seeds. The various aspects of seed dormancy and germination have been extensively reviewed recently (3-6). In addition, it has been shown that there is considerable variation for seed dormancy in nature (7-9). The identification of the genes underlying this natural variation for seed dormancy may help to further understand the mechanisms involved in this process. At the same time, it provides insight into the way nature shaped genetic variability for this trait during adaptive evolution. A common approach to discover genes that control quantitative traits is the use of whole-genome scans to identify quantitative trait loci (QTL). These analyses provide estimates of several genetic parameters that underlie phenotypic variation, including the number of loci, th...

Seed dormancy allows seeds to overcome periods that are unfavourable for seedling established and is therefore important for plant ecology and agriculture. Several processes are known to be involved in the induction of dormancy and in the switch from the dormant to the germinating state. The role of plant hormones, the different tissues and genes involved, including newly identified genes in dormancy and germination are described in this chapter, as well as the use transcriptome, proteome and metabolome analyses to study these mechanistically not well understood processes. of 18 The Arabidopsis BookFinch-Savage and Leubner-Metzger, 2006). Dormancy in Arabidopsis should be described as physiologically non-deep, meaning that embryos released from surrounding structures grow normally, and that dormancy is lost through moist chilling (stratification) or after-ripening (Baskin and Baskin, 2004). However, in addition to the testa and endosperm layer surrounding the embryo, the growth potential of the embryo is also important to overcome the constraint of these structures and thereby affects the dormancy state of a seed (Kucera et al., 2006). Since dormancy is regulated at different developmental phases, in interaction with environmental factors, it is difficult to detect when the genetic and physiological differences are established. This difficulty arises because all dormancy assays are based on seed germination, which is the result of the balance between the degree of dormancy and the capacity of the embryo to overcome dormancy. Mechanistically one can distinguish factors that influence dormancy and germination on the basis of their effect on germination, being either inhibiting or promoting. Mutants that germinate better or faster can represent genes that promote dormancy or those that repress germination. A further distinction can be made by defining the timing and site of action of these factors (during maturation or during imbibition of the seeds, in the embryo, the endosperm or in the testa). The interaction between these factors and the large effect of the environment, both during seed development and during imbibition, make seed dormancy a very complex trait.By definition, germination incorporates those events that commence with the uptake of water by the quiescent dry seed and terminates with the elongation of the embryonic axis (Bewley and Black, 1994). Water uptake by a seed is triphasic; phase I rapid initial uptake; phase II plateau phase and in phase III further increase of water uptake, however, only when germination occurs (Schopfer and Plachy, 1984; Bewley, 1997;Manz et al., 2005). The first signs of germination are the resumption of essential processes, including transcription, translation and DNA repair followed by cell-elongation and eventually at the time of radicle protrusion, resumption of cell division (Barroco et al., 2005;Masubelele et al., 2005). Physically germination is a two-stage process, where testa rupture is followed by endosperm rupture. Following rupture of the micropylar endosper...

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 highresolution 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.