We provide a comprehensive expression map of the different genes (TIR1/AFBs, ARFs and Aux/IAAs) involved in the signalling pathway regulating gene transcription in response to auxin in the shoot apical meristem (SAM).We demonstrate a relatively simple structure of this pathway using a high-throughput yeast two-hybrid approach to obtain the Aux/IAA-ARF full interactome.The topology of the signalling network was used to construct a model for auxin signalling and to predict a role for the spatial regulation of auxin signalling in patterning of the SAM.We used a new sensor to monitor the input in the auxin signalling pathway and to confirm the model prediction, thus demonstrating that auxin signalling is essential to create robust patterns at the SAM.

Early endosperm development involves a series of rapid nuclear divisions in the absence of cytokinesis; thus, many endosperm mutants reveal genes whose functions are essential for mitosis. This work finds that the endosperm of Arabidopsis thaliana endosperm-defective1 (ede1) mutants never cellularizes, contains a reduced number of enlarged polyploid nuclei, and features an aberrant microtubule cytoskeleton, where the specialized radial microtubule systems and cytokinetic phragmoplasts are absent. Early embryo development is substantially normal, although occasional cytokinesis defects are observed. The EDE1 gene was cloned using a map-based approach and represents the pioneer member of a conserved plant-specific family of genes of previously unknown function. EDE1 is expressed in the endosperm and embryo of developing seeds, and its expression is tightly regulated during cell cycle progression. EDE1 protein accumulates in nuclear caps in premitotic cells, colocalizes along microtubules of the spindle and phragmoplast, and binds microtubules in vitro. We conclude that EDE1 is a novel plant-specific microtubule-associated protein essential for microtubule function during the mitotic and cytokinetic stages that generate the Arabidopsis endosperm and embryo.

Many biologically and economically important traits in plants and animals are quantitative/multifactorial, being controlled by several quantitative trait loci (QTL). QTL are dif®cult to locate accurately by conventional methods using molecular markers in segregating populations, particularly for traits of low heritability or for QTL with small effects. In order to resolve this, large (often unrealistically large) populations are required. In this paper we present an alternative approach using a specially developed resource of lines that facilitate QTL location ®rst to a particular chromosome, then to successively smaller regions within a chromosome (`0.5 cM) by means of simple comparisons among a few lines. This resource consists of`Stepped Aligned Inbred Recombinant Strains' (STAIRS) plus single whole Chromosome Substitution Strains (CSSs). We explain the analytical power of STAIRS and illustrate their construction and use with Arabidopsis thaliana, although the principles could be applied to many organisms. We were able to locate¯owering QTL at the top of chromosome 3 known to contain several potential candidate genes.

Transcription-related chromatin decondensation has been studied in mammals for clusters of structurally and/or functionally related genes that are coordinately regulated (e.g., the homeobox locus in mice and the major histocompatability complex locus in humans). Plant genes have generally been considered to be randomly distributed throughout the genome, although several examples of metabolic gene clusters for synthesis of plant defense compounds have recently been discovered. Clustering provides for genetic linkage of genes that together confer a selective advantage and may also facilitate coordinate regulation of gene expression by enabling localized changes in chromatin structure. Here, we use cytological methods to investigate components of a metabolic gene cluster for synthesis of developmentally regulated defense compounds (avenacins) in diploid oat (Avena strigosa). Our experiments reveal that expression of the avenacin gene cluster is associated with cell type-specific chromatin decondensation, providing new insights into regulation of gene clusters in plants. Importantly, chromatin decondensation could be visualized not only at the large-scale level but down to the single gene level. We further show that the avenacin and sterol pathways are likely to be inversely regulated at the level of transcription.