Detlef Weigel

..We advocate here a 1001 Genomes project for Arabidopsis thaliana, the workhorse of plant genetics, which will provide an enormous boost for plant research with a modest financial investment...

..The mysterious agent is not a protein but rather a microRNA that is transcribed at this transition point...

..We present a model in which the decision whether stamens or petals develop is based on the balance between AP2 and AG activities, rather than the two being mutually exclusive...

..This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth...

..Furthermore, our results suggest that the DCL1 is not only involved in miRNA action but also contributes to silencing of a subset of transposons, apparently through an effect on DNA methylation...

..One strategy to increase the power of precisely localizing small effect QTL, is the use of an intercross approach before inbreeding to produce Advanced Intercross RILs (AI-RILs)...

..A complex of FT and FD proteins in turn can activate floral identity genes such as APETALA1 (AP1)...

..Our pipeline for aligning reads and predicting SNPs and indels, SHORE, is available for download at http://1001genomes.org...

..While this finding parallels results obtained for maize, in contrast to maize much of the variation in flowering time in A. thaliana appears to be due to large-effect alleles...

..The effects of both miR156-targeted SPL genes and CYP78A5 on organ size are correlated with changes in plastochron length, suggesting a potential compensatory mechanism that links the rate at which leaves are produced to final leaf size...

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..Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage...

..We propose that miR319-controlled TCP transcription factors coordinate two sequential processes in leaf development: leaf growth, which they negatively regulate, and leaf senescence, which they positively regulate...

..Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations...

..More broadly, we find that the foldback diverges less rapidly than the remainder of the primary transcript. To understand the molecular evolution of miRNA genes, investigations at different levels of phylogenetic divergence are required...

..Our results suggest that natural variation in miRNA biogenesis resulting from cis mutations is a common contributor to phenotypic variation in plants...

..The Bur-0 IIL1 defect thus presents a genetically tractable model for triplet repeat expansions and their variability in natural populations...

..This finding unifies the view of plant miRNA action...

..Together, our findings reveal that functional specialization of miR159 and miR319 is achieved through both expression and sequence differences...

..MIGS can be reliably used for the knockdown of a single gene or of multiple unrelated genes. In addition, we show that MIGS can be applied to other species by co-expression of miR173...

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..Finally, in contrast to Drosophila, there is a clearly positive relationship between interspecific divergence and intraspecific polymorphisms...

..Demonstrated benefits include access to polymorphisms that cannot be identified by alignments against the reference alone. Download GenomeMapper at http://1001genomes.org...

..Our work provides insights into how tandem arrays, which are particularly prone to frequent, complex rearrangements, can produce genetic novelty...

..Our ability to engineer de novo a functional minimal miRNA precursor highlights that we have discovered several elements both necessary and sufficient for accurate miRNA processing...

..Finally, we show that PAN expression persists in ag mutant flowers, suggesting that PAN and AG are engaged in a negative-feedback loop, which might be mediated by the stem-cell-inducing transcription factor WUSCHEL (WUS)...

..thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations...

..Here, we focus on the idea of distinct small RNA-target transcript pairs as nodes within biological networks, and review progress toward understanding the role of small RNA-target nodes in the context of auxin signaling...

..However, genomic resources for studying this important model were not previously widely available...

..We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light-induced mutagenesis...

..Single-end RAD-seq has proven to provide a large number of informative genetic markers in reference as well as non-reference organisms...

..The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution...

..Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions...

..Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process...

..Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html...

..Taken together, our results uncover dual roles in splicing and miRNA processing that distinguish SE and the cap-binding complex from specialized miRNA processing factors such as DCL1 and HYL1...

..In one mapping cross, we observed sex ratio and male phenotype deviations and propose an atypical mode of genetic sex inheritance as its basis...

..We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits...

..In the near future, all these studies will be greatly empowered by complete genome sequences not only for all members of this relatively small genus, but also for many different individuals within each species...

..Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology...

..rubella is likely to be an old S-locus haplotype that only very recently became fixed when C. rubella split off from its SI ancestor, Capsella grandiflora...

..A recently introduced approach is the use of artificial microRNAs (amiRNAs). Here, we review various strategies for small RNA-based gene silencing, and describe in detail the design and application of amiRNAs in many plant species...

..Artificial miRNAs (amiRNAs)-designed to target one or several genes of interest-provide a new and highly specific approach for effective post-transcriptional gene silencing (PTGS) in plants...

..Subsequent stabilization through coevolution with initially fortuitous targets may lead to fixation of a small subset of these proto-miRNA genes...

..Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host-pathogen conflict might cause the evolution of gene flow barriers in plants...

..One challenging aspect of genotyping and association mapping projects is often the identification of markers that are informative between groups of individuals and to convert these into genotyping assays...

..The design principles for amiRNAs have been generalized and integrated into a Web-based tool (http://wmd.weigelworld.org)...

..Here we provide an overview about generation and action of miRNAs and other small RNAs, and their contribution to an important developmental process in plants, flower formation...

..Since opsin variability parallels the extreme male colour polymorphism within guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species...

..We report that the DNA binding domain of LEAFY, although largely conserved, has diverged in activity. On the contrary, other, more rapidly evolving portions of the protein have few effects on LEAFY activity...

..This response has a genetic basis that is distinct from the known genetic pathways of floral transition, and appears to correlate with changes in RNA processing...

..We show that tasiRNAs can be produced from heterologous transcripts containing miR173 or miR390 target sites, indicating that these trigger sequences are the only cis sequences essential for tasiRNA formation...

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..These and related findings on SPL genes suggest that microRNAs play an important role in the regulation of flowering...

..TCP genes with microRNA target sequences are found in a wide range of species, indicating that microRNA-mediated control of leaf morphogenesis is conserved in plants with very different leaf forms...

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..Together, our results reveal a role of PRR7 and PRR9 in regulating CCA1 and LHY activities in response to ambient temperature...

..Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes...

..Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana...

..thaliana and improvements in tools and technology applied to its close relatives are opening doors for combining experimental and comparative analyses to elucidate fundamental mechanisms of evolution...

..thaliana. Our work, together with previous findings, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response...

..We propose that the RNA-induced silencing complex reprogramming occurs during the early steps of miRNA loading, before the miRNA duplex is disassembled and the guide strand is selected...

..rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago...

..In addition to insight into modes of miRNA action, this study provides an important resource for the study of miRNA function in plants...

..Apart from facilitating the investigation of temporal and spatial requirements of gene activity, this technology will permit new types of genetic modifier screens starting with mutations that otherwise confer lethality or sterility...

..Agroinfiltration has been used successfully in many different applications, including the analysis of small RNAs. We describe here a protocol for analysis of miRNA processing using agroinfiltration of N. benthamiana leaves...

..The presence of phenotypic diversity within modern C. rubella suggests that this species will be an interesting model to understand divergence and adaptation, starting from very limited standing genetic variation...

..Our results indicate that miR156 is an evolutionarily conserved regulator of vegetative phase change in both annual herbaceous plants and perennial trees...

..Liljegren and colleagues (2004 [this issue of Cell]) describe a nonlinear network of transcription factor genes controlling this process...

..In agreement with this hypothesis, the silencing signals initiated by different sRNAs differ in their genetic requirements...

..Heterodimers between flower induction and floral organ identity proteins were observed, which point to (auto)regulatory mechanisms that prevent the activity of flower induction proteins in the flower...

..We coin the term 'target mimicry' to define this mechanism of inhibition of miRNA activity. Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics...

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..We show that toc1 affects expression of several floral regulators and a GA biosynthetic gene, but that these effects are independent...

..If misexpressed, JAGGED can induce the formation of bracts, suggesting that the exclusion of JAGGED from the cryptic bract is a cause of bractless flowers in Arabidopsis...

..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...

..These findings show that combinatorial action of WOX transcription factors is essential for Arabidopsis embryonic development...

..These results are combined into a genetic model explaining early second whorl initiation/proliferation, in which UFO functions to inhibit an AG-dependent activity...

..This hypothesis raises the possibility that diffusion is the default state for many macromolecules in the Arabidopsis apex, unless they are specifically retained...

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..CrossLink is available both online and as a standalone version at http://www-ab.informatik.uni-tuebingen.de/software...

..Together, these results suggest that SUP has both indirect and direct effects on the expression of B function homeotic genes...

..This review discusses recent progress in our understanding of floral homeotic genes, with an emphasis on how their region-specific expression is regulated...

..The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions...

..These observations contrast with previous findings that LEAFY acts as a direct activator of floral homeotic genes, supporting the hypothesis that the transcriptional activity of LEAFY is dependent on specific co-regulators...

..These activities are negatively regulated by REPLUMLESS (RPL), which divides FIL/JAG activity, creating two distinct stripes of valve margin...

..As with vernalization and photoperiod, ambient temperature ultimately affects expression of the floral pathway integrator FT...

..The extension of these tools to organisms with complex genomes, such as Arabidopsis, will greatly increase our ability to map and clone quantitative trait loci (QTL)...

..SFPs identified with the gene expression array also provide an empirical hybridization polymorphism background for studies of gene expression polymorphism and are available through the genome browser http://signal.salk.edu/cgi-bin/AtSFP...

..An analysis of the genome-wide pattern of linkage disequilibrium suggests that selfing most likely evolved roughly a million years ago or more...

..Together with earlier studies linking variation in light sensitivity to photoreceptor genes, our work suggests that photoreceptors may be a common target of natural selection...

..The elucidation of a natural strategy for metal hyperaccumulation enables the rational design of technologies for the clean-up of metal-contaminated soils and for bio-fortification...

..This pocket is contacted by a C-terminal peptide, which also contributes to the opposite FT and TFL1 activities. In combination, these results identify a molecular surface likely to be recognized by FT- and/or TFL1-specific interactors...

..The approach is based on a sequence similarity search step followed by a set of structural filters...

..Many discoveries with direct relevance to human health and disease have been elaborated using Arabidopsis, and several processes important to human biology are more easily studied in this versatile model plant...

..All of these results imply conservation and divergence in the functions of FCA between rice and Arabidopsis...

..Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele...

..The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana...

..In the case of PIN proteins, this mechanism enables switches in the direction of intercellular auxin fluxes, which mediate differential growth, tissue patterning, and organogenesis...

..Natural variation in HUA2 activity thus coordinates changes in two important life-history traits, flowering time and shoot morphology...

..The experiments will also reveal how different stem cells communicate to effect coordinated development of the flower. ..

..A second focus will be recent discoveries of how changes in key regulatory factors cause major phenotypic differences in more distantly related taxa. ..