Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, ...also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
Plant microRNAs (miRNAs) are embedded in regulatory networks that coordinate different gene expression programs in support of developmental plasticity. Modification of miRNA-target nodes during ...evolution might in turn underlie morphological and physiological diversity. A survey of the literature indicates that miRNA-target nodes themselves are organized in networks, and here we discuss some of the developmental traits they control along with possible interactions between miRNA and their targets. Because miRNAs and their interactions are not only at the heart of regulating many aspects of developmental plasticity, but because they also have an inherently quantitative mode of action, they present important targets for biotechnology applications.
Genome editing has emerged as a technology with a potential to revolutionize plant breeding. In this study, we report on generating, in less than ten months, Tomelo, a non-transgenic tomato variety ...resistant to the powdery mildew fungal pathogen using the CRISPR/Cas9 technology. We used whole-genome sequencing to show that Tomelo does not carry any foreign DNA sequences but only carries a deletion that is indistinguishable from naturally occurring mutations. We also present evidence for CRISPR/Cas9 being a highly precise tool, as we did not detect off-target mutations in Tomelo. Using our pipeline, mutations can be readily introduced into elite or locally adapted tomato varieties in less than a year with relatively minimal effort and investment.
Plants do not bloom randomly--but how do they know when and where to make flowers? Here, we review molecular mechanisms that integrate spatial and temporal information in day-length-dependent ...flowering. Primarily through genetic analyses in two species, Arabidopsis thaliana and rice, we today understand the essentials of two central issues in plant biology: how the appropriate photoperiod generates an inductive stimulus based on an external coincidence mechanism, and the nature of the mobile flowering signal, florigen, which relays photoperiod-dependent information from the leaf to the growing tip of the plant, the shoot apex.
For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly ...improved when informed by a broader diversity of species and evolutionary context. Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.
In certain plant hybrids, immunity signaling is initiated when immune components interact in the absence of a pathogen trigger. In Arabidopsis thaliana, such autoimmunity and cell death are linked to ...variants of the NLR RPP7 and the RPW8 proteins involved in broad-spectrum resistance. We uncover the molecular basis for this autoimmunity and demonstrate that a homolog of RPW8, HR4Fei-0, can trigger the assembly of a higher-order RPP7 complex, with autoimmunity signaling as a consequence. HR4Fei-0-mediated RPP7 oligomerization occurs via the RPP7 C-terminal leucine-rich repeat (LRR) domain and ATP-binding P-loop. RPP7 forms a higher-order complex only in the presence of HR4Fei-0 and not with the standard HR4 variant, which is distinguished from HR4Fei-0 by length variation in C-terminal repeats. Additionally, HR4Fei-0 can independently form self-oligomers, which directly kill cells in an RPP7-independent manner. Our work provides evidence for a plant resistosome complex and the mechanisms by which RPW8/HR proteins trigger cell death.
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•HR4Fei-0 induces oligomerization of RPP7•HR4Fei-0 and NLR RPP7 association triggers plant autoimmunity•The P-loop and LRR domain are required for oligomerization of RPP7•HR4Fei-0 can also form oligomers and directly kill cells on its own
Plant immunity is activated by intracellular NLR immune receptors. Li et al. identify a two-pronged immune signaling module involving RPW8/HR proteins. HR4 triggers oligomerization of the NLR RPP7 and downstream immune signaling. In addition, HR4 can independently form oligomers that are lethal to cells.
Darwin's theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly ...how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant
Arabidopsis thaliana
. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.
The development of multicellular organisms relies on interconnected genetic programs that control progression through their life cycle. MicroRNAs (miRNAs) and transcription factors (TFs) play key ...roles in such regulatory circuits. Here, we describe how three evolutionary conserved miRNA-TF pairs interact to form multiple checkpoints during reproductive development of Arabidopsis thaliana. Genetic, cellular, and physiological experiments show that miR159- and miR319-regulated MYB and TCP transcription factors pattern the expression of miR167 family members and their ARF6/8 targets. Coordinated action of these miRNA-TF pairs is crucial for the execution of consecutive hormone-dependent transitions during flower maturation. Cross-regulation includes both cis- and trans-regulatory interactions between these miRNAs and their targets. Our observations reveal how different miRNA-TF pairs can be organized into modules that coordinate successive steps in the plant life cycle.
New sequencing technologies are dramatically accelerating progress in forward genetics, and the use of such methods for the rapid identification of mutant alleles will be soon routine in many ...laboratories. A straightforward extension will be the cloning of major-effect genetic variants in crop species. In the near future, it can be expected that mapping by sequencing will become a centerpiece in efforts to discover the genes responsible for quantitative trait loci. The largest impact, however, might come from the use of these strategies to extract genes from non-model, non-crop plants that exhibit heritable variation in important traits. Deployment of such genes to improve crops or engineer microbes that produce valuable compounds heralds a potential paradigm shift for plant biology.
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