Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield

Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.

Reciprocal conversion between annual and polycarpic perennial flowering behavior in the Brassicaceae

The development of perennial crops holds great promise for sustainable agriculture and food security. However, the evolution of the transition between perenniality and annuality is poorly understood. Here, using two Brassicaceae species, Crucihimalaya himalaica and Erysimum nevadense, as polycarpic perennial models, we reveal that the transition from polycarpic perennial to biennial and annual flowering behavior is a continuum determined by the dosage of three closely related MADS-box genes. Diversification of the expression patterns, functional strengths, and combinations of these genes endows species with the potential to adopt various life-history strategies. Remarkably, we find that a single gene among these three is sufficient to convert winter-annual or annual Brassicaceae plants into polycarpic perennial flowering plants. Our work delineates a genetic basis for the evolution of diverse life-history strategies in plants and lays the groundwork for the generation of diverse perennial Brassicaceae crops in the future.

Flowering time: From physiology, through genetics to mechanism

Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.

A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus

Oilseed rape (Brassica napus) is an important global oil crop, with spring and winter varieties grown commercially. To understand the transcriptomic differences between these varieties, we collected transcriptomes from apex and leaf tissue from a spring variety, Westar, and a winter variety, Tapidor, before, during, and after vernalisation treatment, until the plants flowered. Large transcriptomic differences were noted in both varieties during the vernalisation treatment because of temperature and day length changes. Transcriptomic alignment revealed that the apex transcriptome reflects developmental state, whereas the leaf transcriptome is more closely aligned to the age of the plant. Similar numbers of copies of genes were expressed in both varieties during the time series, although key flowering time genes exhibited expression pattern differences. BnaFLC copies on A2 and A10 are the best candidates for the increased vernalisation requirement of Tapidor. Other BnaFLC copies show tissue-dependent reactivation of expression post-cold, with these dynamics suggesting some copies have retained or acquired a perennial nature. BnaSOC1 genes, also related to the vernalisation pathway, have expression profiles which suggest tissue subfunctionalisation. This understanding may help to breed varieties with more consistent or robust vernalisation responses, of special importance due to the milder winters resulting from climate change.

Perenniality: From model plants to applications in agriculture

To compensate for their sessile nature, plants have evolved sophisticated mechanisms enabling them to adapt to ever-changing environments. One such prominent feature is the evolution of diverse life history strategies, particularly such that annuals reproduce once followed by seasonal death, while perennials live longer by cycling growth seasonally. This intrinsic phenology is primarily genetic and can be altered by environmental factors. Although evolutionary transitions between annual and perennial life history strategies are common, perennials account for most species in nature because they survive well under year-round stresses. This proportion, however, is reversed in agriculture. Hence, perennial crops promise to likewise protect and enhance the resilience of agricultural ecosystems in response to climate change. Despite significant endeavors that have been made to generate perennial crops, progress is slow because of barriers in studying perennials, and many developed species await further improvement. Recent findings in model species have illustrated that simply rewiring existing genetic networks can lead to lifestyle variation. This implies that engineering plant life history strategy can be achieved by manipulating only a few key genes. In this review, we summarize our current understanding of genetic basis of perenniality and discuss major questions and challenges that remain to be addressed.

Adaptation of perennial flowering phenology across the European range of Arabis alpina

Flowering phenology is important in the adaptation of many plants to their local environment, but its adaptive value has not been extensively studied in herbaceous perennials. We used Arabis alpina as a model system to determine the importance of flowering phenology to fitness of a herbaceous perennial with a wide geographical range. Individual plants representative of local genetic diversity (accessions) were collected across Europe, including in Spain, the Alps and Scandinavia. The flowering behaviour of these accessions was documented in controlled conditions, in common-garden experiments at native sites and in situ in natural populations. Accessions from the Alps and Scandinavia varied in whether they required exposure to cold (vernalization) to induce flowering, and in the timing and duration of flowering. By contrast, all Spanish accessions obligately required vernalization and had a short duration of flowering. Using experimental gardens at native sites, we show that an obligate requirement for vernalization increases survival in Spain. Based on our analyses of genetic diversity and flowering behaviour across Europe, we propose that in the model herbaceous perennial A. alpina, an obligate requirement for vernalization, which is correlated with short duration of flowering, is favoured by selection in Spain where the plants experience a long growing season.

Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae

MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.

Arabidopsis AGAMOUS-LIKE16 and SUPPRESSOR OF CONSTANS1 regulate the genome-wide expression and flowering time

Flowering transition is tightly coordinated by complex gene regulatory networks, in which AGAMOUS-LIKE 16 (AGL16) plays important roles. Here, we identified the molecular function and binding properties of AGL16 and demonstrated its partial dependency on the SUPPRESSOR OF CONSTANS 1 (SOC1) function in regulating flowering. AGL16 bound to promoters of more than 2,000 genes via CArG-box motifs with high similarity to that of SOC1 in Arabidopsis (Arabidopsis thaliana). Approximately 70 flowering genes involved in multiple pathways were potential targets of AGL16. AGL16 formed a protein complex with SOC1 and shared a common set of targets. Intriguingly, only a limited number of genes were differentially expressed in the agl16-1 loss-of-function mutant. However, in the soc1-2 knockout background, AGL16 repressed and activated the expression of 375 and 182 genes, respectively, with more than a quarter bound by AGL16. Corroborating these findings, AGL16 repressed the flowering time more strongly in soc1-2 than in the Col-0 background. These data identify a partial inter-dependency between AGL16 and SOC1 in regulating genome-wide gene expression and flowering time, while AGL16 provides a feedback regulation on SOC1 expression. Our study sheds light on the complex background dependency of AGL16 in flowering regulation, thus providing additional insights into the molecular coordination of development and environmental adaptation.

Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers

Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.

Gene Silencing through CRISPR Interference in Mycoplasmas

Mycoplasmas are pathogenic, genome-reduced bacteria. The development of such fields of science as system and synthetic biology is closely associated with them. Despite intensive research of different representatives of this genus, genetic manipulations remain challenging in mycoplasmas. Here we demonstrate a single-plasmid transposon-based CRISPRi system for the repression of gene expression in mycoplasmas. We show that selected expression determinants provide a level of dCas9 that does not lead to a significant slow-down of mycoplasma growth. For the first time we describe the proteomic response of genome-reduced bacteria to the expression of exogenous dcas9. The functionality of the resulting vector is confirmed by targeting the three genes coding transcription factors-fur, essential spxA, whiA, and histone-like protein hup1 in Mycoplasma gallisepticum. As a result, the expression level of each gene was decreased tenfold and influenced the mRNA level of predicted targets of transcription factors. To illustrate the versatility of this vector, we performed a knockdown of metabolic genes in a representative member of another cluster of the Mycoplasma genus-Mycoplasma hominis. The developed CRISPRi system is a powerful tool to discover the functioning of genes that are essential, decipher regulatory networks and that can help to identify novel drug targets to control Mycoplasma infections.

Unraveling the role of MADS transcription factor complexes in apple tree dormancy

A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.

The SOC1-like gene BoMADS50 is associated with the flowering of Bambusa oldhamii

Bamboo is known for its edible shoots and beautiful texture and has considerable economic and ornamental value. Unique among traditional flowering plants, many bamboo plants undergo extensive synchronized flowering followed by large-scale death, seriously affecting the productivity and application of bamboo forests. To date, the molecular mechanism of bamboo flowering characteristics has remained unknown. In this study, a SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like gene, BoMADS50, was identified from Bambusa oldhamii. BoMADS50 was highly expressed in mature leaves and the floral primordium formation period during B. oldhamii flowering and overexpression of BoMADS50 caused early flowering in transgenic rice. Moreover, BoMADS50 could interact with APETALA1/FRUITFULL (AP1/FUL)-like proteins (BoMADS14-1/2, BoMADS15-1/2) in vivo, and the expression of BoMADS50 was significantly promoted by BoMADS14-1, further indicating a synergistic effect between BoMADS50 and BoAP1/FUL-like proteins in regulating B. oldhamii flowering. We also identified four additional transcripts of BoMADS50 (BoMADS50-1/2/3/4) with different nucleotide variations. Although the protein-CDS were polymorphic, they had flowering activation functions similar to those of BoMADS50. Yeast one-hybrid and transient expression assays subsequently showed that both BoMADS50 and BoMADS50-1 bind to the promoter fragment of itself and the SHORT VEGETATIVE PHASE (SVP)-like gene BoSVP, but only BoMADS50-1 can positively induce their transcription. Therefore, nucleotide variations likely endow BoMADS50-1 with strong regulatory activity. Thus, BoMADS50 and BoMADS50-1/2/3/4 are probably important positive flowering regulators in B. oldhamii. Moreover, the functional conservatism and specificity of BoMADS50 and BoMADS50-1 might be related to the synchronized and sporadic flowering characteristics of B. oldhamii.

Gene regulatory networks controlled by FLOWERING LOCUS C that confer variation in seasonal flowering and life history

Responses to environmental cues synchronize reproduction of higher plants to the changing seasons. The genetic basis of these responses has been intensively studied in the Brassicaceae. The MADS-domain transcription factor FLOWERING LOCUS C (FLC) plays a central role in the regulatory network that controls flowering of Arabidopsis thaliana in response to seasonal cues. FLC blocks flowering until its transcription is stably repressed by extended exposure to low temperatures in autumn or winter and, therefore, FLC activity is assumed to limit flowering to spring. Recent reviews describe the complex epigenetic mechanisms responsible for FLC repression in cold. We focus on the gene regulatory networks controlled by FLC and how they influence floral transition. Genome-wide approaches determined the in vivo target genes of FLC and identified those whose transcription changes during vernalization or in flc mutants. We describe how studying FLC targets such as FLOWERING LOCUS T, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15, and TARGET OF FLC AND SVP 1 can explain different flowering behaviours in response to vernalization and other environmental cues, and help define mechanisms by which FLC represses gene transcription. Elucidating the gene regulatory networks controlled by FLC provides access to the developmental and physiological mechanisms that regulate floral transition.

The Diverse Roles of FLOWERING LOCUS C in Annual and Perennial Brassicaceae Species

Most temperate species require prolonged exposure to winter chilling temperatures to flower in the spring. In the Brassicaceae, the MADS box transcription factor FLOWERING LOCUS C (FLC) is a major regulator of flowering in response to prolonged cold exposure, a process called vernalization. Winter annual Arabidopsis thaliana accessions initiate flowering in the spring due to the stable silencing of FLC by vernalization. The role of FLC has also been explored in perennials within the Brassicaceae family, such as Arabis alpina. The flowering pattern in A. alpina differs from the one in A. thaliana. A. alpina plants initiate flower buds during vernalization but only flower after subsequent exposure to growth-promoting conditions. Here we discuss the role of FLC in annual and perennial Brassicaceae species. We show that, besides its conserved role in flowering, FLC has acquired additional functions that contribute to vegetative and seed traits. PERPETUAL FLOWERING 1 (PEP1), the A. alpina FLC ortholog, contributes to the perennial growth habit. We discuss that PEP1 directly and indirectly, regulates traits such as the duration of the flowering episode, polycarpic growth habit and shoot architecture. We suggest that these additional roles of PEP1 are facilitated by (1) the ability of A. alpina plants to form flower buds during long-term cold exposure, (2) age-related differences between meristems, which enable that not all meristems initiate flowering during cold exposure, and (3) differences between meristems in stable silencing of PEP1 after long-term cold, which ensure that PEP1 expression levels will remain low after vernalization only in meristems that commit to flowering during cold exposure. These features result in spatiotemporal seasonal changes of PEP1 expression during the A. alpina life cycle that contribute to the perennial growth habit. FLC and PEP1 have also been shown to influence the timing of another developmental transition in the plant, seed germination, by influencing seed dormancy and longevity. This suggests that during evolution, FLC and its orthologs adopted both similar and divergent roles to regulate life history traits. Spatiotemporal changes of FLC transcript accumulation drive developmental decisions and contribute to life history evolution.

Identification and evolution of gene regulatory networks: insights from comparative studies in plants

The availability of genome sequences, genome-wide assays of transcription factor binding, and accessible chromatin maps have unveiled gene regulatory landscapes in plants. This understanding has ushered in comparative gene regulatory network studies that assess network rewiring between species, across time, and between biological tissues. Comparisons of cis-regulatory elements across the plant kingdom have uncovered examples of conserved sequences, but also of divergence, indicating that selective pressures can vary in different plant families. Transcription factor duplication, followed by spatiotemporal expression divergence of the duplicates, also appears to be a key mechanism of network evolution. Here, we review recent literature describing the regulation of gene expression in plants, and how comparative studies provide insights into how these regulatory interactions change and lead to gene regulatory network rewiring.

Evolutionary processes from the perspective of flowering time diversity

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

The Role of FLOWERING LOCUS C Relatives in Cereals

FLOWERING LOCUS C (FLC) is one of the best characterized genes in plant research and is integral to vernalization-dependent flowering time regulation. Yet, despite the abundance of information on this gene and its relatives in Arabidopsis thaliana, the role FLC genes play in other species, in particular cereal crops and temperate grasses, remains elusive. This has been due in part to the comparative reduced availability of bioinformatic and mutant resources in cereals but also on the dominant effect in cereals of the VERNALIZATION (VRN) genes on the developmental process most associated with FLC in Arabidopsis. The strong effect of the VRN genes has led researchers to believe that the entire process of vernalization must have evolved separately in Arabidopsis and cereals. Yet, since the confirmation of the existence of FLC-like genes in monocots, new light has been shed on the roles these genes play in both vernalization and other mechanisms to fine tune development in response to specific environmental conditions. Comparisons of FLC gene function and their genetic and epigenetic regulation can now be made between Arabidopsis and cereals and how they overlap and diversify is coming into focus. With the advancement of genome editing techniques, further study on these genes is becoming increasingly easier, enabling us to investigate just how essential FLC-like genes are to modulating flowering time behavior in cereals.

Networks Consolidate the Core Concepts of Evolution by Natural Selection

Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution.

A regulatory circuit conferring varied flowering response to cold in annual and perennial plants

The reproductive strategies of plants are highly variable. Short-lived annuals flower abundantly soon after germination, whereas longer-lived perennials postpone and spatially restrict flowering. We used CRISPR/Cas9 and interspecies gene transfer to understand divergence in reproductive patterns between annual and perennial crucifers. We show that in perennial Arabis alpina, flowering in response to winter cold depends on the floral integrator SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15 (SPL15), whose activity is limited to older shoots and branches during cold exposure. In annuals, this regulatory system is conserved, but cold-induced flowering occurs in young shoots, without requirement for SPL15, through the photoperiodic pathway when plants return to warm. By reconstructing the annual response in perennials, we conclude that characteristic patterns of reproduction in annuals and perennials are conferred through variation in dependency on distinct flowering pathways acting in parallel.

Gibberellins Act Downstream of Arabis PERPETUAL FLOWERING1 to Accelerate Floral Induction during Vernalization

Regulation of flowering by endogenous and environmental signals ensures that reproduction occurs under optimal conditions to maximize reproductive success. Involvement of the growth regulator gibberellin (GA) in the control of flowering by environmental cues varies among species. Arabis alpina Pajares, a model perennial member of the Brassicaceae, only undergoes floral induction during vernalization, allowing definition of the role of GA specifically in this process. The transcription factor PERPETUAL FLOWERING1 (PEP1) represses flowering until its mRNA levels are reduced during vernalization. Genome-wide analyses of PEP1 targets identified genes involved in GA metabolism and signaling, and many of the binding sites in these genes were specific to the A. alpina lineage. Here, we show that the pep1 mutant exhibits an elongated-stem phenotype, similar to that caused by treatment with exogenous GA, consistent with PEP1 repressing GA responses. Moreover, in comparison with the wild type, the pep1 mutant contains higher GA4 levels and is more sensitive to GA prior to vernalization. Upon exposure to cold temperatures, GA levels fall to low levels in the pep1 mutant and in wild-type plants, but GA still promotes floral induction and the transcription of floral meristem identity genes during vernalization. Reducing GA levels strongly impairs flowering and inflorescence development in response to short vernalization treatments, but longer treatments overcome the requirement for GA. Thus, GA accelerates the floral transition during vernalization in A. alpina, the down-regulation of PEP1 likely increases GA sensitivity, and GA responses contribute to determining the length of vernalization required for flowering and reproduction.

Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants

Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.

Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications

Integration of environmental and endogenous cues at plant shoot meristems determines the timing of flowering and reproductive development. The MADS box transcription factor FLOWERING LOCUS C (FLC) of Arabidopsis thaliana is an important repressor of floral transition, which blocks flowering until plants are exposed to winter cold. However, the target genes of FLC have not been thoroughly described, and our understanding of the mechanisms by which FLC represses transcription of these targets and how this repression is overcome during floral transition is still fragmentary. Here, we identify and characterize TARGET OF FLC AND SVP1 (TFS1), a novel target gene of FLC and its interacting protein SHORT VEGETATIVE PHASE (SVP). TFS1 encodes a B3-type transcription factor, and we show that tfs1 mutants are later flowering than wild-type, particularly under short days. FLC and SVP repress TFS1 transcription leading to deposition of trimethylation of Iysine 27 of histone 3 (H3K27me3) by the Polycomb Repressive Complex 2 at the TFS1 locus. During floral transition, after downregulation of FLC by cold, TFS1 transcription is promoted by SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), a MADS box protein encoded by another target of FLC/SVP. SOC1 opposes PRC function at TFS1 through recruitment of the histone demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) and the SWI/SNF chromatin remodeler ATPase BRAHMA (BRM). This recruitment of BRM is also strictly required for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9) binding at TFS1 to coordinate RNAPII recruitment through the Mediator complex. Thus, we show that antagonistic chromatin modifications mediated by different MADS box transcription factor complexes play a crucial role in defining the temporal and spatial patterns of transcription of genes within a network of interactions downstream of FLC/SVP during floral transition.

The initiation of flowering in plants is exquisitely sensitive to environmental signals, ensuring that reproduction occurs at the appropriate time of year. The sensitivity of these responses depends upon strong repression of flowering under inappropriate conditions. FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) are related transcription factors that act in concert to strongly inhibit flowering in crucifer plants through repressing transcription of their target genes. Many direct FLC/ SVP targets have been identified in genome-wide studies, however few of these genes have been characterized for their roles in regulating flowering time or other aspects of reproductive development. Here, we characterize TARGET OF FLC AND SVP1 (TFS1) as a novel target of FLC and SVP, and demonstrate that TFS1 contributes to proper flowering-time control. Moreover, we provide a detailed mechanistic view of how TFS1 transcription is controlled during reproductive development through the repressive activity of FLC/SVP being overcome by the transcriptional activator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Thus we further elucidate the network of genes repressed by FLC/SVP to block flowering and determine mechanisms by which their repressive activity is overcome during the initiation of flowering.

Photosynthetic activity of reproductive organs

During seed development, carbon is reallocated from maternal tissues to support germination and subsequent growth. As this pool of resources is depleted post-germination, the plant begins autotrophic growth through leaf photosynthesis. Photoassimilates derived from the leaf are used to sustain the plant and form new organs, including other vegetative leaves, stems, bracts, flowers, fruits, and seeds. In contrast to the view that reproductive tissues act only as resource sinks, many studies demonstrate that flowers, fruits, and seeds are photosynthetically active. The photosynthetic contribution to development is variable between these reproductive organs and between species. In addition, our understanding of the developmental control of photosynthetic activity in reproductive organs is vastly incomplete. A further complication is that reproductive organ photosynthesis (ROP) appears to be particularly important under suboptimal growth conditions. Therefore, the topic of ROP presents the community with a challenge to integrate the fields of photosynthesis, development, and stress responses. Here, we attempt to summarize our understanding of the contribution of ROP to development and the molecular mechanisms underlying its control.

Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina

The life cycles of plants are characterized by two major life history transitions-germination and the initiation of flowering-the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an ortholog of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode. We performed greenhouse and garden experiments to compare flowering phenology, fecundity and seed traits between A. alpina accessions that have a functional PEP1 allele and flower seasonally and pep1 mutants and accessions that carry lesions in PEP1 and flower perpetually. In the garden, perpetual genotypes flower asynchronously and show higher winter mortality than seasonal ones. PEP1 also pleiotropically regulates seed dormancy and longevity in a way that is functionally divergent from FLC. Seeds from perpetual genotypes have shallow dormancy and reduced longevity regardless of whether they after-ripened in plants grown in the greenhouse or in the experimental garden. These results suggest that perpetual genotypes have higher mortality during winter but compensate by showing higher seedling establishment. Differences in seed traits between seasonal and perpetual genotypes are also coupled with differences in hormone sensitivity and expression of genes involved in hormonal pathways. Our study highlights the existence of pleiotropic regulation of seed traits by hub developmental regulators such as PEP1, suggesting that seed and flowering traits in perennial plants might be optimized in a coordinated fashion.

Linking genes with ecological strategies in Arabidopsis thaliana

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina

The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 ortholog in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to control flowering through the vernalization pathway via enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the ortholog of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2, we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here, we demonstrate that PEP2 activity prevents the up-regulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY), and APETALA1 (AaAP1), ensuring floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in axillary branches. These multiple roles of PEP2 in the vernalization response contribute to the A. alpina life cycle.

Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C3 photosynthesis. It is widely accepted that CAM plants have evolved from C3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species (Kalanchoë fedtschenkoi) and a C3 model plant species (Arabidopsis thaliana) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi. Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.

Gene networks and the evolution of plant morphology

Elaboration of morphology depends on the precise orchestration of gene expression by key regulatory genes. The hierarchy and relationship among the participating genes is commonly known as gene regulatory network (GRN). Therefore, the evolution of morphology ultimately occurs by the rewiring of gene network structures or by the co-option of gene networks to novel domains. The availability of high-resolution expression data combined with powerful statistical tools have opened up new avenues to formulate and test hypotheses on how diverse gene networks influence trait development and diversity. Here we summarize recent studies based on both big-data and genetics approaches to understand the evolution of plant form and physiology. We also discuss recent genome-wide investigations on how studying open-chromatin regions may help study the evolution of gene expression patterns.

Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.

Extended Vernalization Regulates Inflorescence Fate in Arabis alpina by Stably Silencing PERPETUAL FLOWERING1

The alpine perennial Arabis alpina initiates flower buds during prolonged exposure to cold. In the accession Pajares, we demonstrate that the length of vernalization influences flowering time and inflorescence fate but does not affect the axillary branches that maintain vegetative growth. The expression of floral organ identity genes gradually increases in the main shoot apex during vernalization, correlating with an increase in floral commitment. In northern Arabidopsis (Arabidopsis thaliana) accessions, the length of vernalization modulates the stable silencing of the floral repressor FLOWERING LOCUS C (FLC). We demonstrate that expression of PERPETUAL FLOWERING1 (PEP1), the ortholog of FLC in A. alpina, is similarly influenced by the duration of the exposure to cold. Extended vernalization results in stable silencing of PEP1 in the inflorescence. In contrast, insufficient vernalization leads to PEP1 reactivation after cold treatment, which correlates with delayed flowering and the appearance of floral reversion phenotypes such as bracts and vegetative inflorescence branches. Floral reversion phenotypes are reduced in the pep1-1 mutant, suggesting that PEP1 regulates the fate of the inflorescence after vernalization. The effect of vernalization duration on stable silencing of PEP1 is specific to meristems that initiate flowering during cold treatment. Extended vernalization fails to silence PEP1 in young seedlings and axillary branches that arise from buds initiated during cold treatment, which remain vegetative. We conclude that the duration of vernalization in A. alpina differentially regulates PEP1 in the inflorescence and axillary branches. PEP1 has a dual role regulating meristem fate; it prevents meristems from flowering and antagonizes inflorescence development after vernalization.