Feedback regulation of COOLAIR expression controls seed dormancy and flowering time

Temperature-sensitive pathways may be involved in duck embryonic developmental recovery from blastoderm dormancy during hatching

1. Birds' newly oviposited blastoderms can survive several weeks in a dormant state during low-temperature storage. Previous studies demonstrated that there is a critical temperature range from 19 to 27°C for chicken embryos. Within this range, the embryo will diapause in a dormant state; once the temperature rises above this range, the blastoderm will break dormancy. 2. Clarifying the mechanism that initiates duck embryo developmental recovery from blastoderm dormancy will be helpful to change temperature control to improve hatching in poultry production. It was hypothesised that there might be some temperature-sensitive genes involved in initiating duck embryo developmental recovery from blastoderm dormancy. 3. To test this hypothesis, the transcriptome of the newly oviposited duck blastoderm and duck embryo (incubated for 48 hours) were sequenced to screen for differentially expressed genes with functions that had been predicted by bioinformatics. 4. The results showed that there were 2416 differentially expressed genes between the two groups, 53 of which were involved in temperature-sensitive pathways. The protein-protein interaction network combined these 53 temperature-sensitive genes and another group of 65 genes, which enriched the development pathway. These results suggested that temperature-sensitive genes may be involved in growth and development related pathways.

Molecular Regulation of Plant Responses to Environmental Temperatures

Temperature is a key factor governing the growth and development, distribution, and seasonal behavior of plants. The entire plant life cycle is affected by environmental temperatures. Plants grow rapidly and exhibit specific changes in morphology under mild average temperature conditions, a response termed thermomorphogenesis. When exposed to chilling or moist chilling low temperatures, flowering or seed germination is accelerated in some plant species; these processes are known as vernalization and cold stratification, respectively. Interestingly, once many temperate plants are exposed to chilling temperatures for some time, they can acquire the ability to resist freezing stress, a process termed cold acclimation. In the face of global climate change, heat stress has emerged as a frequent challenge, which adversely affects plant growth and development. In this review, we summarize and discuss recent progress in dissecting the molecular mechanisms regulating plant thermomorphogenesis, vernalization, and responses to extreme temperatures. We also discuss the remaining issues that are crucial for understanding the interactions between plants and temperature.

Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC

In Arabidopsis thaliana, the cold-induced epigenetic regulation of FLOWERING LOCUS C (FLC) involves distinct phases of Polycomb repressive complex 2 (PRC2) silencing. During cold, a PHD-PRC2 complex metastably and digitally nucleates H3K27me3 within FLC On return to warm, PHD-PRC2 spreads across the locus delivering H3K27me3 to maintain long-term silencing. Here, we studied natural variation in this process in Arabidopsis accessions, exploring Lov-1, which shows FLC reactivation on return to warm, a feature characteristic of FLC in perennial Brassicaceae This analysis identifies an additional phase in this Polycomb silencing mechanism downstream from H3K27me3 spreading. In this long-term silencing (perpetuated) phase, the PHD proteins are lost from the nucleation region and silencing is likely maintained by the read-write feedbacks associated with H3K27me3. A combination of noncoding SNPs in the nucleation region mediates instability in this long-term silencing phase with the result that Lov-1 FLC frequently digitally reactivates in individual cells, with a probability that diminishes with increasing cold duration. We propose that this decrease in reactivation probability is due to reduced DNA replication after flowering. Overall, this work defines an additional phase in the Polycomb mechanism instrumental in natural variation of silencing, and provides avenues to dissect broader evolutionary changes at FLC.

The Floral Repressor GmFLC-like Is Involved in Regulating Flowering Time Mediated by Low Temperature in Soybean

Soybean is an important crop that is grown worldwide. Flowering time is a critical agricultural trait determining successful reproduction and yields. For plants, light and temperature are important environmental factors that regulate flowering time. Soybean is a typical short-day (SD) plant, and many studies have elucidated the fine-scale mechanisms of how soybean responds to photoperiod. Low temperature can delay the flowering time of soybean, but little is known about the detailed mechanism of how temperature affects soybean flowering. In this study, we isolated GmFLC-like from soybean, which belongs to the FLOWERING LOCUS C clade of the MADS-box family and is intensely expressed in soybean leaves. Heterologous expression of GmFLC-like results in a delayed-flowering phenotype in Arabidopsis. Additional experiments revealed that GmFLC-like is involved in long-term low temperature-triggered late flowering by inhibiting FT gene expression. In addition, yeast one-hybrid, dual-luciferase reporter assay, and electrophoretic mobility shift assay revealed that the GmFLC-like protein could directly repress the expression of FT2a by physically interacting with its promoter region. Taken together, our results revealed that GmFLC-like functions as a floral repressor involved in flowering time during treatments with various low temperature durations. As the only the FLC gene in soybean, GmFLC-like was meaningfully retained in the soybean genome over the course of evolution, and this gene may play an important role in delaying flowering time and providing protective mechanisms against sporadic and extremely low temperatures.

Arabidopsis MYB4 plays dual roles in flavonoid biosynthesis

Flavonoids are major secondary metabolites derived from the plant phenylpropanoid pathway that play important roles in plant development and also have benefits for human health. So-called MBW ternary complexes involving R2R3-MYB and basic helix-loop-helix (bHLH) transcription factors along with WD-repeat proteins have been reported to regulate expression of the biosynthetic genes in the flavonoid pathway. MYB4 and its closest homolog MYB7 have been suggested to function as repressors of phenylpropanoid metabolism. However, the detailed mechanism by which they act has not been fully elucidated. Here, we show that Arabidopsis thaliana MYB4 and its homologs MYB7 and MYB32 interact with the bHLH transcription factors TT8, GL3 and EGL3 and thereby interfere with the transcriptional activity of the MBW complexes. In addition, MYB4 can also inhibit flavonoid accumulation by repressing expression of the gene encoding Arogenate Dehydratase 6 (ADT6), which catalyzes the final step in the biosynthesis of phenylalanine, the precursor for flavonoid biosynthesis. MYB4 potentially represses not only the conventional ADT6 encoding the plastidial enzyme but also the alternative isoform encoding the cytosolic enzyme. We suggest that MYB4 plays dual roles in modulating the flavonoid biosynthetic pathway in Arabidopsis.

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.

Identification and characterisation of a novel FT orthologous gene in London plane with a distinct expression response to environmental stimuli compared to PaFT

FLOWERING LOCUS T (FT) is a key integrator of environmental signals and internal cues, and codes for florigen-like activity which regulates the transition from vegetative to reproductive growth in flowering plants. Unlike annual plants, perennial tree species undergo several years of vegetative growth prior to the transition to the reproductive stage, as characterised by the ability to form flower buds. Thereafter, trees in temperate regions typically display an annual growth cycle involving distinct vegetative growth, flowering and dormancy stages. In London plane (Platanus acerifolia Willd.), a FT-like gene has previously been identified. Here, we report the isolation of a novel FT orthologous gene, PaFTL, and investigate the functions of PaFT and PaFTL through the analysis of expression profiles and transgenic phenotypes. PaFT displayed the highest levels of expression during tree dormancy, and similarly elevated expression levels were seen under conditions of low temperature and short days (LT/SD). In contrast, PaFTL transcripts were up-regulated during the floral transition phase, the early stages of inflorescence development and throughout the main flowering period, whereas expression levels were low and variable during dormancy and in response to LT/SD treatments. Ectopic expression of 35s::PaFTL in tobacco produced a phenotype similar to that with PaFT, namely, advanced floral initiation. Overall, the results suggest that PaFT and PaFTL have both conserved and diverse functions in floral initiation, floral development and dormancy regulation.

Expression of FRIGIDA in root inhibits flowering in Arabidopsis thaliana

FRIGIDA (FRI), as the major regulator of flowering time in Arabidopsis accessions, can activate its target FLOWERING LOCUS C (FLC) to delay flowering before vernalization. In addition to FLC, other FRI targets also exist in Arabidopsis. Although leaves sense environmental cues to modulate flowering time, it is not known if roots also regulate the floral transition. In this study, we investigated the spatio-temporal effect of FRI on flowering time. Local expression of FRI in the phloem and leaves activated FLC to delay flowering. Furthermore, we found that local expression of FRI in the roots also delayed flowering by activating other targets, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, in the roots. Graft and genetic experiments revealed that the spatial expression of FRI in the root might generate a mobile signal, which is transmitted from roots to shoot and antagonizes the FT signal to delay flowering. Specifically expressing FRI in the embryo efficiently delayed flowering, even expressing FRI as early as the pro-embryo stage is enough to up-regulate FLC expression to delay flowering. Together, our findings demonstrate the spatio-temporal effect of FRI on delaying flowering, and we propose that root tissue also perceives the flowering signal to fine-tune the flowering time through MAF4/5 as novel targets of FRI.

Pleiotropy in developmental regulation by flowering-pathway genes: is it an evolutionary constraint?

Pleiotropy occurs when one gene influences more than one trait, contributing to genetic correlations among traits. Consequently, it is considered a constraint on the evolution of adaptive phenotypes because of potential antagonistic selection on correlated traits, or, alternatively, preservation of functional trait combinations. Such evolutionary constraints may be mitigated by the evolution of different functions of pleiotropic genes in their regulation of different traits. Arabidopsis thaliana flowering-time genes, and the pathways in which they operate, are among the most thoroughly studied regarding molecular functions, phenotypic effects, and adaptive significance. Many of them show strong pleiotropic effects. Here, we review examples of pleiotropy of flowering-time genes and highlight those that also influence seed germination. Some genes appear to operate in the same genetic pathways when regulating both traits, whereas others show diversity of function in their regulation, either interacting with the same genetic partners but in different ways or potentially interacting with different partners. We discuss how functional diversification of pleiotropic genes in the regulation of different traits across the life cycle may mitigate evolutionary constraints of pleiotropy, permitting traits to respond more independently to environmental cues, and how it may even contribute to the evolutionary divergence of gene function across taxa.

The Effect of Ambient Temperature on Brachypodium distachyon Development

Due to climate change, the effect of temperature on crops has become a global concern. It has been reported that minor changes in temperature can cause large decreases in crop yield. While not a crop, the model Brachypodium distachyon can help to efficiently investigate ambient temperature responses of temperate grasses, which include wheat and barley. Here, we use different accessions to explore the effect of ambient temperature on Brachypodium phenology. We recorded leaf initiation, heading time, leaf and branch number at heading, seed set time, seed weight, seed size, seed dormancy, and seed germination at different temperatures. We found that warmer temperatures promote leaf initiation so that leaf number at heading is positively correlated to temperature. Heading time is not correlated to temperature but accessions show an optimal temperature at which heading is earliest. Cool temperatures prolong seed maturation which increases seed weight. The progeny seeds of plants grown at these cool ambient temperatures show stronger dormancy, while imbibition of seeds at low temperature improves germination. Among all developmental stages, it is the duration of seed maturation that is most sensitive to temperature. The results we found reveal that temperature responses in Brachypodium are highly conserved with temperate cereals, which makes Brachypodium a good model to explore temperature responsive pathways in temperate grasses.

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses

A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.

Seed germination and dormancy: The classic story, new puzzles, and evolution

This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.

Multi-tasking as an ancient skill: When one gene does many things well

Multi-tasking is in our DNA. Many genes perform more than one function, and the question is how well it can do them all. Pleiotropy is frequently considered to be an adaptive constraint that prevents optimal phenotypes from evolving because of antagonistic indirect selection acting on genetically correlated traits. However, as geneticists increasingly study the effects of genes under more realistic natural environments, even the most well studied genes are expressing fascinating pleiotropic effects. Pleiotropy appears to be utterly common. The genes involved in the regulation of flowering time in Arabidopsis thaliana, such as FLOWERING LOCUS C (FLC), offer case examples of such pleiotropy. Studying an ortholog of FLC in Arabis alpina, PERPETUAL FLOWERING 1 (PEP1), Hughes, Soppe and Albani (2019) present evidence that such pleiotropy in flowering-time genes persists through taxonomic diversification, albeit the precise function of the genes has evolved in response to taxon-specific natural selection. Their observation that trait-specific function can evolve even in highly pleiotropic genes suggests that pleiotropy may not constrain adaptation as much as is commonly assumed.

A research agenda for seed-trait functional ecology

Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically. Here we suggest broadening the range of morphological, physiological and biochemical seed traits to add new understanding on plant niches, population dynamics and community assembly. The diversity of seed traits and functions provides an important challenge that will require international collaboration in three areas of research. First, we present a conceptual framework for a seed ecological spectrum that builds upon current understanding of plant niches. We then lay the foundation for a seed-trait functional network, the establishment of which will underpin and facilitate trait-based inferences. Finally, we anticipate novel insights and challenges associated with incorporating diverse seed traits into predictive evolutionary ecology, community ecology and applied ecology. If the community invests in standardized seed-trait collection and the implementation of rigorous databases, major strides can be made at this exciting frontier of functional ecology.

An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis

Global warming has profound effects on plant growth and fitness. Plants have evolved sophisticated epigenetic machinery to respond quickly to heat, and exhibit transgenerational memory of the heat-induced release of post-transcriptional gene silencing (PTGS). However, how thermomemory is transmitted to progeny and the physiological relevance are elusive. Here we show that heat-induced HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2) directly activates the H3K27me3 demethylase RELATIVE OF EARLY FLOWERING 6 (REF6), which in turn derepresses HSFA2. REF6 and HSFA2 establish a heritable feedback loop, and activate an E3 ubiquitin ligase, SUPPRESSOR OF GENE SILENCING 3 (SGS3)-INTERACTING PROTEIN 1 (SGIP1). SGIP1-mediated SGS3 degradation leads to inhibited biosynthesis of trans-acting siRNA (tasiRNA). The REF6-HSFA2 loop and reduced tasiRNA converge to release HEAT-INDUCED TAS1 TARGET 5 (HTT5), which drives early flowering but attenuates immunity. Thus, heat induces transmitted phenotypes via a coordinated epigenetic network involving histone demethylases, transcription factors, and tasiRNAs, ensuring reproductive success and transgenerational stress adaptation.

Long Non-Coding RNAs: Rising Regulators of Plant Reproductive Development

Long non-coding RNAs (lncRNAs) exert a multitude of functions in regulating numerous biological processes. Recent studies have uncovered a growing number of lncRNAs within the plant genome. These molecules show striking tissue-specific expression patterns, suggesting that they exert regulatory functions in the growth and development processes of plants. Plant reproductive development is tightly regulated by both environmental and endogenous factors. As plant reproductive development is a crucial aspect of crop breeding, lncRNAs that modulate reproductive development are now particularly worth regarding. Here, we summarize findings that implicate lncRNAs in the control of plant reproductive development, especially in flowering control. Additionally, we elaborate on the regulation mechanisms of lncRNAs, tools for research on their function and mechanism, and potential directions of future research.

MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana

Seed germination in many plant species is triggered by sunlight, which is rich in the red (R) wavelength and repressed by under-the-canopy light rich in far red (FR). R:FR ratios are sensed by phytochromes to regulate levels of gibberellins (GAs) and abscisic acid (ABA), which induce and inhibit germination respectively. In this study we have discovered that, under FR light conditions, germination is repressed by MOTHER-OF-FT-AND-TFL1 (MFT) through the regulation of the ABA and GA signaling pathways. We also show that MFT gene expression is tightly regulated by light quality. Previous work has shown that under FR light conditions the transcription factor PHYOCHROME-INTERACTING-FACTOR1 (PIF1) accumulates and promotes expression of SOMNUS (SOM) that, in turn, leads to increased ABA and decreased GA levels. PIF1 also promotes expression of genes encoding ABA-INSENSITIVE5 (ABI5) and DELLA growth-repressor proteins, which act in the ABA and GA signaling pathways, respectively. Here we show that MFT gene expression is promoted by FR light through the PIF1/SOM/ABI5/DELLA pathway and is repressed by R light via the transcription factor SPATULA (SPT). Consistent with this, we also show that SPT gene expression is repressed under FR light in a PIF1-dependent manner. Furthermore, transcriptomic analyses presented in this study indicate that MFT exerts its function by promoting expression of known ABA-induced genes and repressing cell wall expansion-related genes.