The autonomous flowering-time pathway pleiotropically regulates seed germination in Arabidopsis thaliana

Integrated transcriptome and proteome analysis provides insights into CpFPA1 for floral induction in Chimonanthus praecox (Magnoliidae) without FLC in genome

KEY MESSAGE

We used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud differentiation stages and overexpression of CpFPA1 in Arabidopsis resulted in earlier flowering. Wintersweet (Chimonanthus praecox), a rare winter-flowering woody plant, is well known for its unique blooming time, fragrance and long flowering period. However, the molecular mechanism of flowering in C. praecox remains poorly unclear. In this study, we used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud (FB) differentiation stages (FB.Apr, FB.May and FB.Nov) in C. praecox. The results showed that a total of 952 differential expressed genes (DEGs) and 40 differential expressed proteins (DEPs) were identified. Gene ontology (GO) enrichment revealed that DEGs in FB.Apr/FB.May comparison group were mainly involved in metabolic of biological process, cell and cell part of cellular component and catalytic activity of molecular function. In the EuKaryotic Orthologous Groups (KOG) functional classification, DEPs were predicted mainly in the function of general function prediction only (KOG0118), post-translational modification, protein turnover and chaperones. The autonomous pathway genes play an essential role in the floral induction. Based on transcriptome and proteome correlation analysis, six candidate genes associated with the autonomous pathway were identified, including FPA1, FPA2a, FPA2b, FCA, FLK, FY. Furthermore, CpFPA1 was isolated and functionally characterized, and ectopic expression of CpFPA1 in Arabidopsis Columbia (Col-0) resulted in earlier flowering. These data could contribute to understand the function of CpFPA1 for floral induction and provide information for further research on the molecular mechanisms of flowering in wintersweet.

An overview of floral regulatory genes in annual and perennial plants

The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.

Functional studies of four MiFPF genes in mango revealed their function in promoting flowering in transgenic Arabidopsis

Flowering promoting factor (FPF) genes play a substantial regulatory role in the process of flowering. In the present study, four MiFPF genes, namely, MiFPF1, MiFPF2, MiFPF3a, and MiFPF3b, were obtained from mango (Mangifera indica L.). Tissue expression analysis showed that MiFPFs were expressed in all mango tissues. Specifically, MiFPF1 and MiFPF2 were highly expressed in leaves, while MiFPF3a and MiFPF3b were highly expressed in flowers and buds. The four MiFPF proteins localize to the nucleus. Overexpression of MiFPFs in transgenic Arabidopsis resulted in early flowering and upregulated the expression of APETAL1 (AP1), FLOWERING LOCUS D (FD) and FLOWERING LOCUS T (FT). MiFPF genes increased the root growth of transgenic Arabidopsis plants under gibberellin treatment. BiFC assays showed that MiFPFs can interact with several DELLA proteins. Taken together, our results demonstrate that the MiFPF gene was involved not only in promoting flowering but also in increasing root growth under gibberellin (GA₃) treatment.

Transcriptome analysis and identification of genes associated with floral transition and fruit development in rabbiteye blueberry (Vaccinium ashei)

Flowering and fruit set are important traits affecting fruit quality and yield in rabbiteye blueberry (Vaccinium ashei). Intense efforts have been made to elucidate the influence of vernalization and phytohormones on flowering, but the molecular mechanisms of flowering and fruit set remain unclear. To unravel these mechanisms, we performed transcriptome analysis to explore blueberry transcripts from flowering to early fruit stage. We divided flowering and fruit set into flower bud (S2), initial flower (S3), bloom flower (S4), pad fruit (S5), and cup fruit (S6) based on phenotype and identified 1,344, 69, 658, and 189 unique differentially expressed genes (DEGs) in comparisons of S3/S2, S4/S3, S5/S4, and S6/S5, respectively. There were obviously more DEGs in S3/S2 and S5/S4 than in S4/S3, and S6/S5, suggesting that S3/S2 and S5/S4 represent major transitions from buds to fruit in blueberry. GO and KEGG enrichment analysis indicated these DEGs were mostly enriched in phytohormone biosynthesis and signaling, transporter proteins, photosynthesis, anthocyanins biosynthesis, disease resistance protein and transcription factor categories, in addition, transcript levels of phytohormones and transporters changed greatly throughout the flowering and fruit set process. Gibberellic acid and jasmonic acid mainly acted on the early stage of flowering development like expression of the florigen gene FT, while the expression of auxin response factor genes increased almost throughout the process from bud to fruit development. Transporter proteins were mainly associated with minerals during the early flowering development stage and sugars during the early fruit stage. At the early fruit stage, anthocyanins started to accumulate, and the fruit was susceptible to diseases such as fungal infection. Expression of the transcription factor MYB86 was up-regulated during initial fruit development, which may promote anthocyanin accumulation. These results will aid future studies exploring the molecular mechanism underlying flowering and fruit set of rabbiteye blueberry.

Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time

Dendrobium is a semi-shade epiphytic Orchidaceae herb with important ornamental and medicinal value. Parts of the cultivation of Dendrobium germplasm resources, as well as the identification of medicinal components, are more studied, but the functional characterization of the flowering regulation in Dendrobium plants is less reported. Here, six PEBP family genes (DhFT3, DhFT1, DhMFT, DhTFL1b, DhFT2, and DhTFL1a) were identified from the Dendrobium huoshanense genome. The chromosome-level mapping showed that these genes were sequentially distributed on chromosomes 6, 9, 15, and 17. The paralogous gene DhTFL1b corresponded to DhTFL1a, which was determined through tandem duplication. The gene structure and conserved motif of DhPEBP indicated five PEBP genes apart from DhMFT contained four exons and three introns entirely. The phylogeny analysis showed that the PEBP gene family in A. thaliana, O. sativa, Z. mays, S. lycopersicum, and P. equestris were classified into three subclades, FT, TFL, and MFT, which maintained a high homology with D. huoshanense. The conserved domain of the amino acid demonstrated that two highly conserved short motifs (DPDXP and GXHR) embed in DhPEBPs, which may contribute to the conformation of the ligand binding bag. The 86th position of DhFTs was tyrosine (Y), while the 83th and 87th of DhTFL1s belonged to histidine (H), suggesting they should have distinct functions in flowering regulation. The promoter of six DhPEBPs contained several cis-elements related to hormone induction, light response, and abiotic stress, which indicated they could be regulated by the environmental stress and endogenous signaling pathways. The qRT-PCR analysis of DhPEBPs in short-term days induced by GA indicated the gene expressions of all DhFTs were gradually increased, whereas the expression of DhTFL1 was decreased. The results implied that DhPEBPs have various regulatory functions in modulating flowering, which will provide a scientific reference for the flowering regulation of Dendrobium plants.

Population responses to a historic drought across the range of the common monkeyflower (Mimulus guttatus)

PREMISE

Due to climate change, more frequent and intense periodic droughts are predicted to increasingly pose major challenges to the persistence of plant populations. When a severe drought occurs over a broad geographical region, independent responses by individual populations provide replicated natural experiments for examining the evolution of drought resistance and the potential for evolutionary rescue.

METHODS

We used a resurrection approach to examine trait evolution in populations of the common monkeyflower, Mimulus guttatus, exposed to a record drought in California from 2011 to 2017. Specifically, we compared variation in traits related to drought escape and avoidance from seeds collected from 37 populations pre- and post-drought in a common garden. In a parallel experiment, we evaluated fitness in two populations, one which thrived and one which was nearly extirpated during the drought, under well-watered and dry-down conditions.

RESULTS

We observed substantial variation among populations in trait evolution. In the subset of populations where phenotypes changed significantly, divergence proceeded along trait correlations with some populations flowering rapidly with less vegetative tissue accumulation and others delaying flowering with greater vegetative tissue accumulation. The degree of trait evolution was only weakly correlated with drought intensity but strongly correlated with initial levels of standing variation. Fitness was higher in the post-drought than pre-drought accessions in both treatments for the thriving population, but lower in both treatments for the nearly extirpated population.

CONCLUSIONS

Together, our results indicate that evolutionary responses to drought are context dependent and reflect the standing genetic variation and genetic correlations present within populations.

Changes in phenological events in response to a global warming scenario reveal greater adaptability of winter annual compared with summer annual arabidopsis ecotypes

BACKGROUND AND AIMS

The impact of global warming on life cycle timing is uncertain. We investigated changes in life cycle timing in a global warming scenario. We compared Arabidopsis thaliana ecotypes adapted to the warm/dry Cape Verdi Islands (Cvi), Macaronesia, and the cool/wet climate of the Burren (Bur), Ireland, Northern Europe. These are obligate winter and summer annuals, respectively.

METHODS

Using a global warming scenario predicting a 4 °C temperature rise from 2011 to approx. 2080, we produced F1 seeds at each end of a thermogradient tunnel. Each F1 cohort (cool and warm) then produced F2 seeds at both ends of the thermal gradient in winter and summer annual life cycles. F2 seeds from the winter life cycle were buried at three positions along the gradient to determine the impact of temperature on seedling emergence in a simulated winter life cycle.

KEY RESULTS

In a winter life cycle, increasing temperatures advanced flowering time by 10.1 d °C-1 in the winter annual and 4.9 d °C-1 in the summer annual. Plant size and seed yield responded positively to global warming in both ecotypes. In a winter life cycle, the impact of increasing temperature on seedling emergence timing was positive in the winter annual, but negative in the summer annual. Global warming reduced summer annual plant size and seed yield in a summer life cycle.

CONCLUSIONS

Seedling emergence timing observed in the north European summer annual ecotype may exacerbate the negative impact of predicted increased spring and summer temperatures on their establishment and reproductive performance. In contrast, seedling establishment of the Macaronesian winter annual may benefit from higher soil temperatures that will delay emergence until autumn, but which also facilitates earlier spring flowering and consequent avoidance of high summer temperatures. Such plasticity gives winter annual arabidopsis ecotypes a distinct advantage over summer annuals in expected global warming scenarios. This highlights the importance of variation in the timing of seedling establishment in understanding plant species responses to anthropogenic climate change.

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.

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.

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.

How do Plants Keep their Functional Integrity?

Unlike animals, plants possess a non-strict and sometimes very fuzzy morphology. Mutual proportions of plant parts can vary to a much greater extent than in animals, changing according to the environmental conditions and the plant needs of nutrients, water and light. Despite the existence of this fundamental difference between plants and animals, it passes almost non-reflected in most studies on plants. In this review we make a preliminary attempt to gather together the mechanisms by which plants preserve their integrity, not loosing at the same time the physiological (and morphological) flexibility which allows them adapting to the different environments they can populate.