Flowering time regulation produces much fruit

Unraveling the Secrets of Early-Maturity and Short-Duration Bread Wheat in Unpredictable Environments

In response to the escalating challenges posed by unpredictable environmental conditions, the pursuit of early maturation in bread wheat has emerged as a paramount research endeavor. This comprehensive review delves into the multifaceted landscape of strategies and implications surrounding the unlocking of early maturation in bread wheat varieties. Drawing upon a synthesis of cutting-edge research in genetics, physiology, and environmental science, this review elucidates the intricate mechanisms underlying early maturation and its potential ramifications for wheat cultivation in dynamic environments. By meticulously analyzing the genetic determinants, physiological processes, and environmental interactions shaping early maturation, this review offers valuable insights into the complexities of this trait and its relevance in contemporary wheat breeding programs. Furthermore, this review critically evaluates the trade-offs inherent in pursuing early maturation, navigating the delicate balance between accelerated development and optimal yield potential. Through a meticulous examination of both challenges and opportunities, this review provides a comprehensive framework for researchers, breeders, and agricultural stakeholders to advance our understanding and utilization of early maturation in bread wheat cultivars, ultimately fostering resilience and sustainability in wheat production systems worldwide.

Functional characterization of Arabidopsis hydroxynitrile lyase in response to abiotic stress and the regulation of flowering time

BACKGROUND

Hydroxynitrile lyases (HNLs) are a class of hydrolytic enzymes from a wide range of sources, which play crucial roles in the catalysis of the reversible conversion of carbonyl compounds derived from cyanide and free cyanide in cyanogenic plant species. HNLs were also discovered in non-cyanogenic plants, such as Arabidopsis thaliana, and their roles remain unclear even during plant growth and reproduction.

METHODS AND RESULTS

The pattern of expression of the HNL in A. thaliana (AtHNL) in different tissues, as well as under abiotic stresses and hormone treatments, was examined by real-time quantitative reverse transcription PCR (qRT-PCR) and an AtHNL promoter-driven histochemical β-glucuronidase (GUS) assay. AtHNL is highly expressed in flowers and siliques, and the expression of AtHNL was dramatically affected by abiotic stresses and hormone treatments. The overexpression of AtHNL resulted in transgenic A. thaliana seedlings that were more tolerance to mannitol and salinity. Moreover, transgenic lines of A. thaliana that overexpressed this gene were less sensitive to abscisic acid (ABA). Altered expression of ABA/stress responsive genes was also observed in hnl mutant and AtHNL-overexpressing plants, suggesting AtHNL may play functional roles on regulating Arabidopsis resistance to ABA and abiotic stresses by affecting ABA/stress responsive gene expression. In addition, the overexpression of AtHNL resulted in earlier flowering, whereas the AtHNL mutant flowered later than the wild type (WT) plants. The expression of the floral stimulators CONSTANS (CO), SUPPRESSOR OF OVER EXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS T (FT) was upregulated in plants that overexpressed AtHNL when compared with the WT plants. In contrast, expression of the floral repressor FLOWERING LOCUS C (FLC) was upregulated in AtHNL mutants and downregulated in plants that overexpressed AtHNL compared to the WT plants.

CONCLUSION

This study revealed that AtHNL can be induced under abiotic stresses and ABA treatment, and genetic analysis showed that AtHNL could also act as a positive regulator of abiotic stress and ABA tolerance, as well as flowering time.

How to awaken a sleeping giant: antagonistic expression of Flowering locus T homologs and elements of the age-related pathway are associated with the flowering transition in Agave tequilana

KEY MESSAGE

Antagonistic expression of Flowering locus T proteins and the ageing pathway via miRNAs and sugar metabolism regulate the initiation of flowering in A. tequilana. Flowering in commercial plantations of Agave tequilana signals that plants are ready to harvest for tequila production. However, time of flowering is often unpredictable and a detailed understanding of the process would be beneficial in the field, for breeding and for the development of future research. This report describes the functional analysis of A. tequilana FLOWERING LOCUS T (FT) genes by heterologous expression in A. thaliana and in situ hybridization in agave plants. The gene structures of the Agave tequilana FT family are also described and putative regulatory promoter elements were identified. Most Agave species have monocarpic, perennial life cycles that can last over 25 years during which plants do not respond to the normal environmental signals which induce flowering, suggesting that the ageing pathway as described in Arabidopsis may play an important role in determining flowering time in these species. Elements of this pathway were analyzed and in silico data is presented that supports the regulation of SQUAMOSA PROMOTER BINDING LIKE proteins (SPL), APETALA2 (AP2) proteins and members of Plant Glycoside Hydrolase Family 32 (PGHF32) by interactions with miRNAs 156, 172 and 164 during the initiation of flowering in A. tequilana.

WRKY transcription factors modulate flowering time and response to environmental changes

WRKY transcription factors (TFs), originating in green algae, regulate flowering time and responses to environmental changes in plants. However, the molecular mechanisms underlying the role of WRKY TFs in the correlation between flowering time and environmental changes remain unclear. Therefore, this review summarizes the association of WRKY TFs with flowering pathways to accelerate or delay flowering. WRKY TFs are implicated in phytohormone pathways, such as ethylene, auxin, and abscisic acid pathways, to modulate flowering time. WRKY TFs can modulate salt tolerance by regulating flowering time. WRKY TFs exhibit functional divergence in modulating environmental changes and flowering time. In summary, WRKY TFs are involved in complex pathways and modulate response to environmental changes, thus regulating flowering time.

Regulatory frameworks involved in the floral induction, formation and developmental programming of woody horticultural plants: a case study on blueberries

Flowering represents a crucial stage in the life cycles of plants. Ensuring strong and consistent flowering is vital for maintaining crop production amidst the challenges presented by climate change. In this review, we summarized key recent efforts aimed at unraveling the complexities of plant flowering through genetic, genomic, physiological, and biochemical studies in woody species, with a special focus on the genetic control of floral initiation and activation in woody horticultural species. Key topics covered in the review include major flowering pathway genes in deciduous woody plants, regulation of the phase transition from juvenile to adult stage, the roles of CONSTANS (CO) and CO-like gene and FLOWERING LOCUS T genes in flower induction, the floral regulatory role of GA-DELLA pathway, and the multifunctional roles of MADS-box genes in flowering and dormancy release triggered by chilling. Based on our own research work in blueberries, we highlighted the central roles played by two key flowering pathway genes, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, which regulate floral initiation and activation (dormancy release), respectively. Collectively, our survey shows both the conserved and diverse aspects of the flowering pathway in annual and woody plants, providing insights into the potential molecular mechanisms governing woody plants. This paves the way for enhancing the resilience and productivity of fruit-bearing crops in the face of changing climatic conditions, all through the perspective of genetic interventions.

BnPLP1 Positively Regulates Flowering Time, Plant Height, and Main Inflorescence Length in Brassica napus

Protein prenylation mediated by the Arabidopsis thaliana PLURIPETALA (AtPLP) gene plays a crucial role in plant growth, development, and environmental response by adding a 15-carbon farnesyl group or one to two 20-carbon geranylgeranyl groups onto one to two cysteine residues at the C-terminus of the target protein. However, the homologous genes and their functions of AtPLP in rapeseed are unclear. In this study, bioinformatics analysis and gene cloning demonstrated the existence of two homologous genes of AtPLP in the Brassica napus L. genome, namely, BnPLP1 and BnPLP2. Evolutionary analysis revealed that BnPLP1 originated from the B. rapa L. genome, while BnPLP2 originated from the B. oleracea L. genome. Genetic transformation analysis revealed that the overexpression of BnPLP1 in Arabidopsis plants exhibited earlier flowering initiation, a prolonged flowering period, increased plant height, and longer main inflorescence length compared to the wild type. Contrarily, the downregulation of BnPLP1 expression in B. napus plants led to delayed flowering initiation, shortened flowering period, decreased plant height, and reduced main inflorescence length compared to the wild type. These findings indicate that the BnPLP1 gene positively regulates flowering time, plant height, and main inflorescence length. This provides a new gene for the genetic improvement of flowering time and plant architecture in rapeseed.

MED8 regulates floral transition in Arabidopsis by interacting with FPA

Success in plant reproduction is highly dependent on the correct timing of the floral transition, which is tightly regulated by the flowering pathways. In the model plant Arabidopsis thaliana, the central flowering repressor FLOWERING LOCUS C (FLC) is precisely regulated by multiple flowering time regulators in the vernalization pathway and autonomous pathway, including FPA. Here we report that Arabidopsis MEDIATOR SUBUNIT 8 (MED8) promotes floral transition in Arabidopsis by recruiting FPA to the FLC locus to repress FLC expression. Loss of MED8 function leads to a significant late-flowering phenotype due to increased FLC expression. We further show that MED8 directly interacts with FPA in the nucleus and recruits FPA to the FLC locus. Moreover, MED8 is indispensable for FPA's function in controlling flowering time and regulating FLC expression. Our study thus reveals a flowering mechanism by which the Mediator subunit MED8 represses FLC expression by facilitating the binding of FPA to the FLC locus to ensure appropriate timing of flowering for reproductive success.

PHD finger proteins function in plant development and abiotic stress responses: an overview

The plant homeodomain (PHD) finger with a conserved Cys4-His-Cys3 motif is a common zinc-binding domain, which is widely present in all eukaryotic genomes. The PHD finger is the "reader" domain of methylation marks in histone H3 and plays a role in the regulation of gene expression patterns. Numerous proteins containing the PHD finger have been found in plants. In this review, we summarize the functional studies on PHD finger proteins in plant growth and development and responses to abiotic stresses in recent years. Some PHD finger proteins, such as VIN3, VILs, and Ehd3, are involved in the regulation of flowering time, while some PHD finger proteins participate in the pollen development, for example, MS, TIP3, and MMD1. Furthermore, other PHD finger proteins regulate the plant tolerance to abiotic stresses, including Alfin1, ALs, and AtSIZ1. Research suggests that PHD finger proteins, as an essential transcription regulator family, play critical roles in various plant biological processes, which is helpful in understanding the molecular mechanisms of novel PHD finger proteins to perform specific function.

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.

Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis

Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.

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.

Multiple transcriptome comparisons reveal the essential roles of FLOWERING LOCUS T in floral initiation and SOC1 and SVP in floral activation in blueberry

The flowering mechanisms, especially chilling requirement-regulated flowering, in deciduous woody crops remain to be elucidated. Flower buds of northern highbush blueberry cultivar Aurora require approximately 1,000 chilling hours to bloom. Overexpression of a blueberry FLOWERING LOCUS T (VcFT) enabled precocious flowering of transgenic “Aurora” mainly in non-terminated apical buds during flower bud formation, meanwhile, most of the mature flower buds could not break until they received enough chilling hours. In this study, we highlighted two groups of differentially expressed genes (DEGs) in flower buds caused by VcFT overexpression (VcFT-OX) and full chilling. We compared the two groups of DEGs with a focus on flowering pathway genes. We found: 1) In non-chilled flower buds, VcFT-OX drove a high VcFT expression and repressed expression of a major MADS-box gene, blueberry SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (VcSOC1) resulting an increased VcFT/VcSOC1 expression ratio; 2) In fully chilled flower buds that are ready to break, the chilling upregulated VcSOC1 expression in non-transgenic “Aurora” and repressed VcFT expression in VcFT-OX “Aurora”, and each resulted in a decreased ratio of VcFT to VcSOC1; additionally, expression of a blueberry SHORT VEGETATIVE PHASE (VcSVP) was upregulated in chilled flower buds of both transgenic and non-transgenic’ “Aurora”. Together with additional analysis of VcFT and VcSOC1 in the transcriptome data of other genotypes and tissues, we provide evidence to support that VcFT expression plays a significant role in promoting floral initiation and that VcSOC1 expression is a key floral activator. We thus propose a new hypothesis on blueberry flowering mechanism, of which the ratios of VcFT-to-VcSOC1 at transcript levels in the flowering pathways determine flower bud formation and bud breaking. Generally, an increased VcFT/VcSOC1 ratio or increased VcSOC1 in leaf promotes precocious flowering and flower bud formation, and a decreased VcFT/VcSOC1 ratio with increased VcSOC1 in fully chilled flower buds contributes to flower bud breaking.

The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions

Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.

Fruit growth and development in apple: a molecular, genomics and epigenetics perspective

Fruit growth and development are physiological processes controlled by several internal and external factors. This complex regulatory mechanism comprises a series of events occurring in a chronological order over a growing season. Understanding the underlying mechanism of fruit development events, however, requires consideration of the events occurring prior to fruit development such as flowering, pollination, fertilization, and fruit set. Such events are interrelated and occur in a sequential order. Recent advances in high-throughput sequencing technology in conjunction with improved statistical and computational methods have empowered science to identify some of the major molecular components and mechanisms involved in the regulation of fruit growth and have supplied encouraging successes in associating genotypic differentiation with phenotypic observations. As a result, multiple approaches have been developed to dissect such complex regulatory machinery and understand the genetic basis controlling these processes. These methods include transcriptomic analysis, quantitative trait loci (QTLs) mapping, whole-genome approach, and epigenetics analyses. This review offers a comprehensive overview of the molecular, genomic and epigenetics perspective of apple fruit growth and development that defines the final fruit size and provides a detailed analysis of the mechanisms by which fruit growth and development are controlled. Though the main emphasis of this article is on the molecular, genomic and epigenetics aspects of fruit growth and development, we will also deliver a brief overview on events occurring prior to fruit growth.

Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot

Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.

Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed

Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.

The Genome-Wide Identification of Long Non-Coding RNAs Involved in Floral Thermogenesis in Nelumbo nucifera Gaertn

The sacred lotus (Nelumbo nucifera Gaertn.) can maintain a stable floral chamber temperature when blooming, despite ambient temperature fluctuations; however, the long non-coding RNAs (lncRNAs) involved in floral thermogenesis remain unclear. In the present study, we obtain comprehensive lncRNAs expression profiles from receptacles at five developmental stages by strand-specific RNA sequencing to reveal the lncRNAs regulatory mechanism of the floral thermogenesis of N. nucifera. A total of 22,693 transcripts were identified as lncRNAs, of which approximately 44.78% had stage-specific expression patterns. Subsequently, we identified 2579 differential expressed lncRNAs (DELs) regulating 2367 protein-coding genes mainly involved in receptacle development and reproductive process. Then, lncRNAs with floral thermogenesis identified by weighted gene co-expression network analysis (WGCNA) were mainly related to sulfur metabolism and mitochondrial electron transport chains. Meanwhile, 70 lncRNAs were predicted to act as endogenous target mimics (eTMs) for 29 miRNAs and participate in the regulation of 16 floral thermogenesis-related genes. Our dual luciferase reporter assays indicated that lncRNA LTCONS_00068702 acted as eTMs for miR164a_4 to regulate the expression of TrxL2 gene. These results deepen our understanding of the regulation mechanism of floral thermogenesis by lncRNAs and accumulate data for further research.

C-terminal domain phosphatase-like 1 (CPL1) is involved in floral transition in Arabidopsis

BACKGROUND

RNA polymerase II plays critical roles in transcription in eukaryotic organisms. C-terminal Domain Phosphatase-like 1 (CPL1) regulates the phosphorylation state of the C-terminal domain of RNA polymerase II subunit B1, which is critical in determining RNA polymerase II activity. CPL1 plays an important role in miRNA biogenesis, plant growth and stress responses. Although cpl1 mutant showes delayed-flowering phenotype, the molecular mechanism behind CPL1's role in floral transition is still unknown.

RESULTS

To study the role of CPL1 during the floral transition, we first tested phenotypes of cpl1-3 mutant, which harbors a point-mutation. The cpl1-3 mutant contains a G-to-A transition in the second exon, which results in an amino acid substitution from Glu to Lys (E116K). Further analyses found that the mutated amino acid (Glu) was conserved in these species. As a result, we found that the cpl1-3 mutant experienced delayed flowering under both long- and short-day conditions, and CPL1 is involved in the vernalization pathway. Transcriptome analysis identified 109 genes differentially expressed in the cpl1 mutant, with 2 being involved in floral transition. Differential expression of the two flowering-related DEGs was further validated by qRT-PCR.

CONCLUSIONS

Flowering genetic pathways analysis coupled with transciptomic analysis provides potential genes related to floral transition in the cpl1-3 mutant, and a framework for future studies of the molecular mechanisms behind CPL1's role in floral transition.

Characterization of genes associated with TGA7 during the floral transition

BACKGROUND

The TGACG-binding (TGA) family has 10 members that play vital roles in Arabidopsis thaliana defense responses and development. However, their involvement in controlling flowering time remains largely unknown and requires further investigation.

RESULTS

To study the role of TGA7 during floral transition, we first investigated the tga7 mutant, which displayed a delayed-flowering phenotype under both long-day and short-day conditions. We then performed a flowering genetic pathway analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal the differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 days after germination. For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences, with the majority (84.55 %) of mRNAs being between 500 and 3,000 nt. In total, 325 differentially expressed genes were identified between WT and tga7 mutant seedlings. Among them, four genes were associated with flowering time control. The differential expression of these four flowering-related genes was further validated by qRT-PCR.

CONCLUSIONS

Among these four differentially expressed genes associated with flowering time control, FLC and MAF5 may be mainly responsible for the delayed-flowering phenotype in tga7, as TGA7 expression was regulated by autonomous pathway genes. These results provide a framework for further studying the role of TGA7 in promoting flowering.

Combined Analysis of MicroRNAs and Target Genes Revealed miR156-SPLs and miR172-AP2 Are Involved in a Delayed Flowering Phenomenon After Chromosome Doubling in Black Goji (Lycium ruthencium)

Polyploidy, which is widely distributed in angiosperms, presents extremely valuable commercial applications in plant growth and reproduction. The flower development process of higher plants is essential for genetic improvement. Nevertheless, the reproduction difference between polyploidy and the polyploid florescence regulatory network from the perspective of microRNA (miRNA) remains to be elucidated. In this study, the autotetraploid of Lycium ruthenicum showed late-flowering traits compared with the progenitor. Combining the association of miRNA and next-generation transcriptome technology, the late-flowering characteristics triggered by chromosome duplication may be caused by the age pathway involved in miR156-SPLs and miR172-AP2, which inhibits the messenger RNA (mRNA) transcripts of FT in the leaves. Subsequently, FT was transferred to the shoot apical meristem (SAM) to inhibit the expression of the flowering integration factor SOC1, which can eventually result in delayed flowering time. Our exploration of the flowering regulation network and the control of the flowering time are vital to the goji producing in the late frost area, which provides a new perspective for exploring the intrinsic molecular mechanism of polyploid and the reproductive development of flowering plants.

Exploring PIF4 's contribution to early flowering in plants under daily variable temperature and its tissue-specific flowering gene network

Molecular mechanisms of how constant temperatures affect flowering time have been largely characterized in the model plant Arabidopsis thaliana; however, the effect of natural daily variable temperature outside laboratories is only partly explored. Several flowering genes have been shown to play important roles in temperature responses, including PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and FLOWERING LOCUS C (FLC), the two genes encoding for the transcription factors (TFs) that act antagonistically to regulate flowering time by activating and repressing floral integrator FLOWERING LOCUS T (FT), respectively. In this study, we have taken a multidisciplinary approach to explore the contribution of PIF4 to the early flowering observed in the daily variable temperature (VAR) and to broaden its transcriptional network using publicly available transcriptomic data. We observed early flowering in the natural accessions Col-0, C24 and their late flowering hybrid C24xCol grown under VAR, as compared with a constant temperature (CON). The loss-of-function mutation of PIF4 exhibits later flowering in VAR in both the Col-0 parent and the C24xCol hybrid, suggesting that PIF4, at least in part, contributes to acceleration of flowering in the VAR condition. To investigate the interplay between PIF4 and its flowering regulator counterparts, FLC and FT, we performed transcriptional analyses and found that VAR increased PIF4 transcription at the end of the day when temperature peaked at 32°C, when FT transcription was also elevated. On the other hand, we observed a decrease in FLC transcription in the 4-week-old plants grown in VAR, as well as in the plants with PIF4 overexpression grown in CON. These results raise a possibility that PIF4 might also regulate FT indirectly through the repression of FLC, in addition to the well-characterized direct control of PIF4 over FT. To further expand our view on the PIF4-orientated flowering gene network in response to temperature changes, we have constructed a coexpression-transcriptional regulatory network by combining publicly available transcriptomic data and gene regulatory interactions of PIF4 and its closely related flowering genes, PIF5, FLC, and ELF3. The network model reveals conserved and tissue-specific regulatory functions, which are useful for confirming as well as predicting the functions and regulatory interactions between these key flowering genes.

Genetic and plastic rewiring of food webs under climate change

Climate change is altering ecological and evolutionary processes across biological scales. These simultaneous effects of climate change pose a major challenge for predicting the future state of populations, communities and ecosystems. This challenge is further exacerbated by the current lack of integration of research focused on these different scales.

We propose that integrating the fields of quantitative genetics and food web ecology will reveal new insights on how climate change may reorganize biodiversity across levels of organization. This is because quantitative genetics links the genotypes of individuals to population‐level phenotypic variation due to genetic (G), environmental (E) and gene‐by‐environment (G × E) factors. Food web ecology, on the other hand, links population‐level phenotypes to the structure and dynamics of communities and ecosystems.

We synthesize data and theory across these fields and find evidence that genetic (G) and plastic (E and G × E) phenotypic variation within populations will change in magnitude under new climates in predictable ways. We then show how changes in these sources of phenotypic variation can rewire food webs by altering the number and strength of species interactions, with consequences for ecosystem resilience. We also find evidence suggesting there are predictable asymmetries in genetic and plastic trait variation across trophic levels, which set the pace for phenotypic change and food web responses to climate change. Advances in genomics now make it possible to partition G, E and G × E phenotypic variation in natural populations, allowing tests of the hypotheses we propose.

By synthesizing advances in quantitative genetics and food web ecology, we provide testable predictions for how the structure and dynamics of biodiversity will respond to climate change.

Accession-specific flowering time variation in response to nitrate fluctuation in Arabidopsis thalian a

Flowering time, a key transition point from vegetative to reproductive growth, is regulated by an intrinsic complex of endogenous and exogenous signals including nutrient status. For hundreds of years, nitrogen has been well known to modulate flowering time, but the molecular genetic basis on how plants adapt to ever-changing nitrogen availability remains not fully explored. Here we explore how Arabidopsis natural variation in flowering time responds to nitrate fluctuation. Upon nitrate availability change, we detect accession- and photoperiod-specific flowering responses, which also feature a accession-specific dependency on growth traits. The flowering time variation correlates well with the expression of floral integrators, SOC1 and FT, in an accession-specific manner. We find that gene expression variation of key hub genes in the photoperiod-circadian-clock (GI), aging (SPLs) and autonomous (FLC) pathways associates with the expression change of these integrators, hence flowering time variation. Our results thus shed light on the molecular genetic mechanisms on regulation of accession- and photoperiod-specific flowering time variation in response to nitrate availability.

WRKY transcription factors WRKY12 and WRKY13 interact with SPL10 to modulate age-mediated flowering

WRKY12 and WRKY13 are two WRKY transcription factors that play important roles in the control of flowering time under short-day (SD) conditions. The temporally regulated expression of WRKY12 and WRKY13 indicates that they may be involved in the age-mediated flowering pathway. However, their roles in this pathway are poorly understood. Here, we show that the transcription of WRKY12 and WRKY13 is directly regulated by SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a transcription factor downstream of the age pathway. Binding and activation analyses revealed that SPL10 functions as a positive regulator of WRKY12 and a negative regulator of WRKY13. Further mechanistic investigation revealed that WRKY12 and WRKY13 physically interact with SPL10 and that both of them bind to the promoter of miR172b. Thus, the WRKY12-SPL10 and WRKY13-SPL10 interactions facilitate and inhibit SPL10 transcriptional function, respectively, to regulate miR172b expression. Together, our results show that WRKY12 and WRKY13 participate in the control of age-mediated flowering under SD conditions though physically interacting with SPLs and co-regulating the target gene miR172b.

Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals

Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.

Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa)

Mapping and resequencing of two allelic early bolting mutants ebm5-1 and ebm5-2 revealed that the BrSDG8 gene is related to bolting in Chinese cabbage (Brassica rapa ssp. pekinensis). Bolting influences the leafy head formation and seed yield of Chinese cabbage therefore being an important agronomic trait. Herein, two allelic early bolting mutants, ebm5-1 and ebm5-2, stably inherited in Chinese cabbage were obtained from wild-type 'FT' seeds by ethyl methane sulfonate mutagenesis. Both mutants flowered significantly earlier than 'FT,' and genetic analysis revealed that the early bolting of the two mutants was controlled by one recessive nuclear gene. With BSR-seq, the mutations originating lines ebm5-1 and ebm5-2 were located to the same region in chromosome A07. Using the 1741 F₂ individuals with the ebm5-1 phenotype as the mapping population, this region was narrowed to 56.24 kb between markers InDel18 and InDel45. A single-nucleotide polymorphism (SNP) was aligned to the BraA07g040740.3C (BrSDG8) region by whole-genome resequencing of ebm5-1 mutant and 'FT.' BrSDG8 is a homolog of Arabidopsis thaliana SDG8 encoding a histone methyltransferase affecting H3K4 trimethylation in FLOWERING LOCUS C chromatin. Comparative sequencing established that the SNP occurred on BrSDG8 17th exon in ebm5-1. Genotype analysis showed full co-segregation of the early bolting phenotype with this SNP. Cloning of allelic mutant ebm5-2 indicated that it harbors a deletion mutation on the 12th exon of BrSDG8. Quantitative real-time PCR analysis indicated that BrSDG8 expression level was observably lower in mutant ebm5-1 than in 'FT.' Overall, the present results provide strong evidence that BrSDG8 mutation leads to early bolting in Chinese cabbage, thereby providing a basis to understand the molecular mechanisms underlying this phenotype.

Duration of cold exposure defines the rate of reactivation of a perennial FLC orthologue via H3K27me3 accumulation

Vernalisation is the process in which long-term cold exposure makes plants competent to flower. In vernalisation of Arabidopsis thaliana, a floral repressor, AtFLC, undergoes epigenetic silencing. Although the silencing of AtFLC is maintained under warm conditions after a sufficient duration of cold, FLC orthologues are reactivated under the same conditions in perennial plants, such as A. halleri. In contrast to the abundant knowledge on cold requirements in AtFLC silencing, it has remained unknown how cold duration affects the reactivation of perennial FLC. Here, we analysed the dynamics of A. halleri FLC (AhgFLC) mRNA, H3K4me3, and H3K27me3 over 8 weeks and 14 weeks cold followed by warm conditions. We showed that the minimum levels of AhgFLC mRNA and H3K4me3 were similar between 8 and 14 weeks vernalisation; however, the maximum level of H3K27me3 was higher after 14 weeks than after 8 weeks vernalisation. Combined with mathematical modelling, we showed that H3K27me3 prevents a rapid increase in AhgFLC expression in response to warm temperatures after vernalisation, which controls AhgFT expression and the initiation of flowering. Thus, the duration of cold defines the rate of AhgFLC reactivation via the buffering function of H3K27me3 against temperature increase.

Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines

Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene obtained from population genomic studies to a wild type under long- and short-day conditions. We also did the same for a collection of randomly chosen genes that had not been identified as candidates. We validated the well-known effect of long-day conditions in accelerating flowering time and found that gene disruption caused by insertional mutagenesis tends to delay flowering. Surprisingly, we found that knockouts in random genes were just as likely to produce significant phenotypic effects as knockouts in candidate genes. T-DNA insertions at a handful of candidate genes that had previously been identified as outlier loci showed significant delays in flowering time under both long and short days, suggesting that they are promising candidates for future investigation.

KHZ1 and KHZ2, novel members of the autonomous pathway, repress the splicing efficiency of FLC pre-mRNA in Arabidopsis

As one of the most important events during the life cycle of flowering plants, the floral transition is of crucial importance for plant propagation and requires the precise coordination of multiple endogenous and external signals. There have been at least four flowering pathways (i.e. photoperiod, vernalization, gibberellin, and autonomous) identified in Arabidopsis. We previously reported that two Arabidopsis RNA-binding proteins, KHZ1 and KHZ2, redundantly promote flowering. However, the underlying mechanism was unclear. Here, we found that the double mutant khz1 khz2 flowered late under both long-day and short-day conditions, but responded to vernalization and gibberellin treatments. The late-flowering phenotype was almost completely rescued by mutating FLOWERING LOCUS C (FLC) and fully rescued by overexpressing FLOWERING LOCUS T (FT). Additional experiments demonstrated that the KHZs could form homodimers or interact to form heterodimers, localized to nuclear dots, and repressed the splicing efficiency of FLC pre-mRNA. Together, these data indicate that the KHZs could promote flowering via the autonomous pathway by repressing the splicing efficiency of FLC pre-mRNA.

Nup96 and HOS1 Are Mutually Stabilized and Gate CONSTANS Protein Level, Conferring Long-Day Photoperiodic Flowering Regulation in Arabidopsis

The nuclear pore complex profoundly affects the timing of flowering; however, the underlying mechanisms are poorly understood. Here, we report that Nucleoporin96 (Nup96) acts as a negative regulator of long-day photoperiodic flowering in Arabidopsis (Arabidopsis thaliana). Through multiple approaches, we identified the E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 (HOS1) and demonstrated its interaction in vivo with Nup96. Nup96 and HOS1 mainly localize and interact on the nuclear membrane. Loss of function of Nup96 leads to destruction of HOS1 proteins without a change in their mRNA abundance, which results in overaccumulation of the key activator of long-day photoperiodic flowering, CONSTANS (CO) proteins, as previously reported in hos1 mutants. Unexpectedly, mutation of HOS1 strikingly diminishes Nup96 protein level, suggesting that Nup96 and HOS1 are mutually stabilized and thus form a novel repressive module that regulates CO protein turnover. Therefore, the nup96 and hos1 single and nup96 hos1 double mutants have highly similar early-flowering phenotypes and overlapping transcriptome changes. Together, this study reveals a repression mechanism in which the Nup96-HOS1 repressive module gates the level of CO proteins and thereby prevents precocious flowering in long-day conditions.

Genetic and Epigenetic Understanding of the Seasonal Timing of Flowering

The developmental transition to flowering in many plants is timed by changing seasons, which enables plants to flower at a season that is favorable for seed production. Many plants grown at high latitudes perceive the seasonal cues of changing day length and/or winter cold (prolonged cold exposure), to regulate the expression of flowering-regulatory genes through the photoperiod pathway and/or vernalization pathway, and thus align flowering with a particular season. Recent studies in the model flowering plant Arabidopsis thaliana have revealed that diverse transcription factors engage various chromatin modifiers to regulate several key flowering-regulatory genes including FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) in response to seasonal signals. Here, we summarize the current understanding of molecular and chromatin-regulatory or epigenetic mechanisms underlying the vernalization response and photoperiodic control of flowering in Arabidopsis. Moreover, the conservation and divergence of regulatory mechanisms for seasonal flowering in crops and other plants are briefly discussed.

Overexpression of TCP8 delays Arabidopsis flowering through a FLOWERING LOCUS C-dependent pathway

BACKGROUND

Flowering is a key process in the life cycle of plants. The transition from vegetative to reproductive growth is thus under sophisticated regulation by endogenous and environmental signals. The plant-specific Teosinte Branched 1/Cycloidea/Proliferating Cell Factors (TCP) family transcription factors are involved in many biological processes, but their roles in regulating flowering have not been totally elucidated.

RESULTS

We explored the role of Arabidopsis TCP8 in plant development and, especially, in flowering control. Overexpression of TCP8 significantly delayed flowering under both long-day and short-day conditions and dominant repression by TCP8 led to various growth defects. The upregulation of TCP8 led to more accumulated mRNA level of FLOWERING LOCUS C (FLC), a central floral repressor of Arabidopsis. TCP8 functions in an FLC-dependent manner, as TCP8 overexpression in the flc-6 loss-of-function mutant failed to delay flowering. The vernalization treatment could reverse the late flowering phenotype caused by TCP8 overexpression.

CONCLUSIONS

Our results provide evidence for a role of TCP8 in flowering control and add to our knowledge of the molecular basis of TCP8 function.

GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

Background

Transition to flowering at the right time is critical for local adaptation and to maximize grain yield in crops. Canola is an important oilseed crop with extensive variation in flowering time among varieties. However, our understanding of underlying genes and their role in canola productivity is limited.

Results

We report our analyses of a diverse GWAS panel (300–368 accessions) of canola and identify SNPs that are significantly associated with variation in flowering time and response to photoperiod across multiple locations. We show that several of these associations map in the vicinity of FLOWERING LOCUS T (FT) paralogs and its known transcriptional regulators. Complementary QTL and eQTL mapping studies, conducted in an Australian doubled haploid population, also detected consistent genomic regions close to the FT paralogs associated with flowering time and yield-related traits. FT sequences vary between accessions. Expression levels of FT in plants grown in field (or under controlled environment cabinets) correlated with flowering time. We show that markers linked to the FT paralogs display association with variation in multiple traits including flowering time, plant emergence, shoot biomass and grain yield.

Conclusions

Our findings suggest that FT paralogs not only control flowering time but also modulate yield-related productivity traits in canola.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5964-y) contains supplementary material, which is available to authorized users.

Characterization of Flowering Time Mutants

Timing of flowering, which is adapted to the ambient environment, is one of the key traits to ensure the reproductive success of plants. Our current understanding of the complex genetic control network of this trait is mostly derived from the studies in the model plant species Arabidopsis thaliana. Arabidopsis thaliana is an annual facultative long-day plant, whose flowering time is controlled by numerous environmental and endogenous factors. Here we briefly summarize the genetic pathways that promote flowering of Arabidopsis and describe standard protocols to characterize the flowering time phenotype of Arabidopsis mutants under laboratory conditions.

To Splice or to Transcribe: SKIP-Mediated Environmental Fitness and Development in Plants

Gene expression in eukaryotes is controlled at multiple levels, including transcriptional and post-transcriptional levels. The transcriptional regulation of gene expression is complex and includes the regulation of the initiation and elongation phases of transcription. Meanwhile, the post-transcriptional regulation of gene expression includes precursor messenger RNA (pre-mRNA) splicing, 5' capping, and 3' polyadenylation. Among these events, pre-mRNA splicing, conducted by the spliceosome, plays a key role in the regulation of gene expression, and the efficiency and precision of pre-mRNA splicing are critical for gene function. Ski-interacting protein (SKIP) is an evolutionarily conserved protein from yeast to humans. In plants, SKIP is a bifunctional regulator that works as a splicing factor as part of the spliceosome and as a transcriptional regulator via interactions with the transcriptional regulatory complex. Here, we review how the functions of SKIP as a splicing factor and a transcriptional regulator affect environmental fitness and development in plants.

Arabidopsis U2AF65 Regulates Flowering Time and the Growth of Pollen Tubes

During pre-mRNA splicing, U2 small nuclear ribonucleoprotein auxiliary factor 65 (U2AF65) interacts with U2AF35 and splicing factor 1 (SF1), allowing for the recognition of the 3'-splice site by the ternary complex. The functional characterization of U2AF65 homologs has not been performed in Arabidopsis thaliana yet. Here, we show that normal plant development, including floral transition, and male gametophyte development, requires two Arabidopsis U2AF65 isoforms (AtU2AF65a and AtU2AF65b). Loss-of-function mutants of these two isoforms displayed opposite flowering phenotypes: atu2af65a mutants showed late flowering, whereas atu2af65b mutants were characterized by slightly early flowering, as compared to that in the wild-type (Col-0) plants. These abnormal flowering phenotypes were well-correlated with the expression patterns of the flowering time genes such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT). However, the two atu2af65 mutants did not display any morphological abnormalities or alterations in abiotic stress tests. Double mutation of the AtU2AF65a and AtU2AF65b genes resulted in non-viable seeds due to defective male gametophyte. In vitro pollen germination test revealed that mutations in both AtU2AF65a and AtU2AF65b genes significantly impaired pollen tube growth. Collectively, our findings suggest that two protein isoforms of AtU2AF65 are differentially involved in regulating flowering time and display a redundant role in pollen tube growth.

An invaluable transgenic blueberry for studying chilling-induced flowering in woody plants

BACKGROUND

Many deciduous woody crops require a minimum level of chilling to break dormancy and allow the seasonal growth of vegetative and floral buds. In this study, we report the discovery of an invaluable transgenic event of the blueberry cultivar 'Legacy' (hereafter, Mu-Legacy) for studying chilling-induced flowering in woody plants. Mu-legacy and its progeny provide a unique material to study the unknown mechanism of chilling-mediated flowering in woody plants.

RESULTS

Unlike nontransgenic 'Legacy' and plants of 48 other transgenic events, Mu-Legacy plants were able to flower under nonchilling conditions and had early flower bud formation, reduced plant size, and reduced chilling requirement for normal flowering. These characteristics were heritable and also observed in self-pollinated, transgenic T1 progenies of Mu-Legacy. A 47-Kbp genomic sequence surrounding the transgene insertion position was identified. RNA-sequencing data showed increased expression of a RESPONSE REGULATOR 2-like gene (VcRR2), located adjacent to the insertion position in Mu-Legacy and likely driven by the CaMV 35S promoter of the transgene. The Mu-Legacy showed 209 differentially expressed genes (DEGs) in nonchilled flower buds (compared to nontransgenic 'Legacy'), of which only four DEGs were in the flowering pathway. This suggests altered expression of these few genes, VcRR2 and four flowering DEGs, is sufficient to significantly change flowering behavior in Mu-Legacy.

CONCLUSIONS

The significance of VcRR2 in Mu-Legacy suggests that the VcRR2-involved cytokinin pathway likely contributes to the major differences in chilling-mediated flowering between woody and herbaceous plants. More importantly, Mu-Legacy shows increased yield potential, a decreased chilling requirement, and better winter hardiness than many low-chilling cultivars growing in southern warm winter conditions.

Genome-wide survey of potato MADS-box genes reveals that StMADS1 and StMADS13 are putative downstream targets of tuberigen StSP6A

Background

MADS-box genes encode transcription factors that are known to be involved in several aspects of plant growth and development, especially in floral organ specification. To date, the comprehensive analysis of potato MADS-box gene family is still lacking after the completion of potato genome sequencing. A genome-wide characterization, classification, and expression analysis of MADS-box transcription factor gene family was performed in this study.

Results

A total of 153 MADS-box genes were identified and categorized into MIKC subfamily (MIKC^C and MIKC^*) and M-type subfamily (Mα, Mβ, and Mγ) based on their phylogenetic relationships to the Arabidopsis and rice MADS-box genes. The potato M-type subfamily had 114 members, which is almost three times of the MIKC members (39), indicating that M-type MADS-box genes have a higher duplication rate and/or a lower loss rate during potato genome evolution. Potato MADS-box genes were present on all 12 potato chromosomes with substantial clustering that mainly contributed by the M-type members. Chromosomal localization of potato MADS-box genes revealed that MADS-box genes, mostly MIKC, were located on the duplicated segments of the potato genome whereas tandem duplications mainly contributed to the M-type gene expansion. The potato MIKC subfamily could be further classified into 11 subgroups and the TT16-like, AGL17-like, and FLC-like subgroups found in Arabidopsis were absent in potato. Moreover, the expressions of potato MADS-box genes in various tissues were analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the MIKC^C genes were mainly expressed in flower organs and several of them were highly expressed in stolon and tubers. StMADS1 and StMADS13 were up-regulated in the StSP6A-overexpression plants and down-regulated in the StSP6A-RNAi plant, and their expression in leaves and/or young tubers were associated with high level expression of StSP6A.

Conclusion

Our study identifies the family members of potato MADS-box genes and investigate the evolution history and functional divergence of MADS-box gene family. Moreover, we analyze the MIKC^C expression patterns and screen for genes involved in tuberization. Finally, the StMADS1 and StMADS13 are most likely to be downstream target of StSP6A and involved in tuber development.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5113-z) contains supplementary material, which is available to authorized users.

Transcriptome analysis and identification of genes associated with flower development in Rhododendron pulchrum Sweet (Ericaceae)

Flowering process is essential for plant development. However, the molecular mechanisms driving flower development of ornamental woody Rhododendron pulchrum Sweet are difficult to elucidate due to the lack of genomic data. In this research, high-throughput sequencing and comparative transcriptome analyses of R. pulchrum flowers collected at three key stages were performed: floral bud stage, early flowering stage, and full-flowering stage. Furthermore, expression of genes involved in flower development was also validated with quantitative real-time PCR (qRT-PCR). RNA-seq yielded 96,350,697 bp of clean reads, which were assembled into 98,610 unigenes with an average length of 717 bp. 58,279 (59.10%) unigenes could be annotated, including 324 major unigenes associated with floral development. In addition, ten modules (20,443 mRNAs) were dissected in the co-expression network. Especially, Flowering Locus (FLC) and Flowering Locus T (FT) were co-expressed. 9493 differentially expressed genes (DEGs) were scanned among three stages, and most DEGs existed between flower bud stage and early flowering stage. In particular, 79 DGEs associated with flowering process were enriched in 28 GO terms. Moreover, the expression levels of MYC2, EIN3, and ARR-B were all lowest at early flowering stage, while transcripts of MYC2, TIR1, CYCD3, COL-1, and EIN3 were all peaked at flower bud stage. Transcriptome profile presented here will benefit deep insights into molecular mechanism underlying R. pulchrum flowering process.

Phalaenopsis flowering locus VE regulates floral organ maturation

PaFVE is low ambient temperature-inducible and acts as a systemic regulator in the early stage of floral development in Phalaenopsis. Phalaenopsis aphrodite: subsp. formosana, a native orchid species of Taiwan, is an economically important ornamental crop that requires low ambient temperature for floral transition. Currently, limited genetic information about such orchid species hampers genetic manipulation for specific or improved floral traits, and the control of flowering time independent of temperature regulation. In this study, the sequence of the full-length of Phalaenopsis flowering locus VE (PaFVE) gene was determined. Spatial and temporal expression studies showed that mRNA transcripts of PaFVE were inducible by low ambient temperature, and high levels of expression occurred after spiking initiation and remained high throughout the early stage of floral development. Further investigation revealed that floral organ development was impeded in PaFVE-silenced P. aphrodite, but flowering time and floral organogenesis were not compromised. Analysis of the downstream flowering genes suggested that the delay in floral maturation is associated with a corresponding decrease in the expression of downstream flowering genes, PaSOC1, PaSOC1L and PaAGL24. The ectopic expression of PaFVE in Arabidopsis resulted in an accelerated flowering time, accompanied by an increase in the expression of AtSOC1, thus revealing the functional role of PaFVE as a floral regulator. Overall, our results demonstrate that PaFVE has evolutionarily diverged and conserved functions, and serves as a regulator of floral organ maturation in Phalaenopsis and a regulator of flowering time in Arabidopsis.

SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana

The reproductive success of plants largely depends on the correct programming of developmental phase transitions, particularly the shift from vegetative to reproductive growth. The timing of this transition is finely regulated by the integration of an array of environmental and endogenous factors. Nitrogen is the mineral macronutrient that plants require in the largest amount, and as such its availability greatly impacts on many aspects of plant growth and development, including flowering time. We found that nitrate signaling interacts with the age-related and gibberellic acid pathways to control flowering time in Arabidopsis thaliana. We revealed that repressors of flowering time belonging to the AP2-type transcription factor family including SCHLAFMUTZE (SMZ) and SCHNARCHZAPFEN (SNZ) are important regulators of flowering time in response to nitrate. Our results support a model whereby nitrate activates SMZ and SNZ via the gibberellin pathway to repress flowering time in Arabidopsis thaliana.

Transcription Factor WRKY75 Interacts with DELLA Proteins to Affect Flowering

Flowering time is tightly controlled by both endogenous and exogenous signals. Although several lines of evidence have suggested the involvement of WRKY transcription factors in floral initiation, the underlying mechanisms and signaling pathways involved remain elusive. Here, we newly identified Arabidopsis (Arabidopsis thaliana) WRKY DNA binding protein75 (WRKY75) as a positive regulator of flowering initiation. Mutation of WRKY75 resulted in a delay in flowering, whereas overexpression of WRKY75 significantly accelerated flowering in Arabidopsis. Gene expression analysis showed that the transcript abundance of the flowering time integrator gene FLOWERING LOCUS T (FT) was lower in wrky75 mutants than in the wild type, but greater in WRKY75-overexpressing plants. Chromatin immunoprecipitation assays revealed that WRKY75 directly binds to the promoter of FT Both in vivo and in vitro biochemical analyses demonstrated that WRKY75 interacts with DELLA proteins. We found that both REPRESSOR OF ga1-3 (RGA) RGA-LIKE1 (RGL1) and GA INSENSITIVE (GAI) can repress the activation ability of WRKY75, thereby attenuating expression of its regulon. Genetic analyses indicated that WRKY75 positively regulates flowering in a FT-dependent manner and overexpression of RGL1 or gain-of-function of GAI could partially rescue the early flowering phenotype of WRKY75-overexpressing plants. Taken together, our results demonstrate that WRKY75 may function as a new component of the GA-mediated signaling pathway to positively regulate flowering in Arabidopsis.

TAF15b, involved in the autonomous pathway for flowering, represses transcription of FLOWERING LOCUS C

TATA-binding protein-associated factors (TAFs) are general transcription factors within the transcription factor IID (TFIID) complex, which recognizes the core promoter of genes. In addition to their biochemical function, it is known that several TAFs are involved in the regulation of developmental processes. In this study, we found that TAF15b affects flowering time, especially through the autonomous pathway (AP) in Arabidopsis. The mutant taf15b shows late flowering compared with the wild type plant during both long and short days, and vernalization accelerates the flowering time of taf15b. In addition, taf15b shows strong upregulation of FLOWERING LOCUS C (FLC), a flowering repressor in Arabidopsis, and the flc taf15b double mutant completely offsets the late flowering of taf15b, indicating that TAF15b is a typical AP gene. The taf15b mutant also shows increased transcript levels of COOLAIR, an antisense transcript of FLC. Consistently, chromatin immunoprecipitation (ChIP) analyses showed that the TAF15b protein is enriched around both sense and antisense transcription start sites of the FLC locus. In addition, co-immunoprecipitation showed that TAF15b interacts with RNA polymerase II (Pol II), while ChIP showed increased enrichment of the phosphorylated forms, both serine 2 (Ser2) and Ser5, of the C-terminal domain of Pol II at the FLC locus, which is indicative of transcriptional elongation. Finally, taf15b showed higher enrichment of the active histone marker, H3K4me3, on FLC chromatin. Taken together, our results suggest that TAF15b affects flowering time through transcriptional repression of FLC in Arabidopsis.

RNA-seq analysis of apical meristem reveals integrative regulatory network of ROS and chilling potentially related to flowering in Litchi chinensis

Litchi is an important woody fruit tree. Floral initiation in litchi is triggered by low temperatures. However, defective flowering is a major challenge for litchi production in times of climate change and global warming. Previous studies have shown that the reactive oxygen species (ROS) generated by methyl viologen dichloride hydrate (MV) promotes flowering. In this study, potted trees were transferred to growth chambers for low-temperature (LT), medium-temperature (MT), and high-temperature (HT) treatments. Trees at MT were subjected to ROS treatment to promote flowering, and those at LT were induced to flower. RNA-sequencing was applied to obtain a global transcriptome of the apical meristem and reveal potential gene networks controlling the transformation from vegetative meristems (VM) into inflorescence meristems (IM). We assembled 73,117 unigenes with a mean size of 790 bp and 11741 unigenes were identified as both chilling and ROS responsive genes (CRRGs), of which 48 were identified as flowering-related CRRGs, 59 were plant hormone signal transduction CRRGs, and 146 were plant hormone biosynthesis-related CRRGs. Genes co-expression network analysis indicated inner relationships, suggesting that ROS and chilling promotes the VM to IM transition through a regulatory gene network of transcription factors, hormones, and flowering regulators.

Research progress on the autonomous flowering time pathway in Arabidopsis

The transition from vegetative to reproductive growth phase is a pivotal and complicated process in the life cycle of flowering plants which requires a comprehensive response to multiple environmental aspects and endogenous signals. In Arabidopsis, six regulatory flowering time pathways have been defined by their response to distinct cues, namely photoperiod, vernalization, gibberellin, temperature, autonomous and age pathways, respectively. Among these pathways, the autonomous flowering pathway accelerates flowering independently of day length by inhibiting the central flowering repressor FLC. FCA, FLD, FLK, FPA, FVE, FY and LD have been widely known to play crucial roles in this pathway. Recently, AGL28, CK2, DBP1, DRM1, DRM2, ESD4, HDA5, HDA6, PCFS4, PEP, PP2A-B'γ, PRMT5, PRMT10, PRP39-1, REF6, and SYP22 have also been shown to be involved in the autonomous flowering time pathway. This review mainly focuses on FLC RNA processing, chromatin modification of FLC, post-translational modification of FLC and other molecular mechanisms in the autonomous flowering pathway of Arabidopsis.

Fackel interacts with gibberellic acid signaling and vernalization to mediate flowering in Arabidopsis

Fackel (FK) is involved in the flowering of Arabidopsis mainly via the gibberellin pathway and vernalization pathway. This new function of FK is partially dependent on the FLOWERING LOCUS C ( FLC ). A common transitional process from vegetative stage to reproductive stage exists in higher plants during their life cycle. The initiation of flower bud differentiation, which plays a key role in the reproductive phase, is affected by both external environmental and internal regulatory factors. In this study, we showed that the Arabidopsis weak mutant allele fk-J3158, impaired in the FACKEL (FK) gene, which encodes a C-14 reductase involved in sterol biosynthesis, had a long life cycle and delayed flowering time in different photoperiods. In addition, FK overexpression lines displayed an earlier flowering phenotype than that of the wild type. These processes might be independent of the downstream brassinosteroid (BR) pathway and the autonomous pathway. However, the fk-J3158 plants were more sensitive than wild type in reducing the bolting days and total leaf number under gibberellic acid (GA) treatment. Further studies suggested that FK mutation led to an absence of endogenous GAs in fk-J3158 and FK gene expression was also affected under GA and paclobutrazol (PAC) treatment. Moreover, the delayed flowering time of fk-J3158 could be rescued by a 3-week vernalization treatment, and the expression of FLOWERING LOCUS C (FLC) was accordingly down-regulated in fk-J3158. We also demonstrated that flowering time of fk-J3158 flc double mutant was significantly earlier than that of fk-J3158 under the long-day (LD) conditions. All these results indicated that FK may affect the flowering in Arabidopsis mainly via GA pathway and vernalization pathway. And these effects are partially dependent on the FLOWERING LOCUS C (FLC).

Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants

Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism’s transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants.

The Binding Specificity of the PHD-Finger Domain of VIN3 Moderates Vernalization Response

Vernalization is a response to winter cold to initiate flowering in spring. VERNALIZATION INSENSITIVE3 (VIN3) is induced by winter cold and is essential to vernalization response in Arabidopsis (Arabidopsis thaliana). VIN3 encodes a PHD-finger domain that binds to modified histones in vitro. An alteration in the binding specificity of the PHD-finger domain of VIN3 results in a hypervernalization response. The hypervernalization response is achieved by increased enrichments of VIN3 and trimethylation of Histone H3 Lys 27 at the FLC locus without invoking the increased enrichment of Polycomb Repressive Complex 2. Our result shows that the binding specificity of the PHD-finger domain of VIN3 plays a role in mediating a proper vernalization response in Arabidopsis.

Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay

Eukaryotic cells use nonsense-mediated mRNA decay (NMD) to clear aberrant mRNAs from the cell, thus preventing the accumulation of truncated proteins. In Arabidopsis, two UP-Frameshift (UPF) proteins, UPF1 and UPF3, play a critical role in NMD. Although deficiency of UPF1 and UPF3 leads to various developmental defects, little is known about the mechanism underlying the regulation of flowering time by NMD. Here, we showed that the upf1-5 and upf3-1 mutants had a late-flowering phenotype under long-day conditions and the upf1-5 upf3-1 double mutants had an additive effect in delaying flowering time. RNA sequencing of the upf mutants revealed that UPF3 exerted a stronger effect than UPF1 in the UPF-mediated regulation of flowering time. Among genes known to regulate flowering time, FLOWERING LOCUS C (FLC) mRNA levels increased (up to 8-fold) in upf mutants, as confirmed by qPCR. The upf1-5, upf3-1, and upf1-5 upf3-1 mutants responded to vernalization, suggesting a role of FLC in delayed flowering of upf mutants. Consistent with the high FLC transcript levels and delayed flowering in upf mutants, levels of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) mRNAs were reduced in the upf mutants. However, RNA-seq did not identify an aberrant FLC transcript containing a premature termination codon (PTC), suggesting that FLC is not a direct target in the regulation of flowering time by NMD. Among flowering time regulators that act in an FLC-dependent manner, we found that MAF3, NF-YA2, NF-YA5, and TAF14 showed increased transcript levels in upf mutants. We also found that BBX19 and ATC, which act in an FLC-independent manner, showed increased transcript levels in upf mutants. An aberrant transcript containing a PTC was identified from MAF3 and BBX19 and the levels of the aberrant transcripts increased in upf mutants. Taking these results together, we propose that the late-flowering phenotype of upf mutants is mediated by at least two different pathways, namely, by MAF3 in an FLC-dependent manner and by BBX19 in an FLC-independent manner.