The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals

The RING-type E3 ligase, TaFRFP, regulates flowering by controlling a salicylic acid-mediated floral promotion

The initiation of transition to flowering is carefully managed by endogenous and environmental cues, which is critical for flowering plant reproductive success. Here, we found that wheat RING-type E3 ligase TaFRFP was highly expressed from the double ridge to degeneration stage (WS2.5-WS9). TaFRFP is localized in the nucleus and has E3 ligase activity in vitro. TaFRFP overexpression in Arabidopsis resulted in an early flowering phenotype, but to a lesser extent, under short-day conditions. Under the SA-treated condition, overexpression of TaFRFP shows higher root growth and has more accumulation of SA contents. A proteomic comparison revealed that the amount of FRL4A protein, a FRIGIDA LIKE 4 A, was considerably lower in SA-treated TaFRFP seedlings compared to normal condition. We further found that TaFRFP directly interacts with FRL4A in the nucleus and recruits it to the FLC locus in Arabidopsis. Moreover, an ubiquitination assay showed that TaFRPF physically interact and ubiquitinates TaFRL as a substrate. Our findings support the concept that the TaFRFP E3 ligase works as a positive regulator, and that the ubiquitination of its substrate proteins plays a significant role in controlling flowering time via an SA-dependent pathway.

Genome-wide evolutionary analysis of TKL_CTR1-DRK-2 gene family and functional characterization reveals that TaCTR1 positively regulates flowering time in wheat

BACKGROUND

Flowering time has an important effect on regional adaptation and yields for crops. The tyrosine kinase-like (TKL) gene family is widely existed and participates in many biological processes in plants. Furthermore, only few TKLs have been characterized functions in controlling flowering time in wheat.

RESULTS

Here, we report that TaCTR1, a tyrosine kinase-like (TKL) gene, regulates flowering time in wheat. Based on identification and evolutionary analysis of TKL_CTR1-DRK-2 subfamily in 15 plants, we proposed an evolutionary model for TaCTR1, suggesting that occurrence of some exon fusion events during evolution. The overexpression of TaCTR1 caused early flowering time in transgenic lines. Transcriptomics analysis enabled identification of mass differential expression genes including plant hormone (ET, ABA, IAA, BR) signaling, flavonoid biosynthesis, phenolamides and antioxidant, and flowering-related genes in TaCTR1 overexpression transgenic lines compared with WT plants. qRT-PCR results showed that the expression levels of ethylene (ET) signal-related genes (ETR, EIN, ERF) and flowering-related genes (FT, PPD1, CO, PRR, PHY) were altered in TaCTR1-overexpressing wheat compared with WT plants. Metabonomics analysis showed that flavonoid contents were altered.

CONCLUSIONS

Thus, the results show that TaCTR1 plays a positive role in controlling flowering time by activating various signaling pathways and regulating flowering-related genes, and will provide new insights on the mechanisms of wheat flowering regulation.

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.

Seasonal variation of two floral patterns in Clematis 'Vyvyan Pennell' and its underlying mechanism

BACKGROUND

Floral patterns are crucial for insect pollination and plant reproduction. Generally, once these patterns are established, they exhibit minimal changes under natural circumstances. However, the Clematis cultivar' Vyvyan Pennell', the apetalous lineage in the Ranunculaceae family, produces two distinct types of flowers during different seasons. The regulatory mechanism responsible for this phenomenon remains largely unknown. In this study, we aim to shed light on this floral development with shifting seasonal patterns by conducting extensive morphological, transcriptomic, and hormone metabolic analyses. Our findings are anticipated to contribute valuable insights into the diversity of flowers in the Ranunculaceae family.

RESULTS

The morphological analysis revealed that the presence of extra petaloid structures in the spring double perianth was a result of the transformation of stamens covered with trichomes during the 5th developmental stage. A de novo reference transcriptome was constructed by comparing buds and organs within double and single perianth from both seasons. A total of 209,056 unigenes were assembled, and 5826 genes were successfully annotated in all six databases. Among the 69,888 differentially expressed genes from the comparative analysis, 48 genes of utmost significance were identified. These critical genes are associated with various aspects of floral development. Interestingly, the A-, B-, and C-class genes exhibited a wider range of expression and were distinct within two seasons. The determination of floral organ identity was attributed to the collaborative functioning of all the three classes genes, aligning with a modified "fading border model". The phytohormones GA3, salicylic acid, and trans-zeatin riboside may affect the formation of the spring double perianth, whereas GA7 and abscisic acid may affect single flowers in autumn.

CONCLUSIONS

We presumed that the varying temperatures between the two seasons served as the primary factor in the alteration of floral patterns, potentially affecting the levels of plant hormones and expressions of organ identity genes. However, a more thorough investigation is necessary to fully comprehend the entire regulatory network. Nonetheless, our study provides some valuable informations for understanding the underlying mechanism of floral pattern alterations in Clematis.

Lack of the CCT domain changes the ability of mango MiCOL14A to resist salt and drought stress in Arabidopsis

CONSTANS (CO) is the key gene in the photoperiodic pathway that regulates flowering in plants. In this paper, a CONSTANS-like 14A (COL14A) gene was obtained from mango, and its expression patterns and functions were characterized. Sequence analysis shows that MiCOL14A-JH has an additional A base, which leads to code shifting in subsequent coding boxes and loss of the CCT domain. The MiCOL14A-JH and MiCOL14A-GQ genes both belonged to group Ⅲ of the CO/COL gene family. Analysis of tissue expression patterns showed that MiCOL14A was expressed in all tissues, with the highest expression in the leaves of seedling, followed by lower expression levels in the flowers and stems of adult leaves. However, there was no significant difference between different mango varieties. At different development stages of flowering, the expression level of MiCOL14A-GQ was the highest in the leaves before floral induction period, and the lowest at flowering stage, while the highest expression level of MiCOL14A-JH appeared in the leaves at flowering stage. The transgenic functional analysis showed that both MiCOL14A-GQ and MiCOL14A-JH induced delayed flowering of transgenic Arabidopsis. In addition, MiCOL14A-JH enhanced the resistance of transgenic Arabidopsis to drought stress, while MiCOL14A-GQ increased the sensitivity of transgenic Arabidopsis to salt stress. Further proteinprotein interaction analysis showed that MiCOL14A-JH directly interacted with MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1), CBL-interacting protein kinase 9 (MiCIPK9) and zinc-finger protein 4 (MiZFP4), but MiCOL14A-GQ could not interact with these three stress-related proteins. Together, our results demonstrated that MiCOL14A-JH and MiCOL14A-GQ not only regulate flowering but also play a role in the abiotic stress response in mango, and the lack of the CCT domain affects the proteinprotein interaction, thus affecting the gene response to stress. The insertion of an A base can provide a possible detection site for mango resistance breeding.

Transcriptome Analysis Reveals Key Genes and Pathways Associated with the Regulation of Flowering Time in Cabbage (Brassica oleracea L. var. capitata)

Flowering time is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the molecular regulatory mechanism underlying flowering time regulation in cabbage remains unclear. In this study, transcriptome analysis was performed using two sets of cabbage materials: (1) the early-flowering inbred line C491 (P1) and late-flowering inbred line B602 (P2), (2) the early-flowering individuals F2-B and late-flowering individuals F2-NB from the F2 population. The analysis revealed 9508 differentially expressed genes (DEGs) common to both C491_VS_ B602 and F2-B_VS_F2-NB. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed that plant hormone signal transduction and the MAPK signaling pathway were mainly enriched in up-regulated genes, and ribosome and DNA replication were mainly enriched in down-regulated genes. We identified 321 homologues of Arabidopsis flowering time genes (Ft) in cabbage. Among them, 25 DEGs (11 up-regulated and 14 down-regulated genes) were detected in the two comparison groups, and 12 gene expression patterns closely corresponded with the different flowering times in the two sets of materials. Two genes encoding MADS-box proteins, Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), showed significantly reduced expression in the late-flowering parent B602 compared with the early-flowering parent C491 via qRT-PCR analysis, which was consistent with the RNA-seq data. Next, the expression levels of Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2) were analyzed in two other groups of early-flowering and late-flowering inbred lines, which showed that their expression patterns were consistent with those in the parents. Sequence analysis revealed that three and one SNPs between B602 and C491 were identified in Bo1g157450 (BoSEP2-1) and Bo5g152700 (BoSEP2-2), respectively. Therefore, BoSEP2-1 and BoSEP2-2 were designated as candidates for flowering time regulation through a potential new regulatory pathway. These results provide new insights into the molecular mechanisms underlying flowering time regulation in cabbage.

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.

DnFCA Isoforms Cooperatively Regulate Temperature-Related Flowering in Dendrobium nobile

Timely flowering is a determinative trait for many economically valuable species in the Dendrobium genus of the Orchidaceae family, some of which are used for ornamental and medicinal purposes. D. nobile, a representative species of nobile-type Dendrobium, normally flowers in spring after exposure to sufficient low temperatures in winter. However, flowering can be stopped or disrupted by the untimely application of high temperatures. Little is known about the regulation and the mechanisms behind this switch. In this study, we report two isoforms from the KFK09_017173 locus of the D. nobile genome, named DnFCAγ and DnFCAβ, respectively, that cooperatively regulate flowering in D. nobile. These two isoforms are generated by alternative 3' polyadenylation of DnFCA (FLOWERING CONTROL LOCUS C in D. nobile) pre-mRNA and contain a distinct 3'-terminus. Both can partially rescue late flowering in the Arabidopsis fca-1 mutant, while in wild-type Arabidopsis, they tend to delay the flowering time. When introduced into the detached axillary buds or young seedlings of D. nobile, both were able to induce the transcription of DnAGL19 (AGAMOUS LIKE 19 in D. nobile) in seedlings, whereas only DnFCAγ was able to suppress the transcription of DnAPL1 (AP1-LIKE 1 in D. nobile) in axillary buds. Furthermore, the time-course change of DnFCAγ accumulation was opposite to that of DnAPL1 in axillary buds, which was remarkable under low temperatures and within a short time after the application of high temperatures, supporting the suggestion that the expression of DnAPL1 can be inhibited by a high accumulation of DnFCAγ in floral buds. In leaves, the accumulation of DnFCAβ was in accordance with that of DnAGL19 and DnFT (FLOWERING LOCUS T in D. nobile) to a large extent, suggesting the activation of the DnAGL19-DnFT pathway by DnFCAβ. Taken together, these results suggest that the DnFCAγ-DnAPL1 pathway in axillary buds and the DnFCAβ-DnAGL19 pathway in the leaves cooperatively promote flowering under low temperatures. The long-term and constant, or untimely, application of high temperatures leads to the constitutive suppression of DnAPL1 by a high level of DnFCAγ in axillary buds, which consequently delays floral development.

Independent recruitment of FRUITFULL-like transcription factors in the convergent origins of vernalization-responsive grass flowering

Flowering in response to low temperatures (vernalization) has evolved multiple times independently across angiosperms as an adaptation to match reproductive development with the short growing season of temperate habitats. Despite the context of a generally conserved flowering time network, evidence suggests that the genes underlying vernalization responsiveness are distinct across major plant clades. Whether different or similar mechanisms underlie vernalization-induced flowering at narrower (e.g., family-level) phylogenetic scales is not well understood. To test the hypothesis that vernalization responsiveness has evolved convergently in temperate species of the grass family (Poaceae), we carried out flowering time experiments with and without vernalization in several representative species from different subfamilies. We then determined the likelihood that vernalization responsiveness evolved through parallel mechanisms by quantifying the response of Pooideae vernalization pathway FRUITFULL (FUL)-like genes to extended periods of cold. Our results demonstrate that vernalization-induced flowering has evolved multiple times independently in at least five grass subfamilies, and that different combinations of FUL-like genes have been recruited to this pathway on several occasions.

Molecular Links between Flowering and Abiotic Stress Response: A Focus on Poaceae

Extreme temperatures, drought, salinity and soil pollution are the most common types of abiotic stresses crops can encounter in fields; these variations represent a general warning to plant productivity and survival, being more harmful when in combination. Plant response to such conditions involves the activation of several molecular mechanisms, starting from perception to signaling, transcriptional reprogramming and protein modifications. This can influence the plant's life cycle and development to different extents. Flowering developmental transition is very sensitive to environmental stresses, being critical to reproduction and to agricultural profitability for crops. The Poacee family contains some of the most widespread domesticated plants, such as wheat, barley and rice, which are commonly referred to as cereals and represent a primary food source. In cultivated Poaceae, stress-induced modifications of flowering time and development cause important yield losses by directly affecting seed production. At the molecular level, this reflects important changes in gene expression and protein activity. Here, we present a comprehensive overview on the latest research investigating the molecular pathways linking flowering control to osmotic and temperature extreme conditions in agronomically relevant monocotyledons. This aims to provide hints for biotechnological strategies that can ensure agricultural stability in ever-changing climatic conditions.

Molecular epigenetic mechanisms for the memory of temperature stresses in plants

The sessile plants encounter various stresses; some are prolonged, whereas some others are recurrent. Temperature is crucial for plant growth and development, and plants often encounter adverse high temperature fluctuations (heat stresses) as well as prolonged cold exposure such as seasonal temperature drops in winter when grown in temperate regions. Many plants can remember past temperature stresses to get adapted to adverse local temperature changes to ensure survival and/or reproductive success. Here, we summarize chromatin-based mechanisms underlying acquired thermotolerance or thermomemory in plants and review recent progresses on molecular epigenetic understanding of 'remembering of prolonged cold in winter' or vernalization, a process critical for various over-wintering plants to acquire competence to flower in the coming spring. In addition, perspectives on future study in temperature stress memories of economically-important crops are discussed.

Tuning of meristem maturation rate increases yield in multiple Triticum aestivum cultivars

Breeding programs aim to improve crop yield and environmental stability for enhanced food security. The principal methodology in breeding for stable yield gain relies on the indirect selection of beneficial genetics by yield evaluation across diverse environmental conditions. This methodology requires substantial resources while delivering a slow pace of yield gain and environmental adaptation. Alternative methods are required to accelerate gain and adaptation, becoming even more imperative in a changing climate. New molecular tools and approaches can enable accelerated creation and deployment of multiple alleles of genes identified to control key traits. With the advent of tools that enable breeding by targeted allelic selection, identifying gene targets associated with an improved crop performance ideotype will become crucial. Previous studies have shown that altered photoperiod regimes increase yield in wheat (Triticum aestivum). In the current study, we have employed such treatments to study the resulting yield ideotype in five spring wheat cultivars. We found that the photoperiod treatment creates a yield ideotype arising from delayed spike establishment rates that are accompanied by increased early shoot expression of TARGET OF EAT1 (TaTOE1) genes. Genes identified in this way could be used for ideotype-based improve crop performance through targeted allele creation and selection in relevant environments.

Major niche transitions in Pooideae correlate with variation in photoperiodic flowering and evolution of CCT domain genes

The external cues that trigger timely flowering vary greatly across tropical and temperate plant taxa, the latter relying on predictable seasonal fluctuations in temperature and photoperiod. In the grass family (Poaceae) for example, species of the subfamily Pooideae have become specialists of the northern temperate hemisphere, generating the hypothesis that their progenitor evolved a flowering response to long days from a short-day or day-neutral ancestor. Sampling across the Pooideae, we found support for this hypothesis, and identified several secondary shifts to day-neutral flowering and one to short-day flowering in a tropical highland clade. To explain the proximate mechanisms for the secondary transition back to short-day-regulated flowering, we investigated the expression of CCT domain genes, some of which are known to repress flowering in cereal grasses under specific photoperiods. We found a shift in CONSTANS 1 and CONSTANS 9 expression that coincides with the derived short-day photoperiodism of our exemplar species Nassella pubiflora. This sets up the testable hypothesis that trans- or cis-regulatory elements of these CCT domain genes were the targets of selection for major niche shifts in Pooideae grasses.

Dynamic QTL-based ecophysiological models to predict phenotype from genotype and environment data

BACKGROUND

Predicting the phenotype from the genotype is one of the major contemporary challenges in biology. This challenge is greater in plants because their development occurs mostly post-embryonically under diurnal and seasonal environmental fluctuations. Most current crop simulation models are physiology-based models capable of capturing environmental fluctuations but cannot adequately capture genotypic effects because they were not constructed within a genetics framework.

RESULTS

We describe the construction of a mixed-effects dynamic model to predict time-to-flowering in the common bean (Phaseolus vulgaris L.). This prediction model applies the developmental approach used by traditional crop simulation models, uses direct observational data, and captures the Genotype, Environment, and Genotype-by-Environment effects to predict progress towards time-to-flowering in real time. Comparisons to a traditional crop simulation model and to a previously developed static model shows the advantages of the new dynamic model.

CONCLUSIONS

The dynamic model can be applied to other species and to different plant processes. These types of models can, in modular form, gradually replace plant processes in existing crop models as has been implemented in BeanGro, a crop simulation model within the DSSAT Cropping Systems Model. Gene-based dynamic models can accelerate precision breeding of diverse crop species, particularly with the prospects of climate change. Finally, a gene-based simulation model can assist policy decision makers in matters pertaining to prediction of food supplies.

Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis

Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.

The wild grass Brachypodium distachyon as a developmental model system

The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.

Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

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.

The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat

Vernalization is a physiological process in which prolonged cold exposure establishes flowering competence in winter plants. In hexaploid wheat, TaVRN1 is a cold-induced key regulator that accelerates floral transition. However, the molecular mechanism underlying the gradual activation of TaVRN1 during the vernalization process remains unknown. In this study, we identified the novel transcript VAS (TaVRN1 alternative splicing) as a non-coding RNA derived from the sense strand of the TaVRN1 gene only in winter wheat, which regulates TaVRN1 transcription for flowering. VAS was induced during the early period of vernalization, and its overexpression promoted TaVRN1 expression to accelerate flowering in winter wheat. VAS physically associates with TaRF2b and facilitates docking of the TaRF2b-TaRF2a complex at the TaVRN1 promoter during the middle period of vernalization. TaRF2b recognizes the Sp1 motif within the TaVRN1 proximal promoter region, which is gradually exposed along with the disruption of a loop structure at the TaVRN1 locus during vernalization, to activate the transcription of TaVRN1. The tarf2b mutants exhibited delayed flowering, whereas transgenic wheat lines overexpressing TaRF2b showed earlier flowering. Taken together, our data reveal a distinct regulatory mechanism by which a long non-coding RNA facilitates the transcription factor targeting to regulate wheat flowering, providing novel insights into the vernalization process and a potential target for wheat genetic improvement.

The Breeding of Winter-Hardy Malting Barley

In breeding winter malting barley, one recurring strategy is to cross a current preferred spring malting barley to a winter barley. This is because spring malting barleys have the greatest amalgamation of trait qualities desirable for malting and brewing. Spring barley breeding programs can also cycle their material through numerous generations each year-some managing even six-which greatly accelerates combining desirable alleles to generate new lines. In a winter barley breeding program, a single generation per year is the limit when the field environment is used and about two generations per year if vernalization and greenhouse facilities are used. However, crossing the current favored spring malting barley to a winter barley may have its downsides, as winter-hardiness too may be an amalgamation of desirable alleles assembled together that confers the capacity for prolonged cold temperature conditions. In this review I touch on some general criteria that give a variety the distinction of being a malting barley and some of the general trends made in the breeding of spring malting barleys. But the main objective of this review is to pull together different aspects of what we know about winter-hardiness from the seemingly most essential aspect, which is survival in the field, to molecular genetics and gene regulation, and then finish with ideas that might help further our insight for predictability purposes.

Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage (Brassica rapa)

Chinese cabbage is one of the most important and widely consumed vegetables in China. The developmental transition from the vegetative to reproductive phase is a crucial process in the life cycle of flowering plants. In spring-sown Chinese cabbage, late bolting is desirable over early bolting. In this study, we analyzed double haploid (DH) lines of late bolting (“Y410-1” and “SY2004”) heading Chinese cabbage (Brassica rapa var. pekinensis) and early-bolting Chinese cabbage (“CX14-1”) (B. rapa ssp. chinensis var. parachinensis) by comparative transcriptome profiling using the Illumina RNA-seq platform. We assembled 721.49 million clean high-quality paired-end reads into 47,363 transcripts and 47,363 genes, including 3,144 novel unigenes. There were 12,932, 4,732, and 4,732 differentially expressed genes (DEGs) in pairwise comparisons of Y410-1 vs. CX14-1, SY2004 vs. CX14-1, and Y410-1 vs. SY2004, respectively. The RNA-seq results were confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs revealed significant enrichment for plant hormone and signal transduction as well as starch and sucrose metabolism pathways. Among DEGs related to plant hormone and signal transduction, six unigenes encoding the indole-3-acetic acid-induced protein ARG7 (BraA02g009130), auxin-responsive protein SAUR41 (BraA09g058230), serine/threonine-protein kinase BSK11 (BraA07g032960), auxin-induced protein 15A (BraA10g019860), and abscisic acid receptor PYR1 (BraA08g012630 and BraA01g009450), were upregulated in both late bolting Chinese cabbage lines (Y410-1 and SY2004) and were identified as putative candidates for the trait. These results improve our understanding of the molecular mechanisms underlying flowering in Chinese cabbage and provide a foundation for studies of this key trait in related species.

Interactions between ScNAC23 and ScGAI regulate GA-mediated flowering and senescence in sugarcane

Control of gene transcription is crucial to regulate plant growth and development events, such as flowering, leaf senescence, and seed germination. Here we identified a NAC transcription factor (ScNAC23) isolated from sugarcane (cv. ROC22). Analysis by qRT-PCR indicated that ScNAC23 expression was strongly induced in mature leaves and flowering varieties and was also responsive to exogenous treatment with the hormone gibberellin (GA). Ectopic expression of ScNAC23 in Arabidopsis accelerated bolting, flowering, and leaf senescence compared to wild type plants. Furthermore, Arabidopsis overexpressed ScNAC23 were more sensitive to GA than the wild type, and exogenous GA significantly accelerated flowering and senescence in the ScNAC23-overexpressed ones. A direct interaction between ScNAC23 and ScGAI, an inhibitor of GA signaling, was confirmed by yeast-two hybrid, bimolecular fluorescence complementation, and GST-pull down assay. The putative GA-ScNAC23-LFY/SAGs regulator module might provide a new sight into the molecular action of GA to accelerating flowering and leaf senescence in sugarcane.

Combined effects of a glycine-rich RNA-binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance

Two key barley genes independently control anthesis and senescence timing, enabling the manipulation of grain fill duration, grain size/plumpness, and grain protein concentration. Plant developmental processes such as flowering and senescence have direct effects on cereal yield and quality. Previous work highlighted the importance of two tightly linked genes encoding a glycine-rich RNA-binding protein (HvGR-RBP1) and a NAC transcription factor (HvNAM1), controlling barley anthesis timing, senescence, and percent grain protein. Varieties that differ in HvGR-RBP1 expression, 'Karl'(low) and 'Lewis'(high), also differ in sequence 1 KB upstream of translation start site, including an ~ 400 bp G rich insertion in the 5'-flanking region of the 'Karl' allele, which could disrupt gene expression. To improve malt quality, the (low-grain protein, delayed-senescence) 'Karl' HvNAM1 allele was introgressed into Montana germplasm. After several seasons of selection, the resulting germplasm was screened for the allelic combinations of HvGR-RBP1 and HvNAM1, finding lines combining 'Karl' alleles for both genes (-/-), lines combining 'Lewis' (functional, expressed) HvGR-RBP1 with 'Karl' HvNAM1 alleles ( ±), and lines combining 'Lewis' alleles for both genes (+ / +). Field experiments indicate that the functional ('Lewis,'  +) HvGR-RBP1 allele is associated with earlier anthesis and with slightly shorter plants, while the 'Karl' (-) HvNAM1 allele delays maturation. Genotypes carrying the ± allele combination therefore had a significantly (3 days) extended grain fill duration, leading to a higher percentage of plump kernels, slightly enhanced test weight, and lower grain protein concentration when compared to the other allele combinations. Overall, our data suggest an important function for HvGR-RBP1 in the control of barley reproductive development and set the stage for a more detailed functional analysis of this gene.

Morphological Characteristics and Transcriptome Comparisons of the Shoot Buds from Flowering and Non-Flowering Pleioblastus pygmaeus

Bamboo plants have a distinctive life cycle with long flowering periodicity. Many species remain in vegetative growth for decades, followed by large-scale flowering and subsequent death. Floral transition is activated while shoot buds are still dormant in bamboo plants. In this study, we performed morphological characterization and transcriptome analysis of the shoot buds at different growth stages from flowering and non-flowering Pleioblastus pygmaeus. The morphological and anatomical structures of the dormant shoot buds were similar in flowering and non-flowering plants, while there was an obvious difference between the flower buds from flowering plants and the leaf buds from non-flowering plants. The transcriptomes of the dormant shoot buds, germinated shoots, and flower buds from flowering P. pygmaeus, and the dormant shoot buds, germinated shoots, and leaf buds from non-flowering P. pygmaeus were profiled and compared by RNA-Seq. The identified sequences were mostly related to metabolic synthesis, signal transmission, translation, and other functions. A total of 2434 unigenes involved in different flowering pathways were screened from transcriptome comparisons. The differentially expressed unigenes associated with the photoperiod pathway were related to circadian rhythm and plant hormone signal transduction. Moreover, the relative expression levels of a few key flowering-related genes such as CO, FT, FLC, and SOC1 were quantified by qRT-PCR, which was in accordance with RNA-Seq. The study revealed morphological differences in the shoot buds at different growth stages and screened flowering-related genes by transcriptome comparisons of the shoot buds from flowering and non-flowering P. pygmaeus, which will enrich the research on reproductive biology of bamboo plants and shed light on the molecular mechanism of the floral transition in bamboo plants.

The molecular mechanism of vernalization in Arabidopsis and cereals: role of Flowering Locus C and its homologs

Winter varieties of plants can flower only after exposure to prolonged cold. This phenomenon is known as vernalization and has been widely studied in the model plant Arabidopsis thaliana as well as in monocots. Through the repression of floral activator genes, vernalization prevents flowering in winter. In Arabidopsis, FLOWERING LOCUS C or FLC is the key repressor during vernalization, while in monocots vernalization is regulated through VRN1, VRN2 and VRN3 (or FLOWERING LOCUS T). Interestingly, VRN genes are not homologous to FLC but FLC homologs are found to have a significant role in vernalization response in cereals. The presence of FLC homologs in monocots opens new dimensions to understand, compare and retrace the evolution of vernalization pathways between monocots and dicots. In this review, we discuss the molecular mechanism of vernalization-induced flowering along with epigenetic regulations in Arabidopsis and temperate cereals. A better understanding of cold-induced flowering will be helpful in crop breeding strategies to modify the vernalization requirement of economically important temperate cereals.

MiR396 is involved in plant response to vernalization and flower development in Agrostis stolonifera

MicroRNA396 (miR396) has been demonstrated to regulate flower development by targeting growth-regulating factors (GRFs) in annual species. However, its role in perennial grasses and its potential involvement in flowering time control remain unexplored. Here we report that overexpression of miR396 in a perennial species, creeping bentgrass (Agrostis stolonifera L.), alters flower development. Most significantly, transgenic (TG) plants bypass the vernalization requirement for flowering. Gene expression analysis reveals that miR396 is induced by long-day (LD) photoperiod and vernalization. Further study identifies VRN1, VRN2, and VRN3 homologs whose expression patterns in wild-type (WT) plants are similar to those observed in wheat and barley during transition from short-day (SD) to LD, and SD to cold conditions. However, compared to WT controls, TG plants overexpressing miR396 exhibit significantly enhanced VRN1 and VRN3 expression, but repressed VRN2 expression under SD to LD conditions without vernalization, which might be associated with modified expression of methyltransferase genes. Collectively, our results unveil a potentially novel mechanism by which miR396 suppresses the vernalization requirement for flowering which might be related to the epigenetic regulation of VRN genes and provide important new insight into critical roles of a miRNA in regulating vernalization-mediated transition from vegetative to reproductive growth in monocots.

A light-regulated gene, TaLWD1L-A, affects flowering time in transgenic wheat (Triticum aestivum L.)

Flowering time is an important agronomic trait that greatly influences plant architecture and grain yield in cereal crops. The present study identified a light-regulated gene, TaLWD1L-A, from hexaploid wheat that encodes a WD40 domain-containing protein. TaLWD1L-A was localized in the nucleus. Phenotypic analysis demonstrated that TaLWD1L-A overexpression in transgenic wheat led to an obvious early flowering phenotype. Upregulation of the floral activator gene TaFT1 caused the early flowering phenotype in transgenic wheat plants. TaLWD1L-A also affected the expression of circadian clock genes, including TaTOC1, TaLHY, TaPRR59, TaPRR73 and TaPRR95, and indirectly regulated the expression of the TaFT1 in transgenic plants by affecting the expression of vernalization-related genes TaVRN1 and TaVRN2 and photoperiod-related genes TaPpd-1 and TaGI. The early flowering phenotype in TaLWD1L-A-overexpressing transgenic lines led to a relatively shorter phenotype and yield reduction. Our results revealed that TaLWD1L-A affected the expression of circadian clock-related genes and played an important role in wheat flowering regulation by influencing the expression of genes related to vernalization and photoperiod pathways.

MawuAP1 promotes flowering and fruit development in the basal angiosperm Magnolia wufengensis (Magnoliaceae)

The APETALA1/SQUAMOSA (AP1/SQUA)-like genes of flowering plants play crucial roles in the development processes of floral meristems, sepals, petals and fruits. Although many of the AP1/SQUA-like genes have been characterized in angiosperms, few have been identified in basal angiosperm taxa. Therefore, the functional evolution of the AP1/SQUA subfamily is still unclear. We characterized an AP1 homolog, MawuAP1, from Magnolia wufengensis that is an ornamental woody plant belonging to the basal angiosperms. Gene sequence and phylogenetic analyses suggested that MawuAP1 was clustered with the FUL-like homologous genes of basal angiosperms and had FUL motif and paleoAP1 motif domain, but it did not have the euAP1 motif domain of core eudicots. Expression pattern analysis showed that MawuAP1 was highly expressed in vegetative and floral organs, particularly in the early stage of flower bud development and pre-anthesis. Protein-protein interaction pattern analysis revealed that MawuAP1 has interaction with an A-class gene (MawuAP1), C-class gene (MawuAG-1) and E-class gene (MawuAGL9) of the MADS-box family genes. Ectopic expression in Arabidopsis thaliana indicated that MawuAP1 could significantly promote flowering and fruit development, but it could not restore the sepal and petal formation of ap1 mutants. These results demonstrated that there are functional differences in the specification of sepal and petal floral organs and development of fruits among the AP1/SQUA-like genes, and functional conservation in the regulation of floral meristem. These findings provide strong evidence for the important functions of MawuAP1 in floral meristem determination, promoting flowering and fruit development, and further highlight the importance of AP1/SQUA subfamily in biological evolution and diversity.

Transcriptome profiling of the flowering transition in saffron (Crocus sativus L.)

Saffron, derived from the stigma of Crocus sativus, is not only a valuable traditional Chinese medicine but also the expensive spice and dye. Its yield and quality are seriously influenced by its flowering transition. However, the molecular regulatory mechanism of the flowering transition in C. sativus is still unknown. In this study, we performed morphological, physiological and transcriptomic analyses using apical bud samples from C. sativus during the floral transition process. Morphological results indicated that the flowering transition process could be divided into three stages: an undifferentiated period, the early flower bud differentiation period, and the late flower bud differentiation period. Sugar, gibberellin (GA₃), auxin (IAA) and zeatin (ZT) levels were steadily upregulated, while starch and abscisic acid (ABA) levels were gradually downregulated. Transcriptomic analysis showed that a total of 60 203 unigenes were identified, among which 19 490 were significantly differentially expressed. Of these, 165 unigenes were involved in flowering and were significantly enriched in the sugar metabolism, hormone signal transduction, cell cycle regulatory, photoperiod and autonomous pathways. Based on the above analysis, a hypothetical model for the regulatory networks of the saffron flowering transition was proposed. This study lays a theoretical basis for the genetic regulation of flowering in C. sativus.

Proteomic Analysis of the Early Development of the Phalaenopsis amabilis Flower Bud under Low Temperature Induction Using the iTRAQ/MRM Approach

Phalaenopsis amabilis, one of the most important plants in the international flower market due to its graceful shape and colorful flowers, is an orchid that undergoes vernalization and requires low-temperature treatment for flowering. There have been few reports on the proteomics of the development of flower buds. In this study, isobaric tags for relative and absolute quantification (iTRAQ) were used to identify 5064 differentially expressed proteins in P. amabilis under low-temperature treatment; of these, 42 were associated with early floral induction, and 18 were verified by mass spectrometry multi-reaction monitoring (MRM). The data are available via ProteomeXchange under identifier PXD013908. Among the proteins associated with the vernalization pathway, PEQU_11434 (glycine-rich RNA-binding protein GRP1A-like) and PEQU_19304 (FT, VRN3 homolog) were verified by MRM, and some other important proteins related to vernalization and photoperiod pathway that were detected by iTRAQ but not successfully verified by MRM, such as PEQU_11045 (UDP-N-acetylglucosamine diphosphorylase), phytochromes A (PEQU_13449, PEQU_35378), B (PEQU_09249), and C (PEQU_41401). Our data revealed a regulation network of the early development of flower buds in P. amabilis under low temperature induction.

Temperature and Light-Quality-Dependent Regulation of Freezing Tolerance in Barley

It is established that, besides the cold, incident light also has a crucial role in the cold acclimation process. To elucidate the interaction between these two external hardening factors, barley plantlets were grown under different light conditions with low, normal, and high light intensities at 5 and 15 °C. The expression of the HvCBF14 gene and two well-characterized members of the C-repeat binding factor (CBF)-regulon HvCOR14b and HvDHN5 were studied. In general, the expression level of the studied genes was several fold higher at 5 °C than that at 15 °C independently of the applied light intensity or the spectra. The complementary far-red (FR) illumination induced the expression of HvCBF14 and also its target gene HvCOR14b at both temperatures. However, this supplementation did not affect significantly the expression of HvDHN5. To test the physiological effects of these changes in environmental conditions, freezing tests were also performed. In all the cases, we found that the reduced R:FR ratio increased the frost tolerance of barley at every incident light intensity. These results show that the combined effects of cold, light intensity, and the modification of the R:FR light ratio can greatly influence the gene expression pattern of the plants, which can result in increased plant frost tolerance.

Negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in Betula platyphylla × B. pendula

MADS-box genes encode transcription factors involved in the control of many important developmental processes, especially the flower development of angiosperms. Analysis on gene regulatory relationship between MADS-box genes is useful for understanding the molecular mechanism of flower development. In this study, we focused on the regulatory relationship between MADS-box transcription factors APETALA1 (AP1) and PISTILLATA(PI)/DEFICIENS (DEF) in birch. We found that BpPI was an authentic target gene of BpAP1, and BpAP1 activated the expression of BpPI via directly binding to the CArG box motif. Functional analysis of BpPI showed that overexpression of BpPI may delay flowering via restricting flowering activators, in which BpAP1 was significantly down-regulated. We further investigated the regulatory of BpAP1 by BpPI, and found that BpPI could directly bind to the promoter of BpAP1 to restrict BpAP1 expression. In addition, we also found that BpPI could interact with its hypothetical partner BpDEF to co-regulate BpAP1 in birch. Our results suggested that overexpression of BpPI may delay flowering via restricting flowering activators, and there is a negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in birch. Our results will bring new evidences for further analysis of the molecular mechanism of flower formation in plants that produced unisexual flowers.

Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa

Flowering is a key agronomic trait that directly influences crop yield and quality and serves as a model system for elucidating the molecular basis that controls successful reproduction, adaptation, and diversification of flowering plants. Adequate knowledge of continuous series of expression data from the floral transition to maturation is lacking in Brassica rapa. To unravel the genome expression associated with the development of early small floral buds (< 2 mm; FB2), early large floral buds (2-4 mm; FB4), stamens (STs) and carpels (CPs), transcriptome profiling was carried out with a Br300K oligo microarray. The results showed that at least 6848 known nonredundant genes (30% of the genes of the Br300K) were differentially expressed during the floral transition from vegetative tissues to maturation. Functional annotation of the differentially expressed genes (DEGs) (fold change ≥ 5) by comparison with a close relative, Arabidopsis thaliana, revealed 6552 unigenes (4579 upregulated; 1973 downregulated), including 131 Brassica-specific and 116 functionally known floral Arabidopsis homologs. Additionally, 1723, 236 and 232 DEGs were preferentially expressed in the tissues of STs, FB2, and CPs. These DEGs also included 43 transcription factors, mainly AP2/ERF-ERF, NAC, MADS-MIKC, C2H2, bHLH, and WRKY members. The differential gene expression during flower development induced dramatic changes in activities related to metabolic processes (23.7%), cellular (22.7%) processes, responses to the stimuli (7.5%) and reproduction (1%). A relatively large number of DEGs were observed in STs and were overrepresented by photosynthesis-related activities. Subsequent analysis via semiquantitative RT-PCR, histological analysis performed with in situ hybridization of BrLTP1 and transgenic reporter lines (BrLTP promoter::GUS) of B. rapa ssp. pekinensis supported the spatiotemporal expression patterns. Together, these results suggest that a temporally and spatially regulated process of the selective expression of distinct fractions of the same genome leads to the development of floral organs. Interestingly, most of the differentially expressed floral transcripts were located on chromosomes 3 and 9. This study generated a genome expression atlas of the early floral transition to maturation that represented the flowering regulatory elements of Brassica rapa.

Expression Analysis and Regulation Network Identification of the CONSTANS-Like Gene Family in Moso Bamboo (Phyllostachys edulis) Under Photoperiod Treatments

CONSTANS (CO)/CONSTANS-like (COL) genes that have been studied in annual model plants such as Arabidopsis thaliana and Oryza sativa play key roles in the photoperiodic flowering pathway. Moso bamboo is a perennial plant characterized by a long vegetative stage and flowers synchronously followed by widespread death. However, the characteristics of COL in moso bamboo remain unclear. In view of this, we performed a genome-wide identification and expression analysis of the COL gene family in moso bamboo. Fourteen nonredundant PheCOL genes were identified, and we analyzed gene structures, phylogeny, and subcellular location predictions. Phylogenetic analyses indicated that 14 PheCOLs could be clustered into three groups, and each clade was well supported by conserved intron/exon structures and motifs. A number of light-related and tissue-specific cis-elements were randomly distributed within the promoter sequences of the PheCOLs. The expression profiling of PheCOL genes in various tissues and developmental stages revealed that most of PheCOL genes were most highly expressed in the leaves and took part in moso bamboo flower development and rapid shoot growth. In addition, the transcription of PheCOLs exhibited a clear diurnal oscillation in both long-day and short-day conditions. Most of the PheCOL genes were inhibited under light treatment and upregulated in dark conditions. PheCOLs can interact with each other. Subcellular localization result showed that PheCOL14 encoded a cell membrane protein, and it bound to the promoter of PheCOL3. Taken together, the results of this study will be useful not only as they contribute to comprehensive information for further analyses of the molecular functions of the PheCOL gene family, but also will provide a theoretical foundation for the further construction of moso bamboo photoperiod regulation networks.

BpAP1 directly regulates BpDEF to promote male inflorescence formation in Betula platyphylla × B. pendula

Flowering is a crucial process for plants that is under complex genetic control. AP1 acts as an organizer and a switch for the transition from vegetative to reproductive growth. In our previous study, we found that overexpression of BpAP1 significantly promoted the formation of male inflorescence in birch (Betula platyphlla × B. pendula). In this study, we aimed at investigating the molecular regulatory mechanism of BpAP1 during the process of male inflorescence formation in birch. We found that overexpression of BpAP1 affected the expression of many flowering-related genes, and had significant effect on B class MADS-box genes. A BpAP1-mediated gene regulatory network was constructed and B class gene BpDEF was finally predicted as a key target gene of BpAP1. Chromatin immunoprecipitation results indicated that BpAP1 could directly regulate BpDEF during the process of male inflorescence formation. Yeast one-hybrid assays and its validation in tobacco results suggested that BpAP1 regulated BpDEF via binding to a consensus DNA sequence known as CArG box. Gene function analysis of BpDEF indicated that BpDEF may function in sex-determination, and in particular specify the identity of male inflorescence in birch. Our results provide valuable clues for our understanding of the molecular mechanism of BpAP1 during the process of male inflorescence formation in birch.

TaZIM-A1 negatively regulates flowering time in common wheat (Triticum aestivum L.)

Flowering time is a critical determinant of regional adaptation for crops and has strong effects on crop yields. Here, we report that TaZIM-A1, an atypical GATA-like transcription factor, is a negative regulator of flowering in wheat. TaZIM-A1 possessed weak transcriptional repression activity, with its CCT domain functioning as the major inhibitory region. TaZIM-A1 expression exhibited a typical circadian oscillation pattern under various light regimes. Overexpression of TaZIM-A1 caused a delay in flowering time and a decrease in thousand-kernel weight (TKW) in wheat under long-day conditions. Moreover, TaZIM-A1 directly bound to the promoters of TaCO-1 and TaFT-1 and downregulated their expression. Sequence analysis of a collection of common wheat cultivars identified three and two haplotypes for TaZIM-A1 and TaZIM-B1, respectively. Association analysis revealed that TaZIM-A1-HapI/-HapIII and TaZIM-B1-HapI have undergone strong positive selection during modern wheat breeding, likely due to their association with earlier heading and higher TKW. Diagnostic markers were developed for these haplotypes that can be used for wheat cultivar improvement, via marker-assisted breeding.

Expression of sugarcane genes associated with perception of photoperiod and floral induction reveals cycling over a 24-hour period

The genetic network resulting in the production of an inflorescence is complex, involving one or more pathways including the photoperiod, maturity, gibberellin and autonomous pathways, and induction and repression of genes along the pathways. Understanding the cyclic expression profile of genes involved with photoperiod perception and floral pathway induction in sugarcane, an intermediate-short day plant (ISD), is crucial for identifying key genes and understanding how the profile changes in response to floral induction signals under decreasing daylengths. Homologues of 21 genes, and some gene alleles, associated with photoperiod perception and the flower induction pathway were examined in sugarcane variety Q174 over a 24-h light-dark cycle. The strongest expression of these genes was seen in the immature spindle leaves and levels of expression generally decreased with increasing leaf age. Significant changes in gene expression levels during a 24-h cycle were observed for 16 of the 21 genes tested. We have now defined an important baseline for expression patterns over a 24-h cycle in non-inductive conditions in sugarcane. These results can be utilised to select the optimal time for detecting changes during floral induction, differences between varieties that are responsive/non-responsive to photoperiod induction, and to identify genes that may be manipulated to enhance or inhibit flowering.

The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought

The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0-2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3-1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids.

Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat

BACKGROUND

The extensive adaptability of polyploidy wheat is attributed to its complex genome, and accurately controlling heading stage is a prime target in wheat breeding process. Wheat heading stage is an essential growth and development processes since it starts at a crucial point in the transition from vegetative phase to reproductive phase.

MAIN BODY

Heading stage is mainly decided by vernalization, photoperiod, hormone (like gibberellic acid, GA), and earliness per se (Eps). As a polyploidy species, common wheat possesses the abundant genetic variation, such as allelic variation, copy number variation etc., which have a strong effect on regulation of wheat growth and development. Therefore, understanding genetic manipulation of heading stage is pivotal for controlling the heading stage in wheat. In this review, we summarized the recent advances in the genetic regulatory mechanisms and abundant variation in genetic diversity controlling heading stage in wheat, as well as the interaction mechanism of different signals and the contribution of different genetic variation. We first summarized the genes involved in vernalization, photoperoid and other signals cross-talk with each other to control wheat heading stage, then the abundant genetic variation related to signal components associated with wheat heading stage was also elaborated in detail.

CONCLUSION

Our knowledge of the regulatory network of wheat heading can be used to adjust the duration of the growth phase for the purpose of acclimatizing to different geographical environments.

Deterministic and Stochastic Models of Arabidopsis thaliana Flowering

Experimental studies of the flowering of Arabidopsis thaliana have shown that a large complex gene regulatory network (GRN) is responsible for its regulation. This process has been mathematically modelled with deterministic differential equations by considering the interactions between gene activators and inhibitors (Valentim et al. in PLoS ONE 10(2):e0116973, 2015; van Mourik et al. in BMC Syst Biol 4(1):1, 2010). However, due to complexity of the model, the properties of the network and the roles of the individual genes cannot be deducted from the numerical solution the published work offers. Here, we propose simplifications of the model, based on decoupling of the original GRN to motifs, described with three and two differential equations. A stable solution of the original model is sought by linearisation of the original model which contributes to further investigation of the role of the individual genes to the flowering. Furthermore, we study the role of noise by introducing and investigating two types of stochastic elements into the model. The deterministic and stochastic nonlinear dynamic models of Arabidopsis flowering time are considered by following the deterministic delayed model introduced in Valentim et al. (2015). Steady-state regimes and stability of the deterministic original model are investigated analytically and numerically. By decoupling some concentrations, the system was reduced to emphasise the role played by the transcription factor Suppressor of Overexpression of Constants1 ([Formula: see text]) and the important floral meristem identity genes, Leafy ([Formula: see text]) and Apetala1 ([Formula: see text]). Two-dimensional motifs, based on the dynamics of [Formula: see text] and [Formula: see text], are obtained from the reduced network and parameter ranges ensuring flowering are determined. Their stability analysis shows that [Formula: see text] and [Formula: see text] are regulating each other for flowering, matching experimental findings. New sufficient conditions of mean square stability in the stochastic model are obtained using a stochastic Lyapunov approach. Our numerical simulations demonstrate that the reduced models of Arabidopsis flowering time, describing specific motifs of the GRN, can capture the essential behaviour of the full system and also introduce the conditions of flowering initiation. Additionally, they show that stochastic effects can change the behaviour of the stability region through a stability switch. This study thus contributes to a better understanding of the role of [Formula: see text] and [Formula: see text] in Arabidopsis flowering.

VcRR2 regulates chilling-mediated flowering through expression of hormone genes in a transgenic blueberry mutant

The molecular mechanism underlying dormancy release and the induction of flowering remains poorly understood in woody plants. Mu-legacy is a valuable blueberry mutant, in which a transgene insertion caused increased expression of a RESPONSE REGULATOR 2-like gene (VcRR2). Mu-legacy plants, compared with nontransgenic 'Legacy' plants, show dwarfing, promotion of flower bud formation, and can flower under nonchilling conditions. We conducted transcriptomic comparisons in leaves, chilled and nonchilled flowering buds, and late-pink buds, and analyzed a total of 41 metabolites of six groups of hormones in leaf tissues of both Mu-legacy and 'Legacy' plants. These analyses uncovered that increased VcRR2 expression promotes the expression of a homolog of Arabidopsis thaliana ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 (VcGA1), which induces new homeostasis of hormones, including increased gibberellin 4 (GA4) levels in Mu-legacy leaves. Consequently, increased expression of VcRR2 and VcGA1, which function in cytokinin responses and gibberellin synthesis, respectively, initiated the reduction in plant height and the enhancement of flower bud formation of the Mu-legacy plants through interactions of multiple approaches. In nonchilled flower buds, 29 differentially expressed transcripts of 17 genes of five groups of hormones were identified in transcriptome comparisons between Mu-legacy and 'Legacy' plants, of which 22 were chilling responsive. Thus, these analyses suggest that increased expression of VcRR2 was collectively responsible for promoting flower bud formation in highbush blueberry under nonchilling conditions. We report here for the first time the importance of VcRR2 to induce a suite of downstream hormones that promote flowering in woody plants.

Remembering winter through vernalisation

Vernalisation is the programmed physiological process in which prolonged cold-exposure provides competency to flower in plants; widely found in winter and biennial species, such as Arabidopsis, fruit trees, vegetables and wheat. This phenomenon is regulated by diverse genetic networks, and memory of vernalisation in a life cycle mainly depends on epigenetic mechanisms. However, less is known about how to count winter-dosage for flowering in plants. Here, we compare the vernalisation genetic framework between the dicots Arabidopsis, temperate grasses, wheat, barley and Brachypodium. We discuss vernalisation mechanisms involving crosstalk between phosphorylation and O-GlcNAcylation modification of key proteins, and epigenetic modifications of the key gene VRN1 in wheat. We also highlight the potential evolutionary origins of vernalisation in various species. Current progress toward understanding the regulation of vernalisation requirements provides insight that will inform the design of molecular breeding strategies for winter crops.

Overexpression of the MADS-box gene K-domain increases the yield potential of blueberry

MADS-box genes play a significant role for plant flowering. Keratin-like (K) domains are involved in protein-to-protein interactions in the formation of the MIKC-type MADS-box domain proteins. In this study, the potential of utilizing the K domain of a Vaccinium corymbosum SOC1-like gene (VcSOC1K) was investigated to modulate expression of other blueberry MADS-box genes for increasing blueberry productivity. Chilled transgenic blueberry plants overexpressing the VcSOC1K showed a significant increase in the number of canes, floral buds, and flower and fruit clusters compared to chilled non-transgenic plants. Additionally, nonchilled transgenic plants flowered whereas nonchilled non-transgenic plants did not. Transgenic plants showed an increase in tolerance to high soil pH. Comparative transcriptome analysis of transgenic and non-transgenic leaves showed differential expression of 17% of the MADS-box genes identified in blueberry. These differentially expressed (DE) MADS-box genes were associated with genes related to plant flowering, phytohormones, and response to various biotic and abiotic stimuli. The phenotypic changes and the DE MADS-box genes caused by the overexpression of VcSOC1K not only reveal that the MADS-box genes are involved in chilling/vernalization-mediated flowering in blueberry but also demonstrated that the overexpression of the K domain can effectively modulate plant reproductive processes.

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.

Global spatial analysis of Arabidopsis natural variants implicates 5'UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature

How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception and signal transduction may occur through temperature-sensitive intramolecular folding of primary mRNA transcripts. Recent studies suggested a role for retention of the first intron in the 5'UTR of the clock component LATE ELONGATED HYPOCOTYL (LHY) in response to changes in temperature. Here, we identified a set of haplotypes in the LHY 5'UTR, examined their global spatial distribution, and obtained evidence that haplotype can affect temperature-dependent splicing of LHY transcripts. Correlations of haplotype spatial distributions with global bioclimatic variables and altitude point to associations with annual mean temperature and temperature fluctuation. Relatively rare relict type accessions correlate with lower mean temperature and greater temperature fluctuation and the spatial distribution of other haplotypes may be informative of evolutionary processes driving colonization of ecosystems. We propose that haplotypes may possess distinct 5'UTR pre-mRNA folding thermodynamics and/or specific biological stabilities based around the binding of trans-acting RNA splicing factors, a consequence of which is scalable splicing sensitivity of a central clock component that is likely tuned to specific temperature environments.

Developmental responses of bread wheat to changes in ambient temperature following deletion of a locus that includes FLOWERING LOCUS T1

FLOWERING LOCUS T (FT) is a central integrator of environmental signals that regulates the timing of vegetative to reproductive transition in flowering plants. In model plants, these environmental signals have been shown to include photoperiod, vernalization, and ambient temperature pathways, and in crop species, the integration of the ambient temperature pathway remains less well understood. In hexaploid wheat, at least 5 FT-like genes have been identified, each with a copy on the A, B, and D genomes. Here, we report the characterization of FT-B1 through analysis of FT-B1 null and overexpression genotypes under different ambient temperature conditions. This analysis has identified that the FT-B1 alleles perform differently under diverse environmental conditions; most notably, the FT-B1 null produces an increase in spikelet and tiller number when grown at lower temperature conditions. Additionally, absence of FT-B1 facilitates more rapid germination under both light and dark conditions. These results provide an opportunity to understand the FT-dependent pathways that underpin key responses of wheat development to changes in ambient temperature. This is particularly important for wheat, for which development and grain productivity are sensitive to changes in temperature.

Comparative transcriptome analysis of nonchilled, chilled, and late-pink bud reveals flowering pathway genes involved in chilling-mediated flowering in blueberry

BACKGROUND

Blueberry cultivars require a fixed quantity of chilling hours during winter endo-dormancy for vernalization. In this study, transcriptome analysis using RNA sequencing data from nonchilled, chilled, and late pink buds of southern highbush blueberry 'Legacy' was performed to reveal genes associated with chilling accumulation and bud break.

RESULTS

Fully chilled 'Legacy' plants flowered normally whereas nonchilled plants could not flower. Compared to nonchilled flower buds, chilled flower buds showed differential expression of 89% of flowering pathway genes, 86% of MADS-box genes, and 84% of cold-regulated genes. Blueberry orthologues of FLOWERING LOCUS T (FT) did not show a differential expression in chilled flower buds (compared to nonchilled flower bud) but were up-regulated in late-pink buds (compared to chilled flower bud). Orthologoues of major MADS-box genes were significantly up-regulated in chilled flower buds and down-regulated in late-pink buds. Functional orthologues of FLOWERING LOCUS C (FLC) were not found in blueberry. Orthologues of Protein FD (FD), TERMINAL FLOWER 1 (TFL1), and LEAFY (LFY) were down-regulated in chilled flower buds and in late-pink buds compared to nonchilled flower bud.

CONCLUSIONS

The changes from nonchilled to chilled and chilled to late-pink buds are associated with transcriptional changes in a large number of differentially expressed (DE) phytohormone-related genes and DE flowering pathway genes. The profile of DE genes suggests that orthologues of FT, FD, TFL1, LFY, and MADS-box genes are the major genes involved in chilling-mediated blueberry bud-break. The results contribute to the comprehensive investigation of the vernalization-mediated flowering mechanism in woody plants.

MADS-box genes and crop domestication: the jack of all traits

MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.

Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping

Barley is cultivated more widely than the other major world crops because it adapts well to environmental constraints, such as drought, heat, and day length. To better understand the genetic control of local adaptation in barley, we studied development in the nested association mapping population HEB-25, derived from crossing 25 wild barley accessions with the cultivar 'Barke'. HEB-25 was cultivated in replicated field trials in Dundee (Scotland) and Halle (Germany), differing in regard to day length, precipitation, and temperature. Applying a genome-wide association study, we located 60 and 66 quantitative trait locus (QTL) regions regulating eight plant development traits in Dundee and Halle, respectively. A number of QTLs could be explained by known major genes such as PHOTOPERIOD 1 (Ppd-H1) and FLOWERING LOCUS T (HvFT-1) that regulate plant development. In addition, we observed that developmental traits in HEB-25 were partly controlled via genotype × environment and genotype × donor interactions, defined as location-specific and family-specific QTL effects. Our findings indicate that QTL alleles are available in the wild barley gene pool that show contrasting effects on plant development, which may be deployed to improve adaptation of cultivated barley to future environmental changes.