Long-distance regulation of 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.

Flowering and Runnering of Seasonal Strawberry under Different Photoperiods Are Affected by Intensity of Supplemental or Night-Interrupting Blue Light

The strawberry (Fragaria × ananassa Duch.) "Sulhyang" is a typical seasonal flowering (SF) strawberry that produces flower buds in day lengths shorter than a critical limit (variable, but often defined as <12 h). There is a trade-off between photoperiod-controlled flowering and gibberellin (GA) signaling pathway-mediated runnering. Some related genes (such as CO, FT1, SOC1, and TFL1) participating in light signaling and circadian rhythm in plants are altered under blue light (BL). Sugars for flowering and runnering are mainly produced by photosynthetic carbon assimilation. The intensity of light could affect photosynthesis, thereby regulating flowering and runnering. Here, we investigated the effect of the intensity of supplemental blue light (S-BL) or night-interrupting blue light (NI-BL) in photoperiodic flowering and runnering regulation by applying 4 h of S-BL or NI-BL with either 0, 10, 20, 30, or 40 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) in a 10 h short-day (SD10) (SD10 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)) or 14 h long-day (LD14) conditions (LD14 + S-BL4 or + NI-BL4 (0, 10, 20, 30, or 40)). Approximately 45 days after the photoperiodic light treatment, generally, whether S-BL or NI-BL, BL (20) was the most promotive in runnering, leading to more runners in both the LD and SD conditions. For flowering, except the treatment LD14 + S-BL, BL (20) was still the key light, either from BL (20) or BL (40), promoting flowering, especially when BL acted as the night-interrupting light, regardless of the photoperiod. At the harvest stage, larger numbers of inflorescences and runners were observed in the LD14 + NI-BL4 treatment, and the most were observed in the LD14 + NI-BL (20). Moreover, the SD10 + NI-BL4 was slightly inferior to the LD14 + NI-BL4 in increasing the numbers of inflorescences and runners, but it caused earlier flowering. Additionally, the circadian rhythm expression of flowering-related genes was affected differently by the S-BL and NI-BL. After the application of BL in LD conditions, the expression of an LD-specific floral activator FaFT1 was stimulated, while that of a flowering suppressor FaTFL1 was inhibited, resetting the balance of expression between these two opposite flowering regulators. The SD runnering was caused by BL in non-runnering SD conditions associated with the stimulation of two key genes that regulate runner formation in the GA pathway, FaGRAS32 and FaGA20ox4. In addition, the positive effects of BL on enhancing photosynthesis and carbohydrate production also provided an abundant energy supply for the flowering and runnering processes.

The central role of stem cells in determining plant longevity variation

Vascular plants display a huge variety of longevity patterns, from a few weeks for several annual species up to thousands of years for some perennial species. Understanding how longevity variation is structured has long been considered a fundamental aspect of the life sciences in view of evolution, species distribution, and adaptation to diverse environments. Unlike animals, whose organs are typically formed during embryogenesis, vascular plants manage to extend their life by continuously producing new tissues and organs in apical and lateral directions via proliferation of stem cells located within specialized tissues called meristems. Stem cells are the main source of plant longevity. Variation in plant longevity is highly dependent on the activity and fate identity of stem cells. Multiple developmental factors determine how stem cells contribute to variation in plant longevity. In this review, we provide an overview of the genetic mechanisms, hormonal signaling, and environmental factors involved in controlling plant longevity through long-term maintenance of stem cell fate identity.

Genome-wide identification and functional prediction of BYPASS1-related (BPS1) homologs in soybean

The BYPASS1-related gene (BPS1) encodes a protein with an unknown functional domain that regulates plant organ growth and development by inhibiting the continuous production of a root-derived long-distance signaling molecule called bypass (bps). We conducted a comprehensive study to investigate the BPS gene family in soybean and identified twenty-three BPS genes in Glycine max and twenty BPS genes in Glycine soja (wild soybean). Collinearity analysis revealied the existence of multiple orthologs of soybean BPS genes in wild soybean, indicating incomplete conservation between the BPS genes of soybean and wild soybean. Phylogenetic analysis successfully categorized all BPS genes into five distinct groups. We further scrutinized their chromosomal locations, gene structures, conserved motifs, cis-acting elements, and expression patterns. Leveraging publicly available data on genetic variation, phenotypic variation, and single-cell transcriptome sequencing of root nodules, we discovered a potential association between BPS genes and multiple soybean traits, particularly those related to the root nodule phenotype. This pioneering study provides a systematic and comprehensive examination of the BPS gene family in soybean. The findings establish a robust foundation for future investigations into the functional roles of BPS genes in plant growth and development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01403-2.

Sorbitol induces flower bud formation via the MADS-box transcription factor EjCAL in loquat

Sorbitol is an important signaling molecule in fruit trees. Here, we observed that sorbitol increased during flower bud differentiation (FBD) in loquat (Eriobotrya japonica Lindl.). Transcriptomic analysis suggested that bud formation was associated with the expression of the MADS-box transcription factor (TF) family gene, EjCAL. RNA fluorescence in situ hybridization showed that EjCAL was enriched in flower primordia but hardly detected in the shoot apical meristem. Heterologous expression of EjCAL in Nicotiana benthamiana plants resulted in early FBD. Yeast-one-hybrid analysis identified the ERF12 TF as a binding partner of the EjCAL promoter. Chromatin immunoprecipitation-PCR confirmed that EjERF12 binds to the EjCAL promoter, and β-glucuronidase activity assays indicated that EjERF12 regulates EjCAL expression. Spraying loquat trees with sorbitol promoted flower bud formation and was associated with increased expression of EjERF12 and EjCAL. Furthermore, we identified EjUF3GaT1 as a target gene of EjCAL and its expression was activated by EjCAL. Function characterization via overexpression and RNAi reveals that EjUF3GaT1 is a biosynthetic gene of flavonoid hyperoside. The concentration of the flavonoid hyperoside mirrored that of sorbitol during FBD and exogenous hyperoside treatment also promoted loquat bud formation. We identified a mechanism whereby EjCAL might regulate hyperoside biosynthesis and confirmed the involvement of EjCAL in flower bud formation in planta. Together, these results provide insight into bud formation in loquat and may be used in efforts to increase yield.

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 flowering of SDP chrysanthemum in response to intensity of supplemental or night-interruptional blue light is modulated by both photosynthetic carbon assimilation and photoreceptor-mediated regulation

The photoreceptor-mediated photoperiodic sensitivity determines the obligate short-day flowering in chrysanthemum (Chrysanthemum morifolium Ramat.) when the night length is longer than a critical minimum, otherwise, flowering is effectively inhibited. The reversal of this inhibition by subsequent exposure to a short period of supplemental (S) or night-interruptional (NI) blue (B) light (S-B; NI-B) indicates the involvement of B light-received photoreceptors in the flowering response. Flowering is mainly powered by sugars produced through photosynthetic carbon assimilation. Thus, the light intensity can be involved in flowering regulation by affecting photosynthesis. Here, it is elucidated that the intensity of S-B or NI-B in photoperiodic flowering regulation of chrysanthemums by applying 4-h of S-B or NI-B with either 0, 10, 20, 30, or 40 μmol·m^-2·s^-1 photosynthetic photon flux density (PPFD) in a 10-h short-day (SD10) [SD10 + 4B or + NI-4B (0, 10, 20, 30, or 40)] or 13-h long-day (LD13) condition [LD13 + 4B or + NI-4B (0, 10, 20, 30, or 40)] provided by 300 ± 5 μmol·m^-2·s^-1 PPFD white (W) LEDs. After 60 days of photoperiodic light treatments other than the LD13 and LD13 + NI-4B (40), flowering with varying degrees was observed, although the SD10 gave the earliest flowering. And the LD13 + 4B (30) produced the greatest number of flowers. The flowering pattern in response to the intensity of S-B or NI-B was consistent as it was gradually promoted from 10 to 30 μmol m^-2 s^-1 PPFD and inhibited by 40B regardless of the photoperiod. In SD conditions, the same intensity of S-B and NI-B did not significantly affect flowering, while differential flowering inhibition was observed with any intensity of NI-B in LDs. Furthermore, the 30 μmol·m^-2·s^-1 PPFD of S-B or NI-B up-regulated the expression of floral meristem identity or florigen genes, as well as the chlorophyll content, photosynthetic efficiency, and carbohydrate accumulation. The 40B also promoted these physiological traits but led to the unbalanced expression of florigen or anti-florigen genes. Overall, the photoperiodic flowering in response to the intensity of S-B or NI-B of the SDP chrysanthemum suggests the co-regulation of photosynthetic carbon assimilation and differential photoreceptor-mediated control.

Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton

Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.

SDG102, a H3K36-Methyltransferase-Encoding Gene, Plays Pleiotropic Roles in Growth and Development of Maize (Zea mays L.)

Although histone lysine methylation has been studied in thale cress (Arabidopsis thaliana (L.) Heynh.) and rice (Oryza sativa L.) in recent years, its function in maize (Zea mays L.) remains poorly characterized. To better understand the function of histone lysine methylation in maize, SDG102, a H3 lysine 36 (H3K36) methylase, was chosen for functional characterization using overexpressed and knockout transgenic plants. SDG102-deficiency in maize caused multiple phenotypes including yellow leaves in seedlings, late-flowering, and increased adult plant height, while the overexpression of SDG102 led to reduced adult plant height. The key flowering genes, ZCN8/ZCN7 and MADS4/MADA67, were downregulated in SDG102-deficient plants. Chromatin immunoprecipitation (ChIP) experiments showed that H3 lysine 36 trimethylation (H3K36me3) levels were reduced at these loci. Perturbation of SDG102 expression caused the misexpression of multiple genes. Interestingly, the overexpression or knockout of SDG102 also led to genome-wide decreases and increases in the H3K36me3 levels, respectively. Together, our results suggest that SDG102 is a methyltransferase that catalyzes the trimethylation of H3K36 of many genes across the maize genome, which are involved in multiple biological processes including those controlling flowering time.

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa

Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F₂ populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.

Integrative mRNA and Long Noncoding RNA Analysis Reveals the Regulatory Network of Floral Bud Induction in Longan (Dimocarpus longan Lour.)

Longan (Dimocarpus longan Lour.) is a tropical/subtropical fruit tree of significant economic importance. Floral induction is an essential process for longan flowering and plays decisive effects on the longan yield. Due to the instability of flowering, it is necessary to understand the molecular mechanisms of floral induction in longan. In this study, mRNA and long noncoding RNA (lncRNA) transcriptome sequencing were performed using the apical buds of fruiting branches as materials. A total of 7,221 differential expressions of mRNAs (DEmRNAs) and 3,238 differential expressions of lncRNAs (DElncRNAs) were identified, respectively. KEGG enrichment analysis of DEmRNAs highlighted the importance of starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways during floral induction. Combining the analysis of weighted gene co-expression network (WGCNA) and expression pattern of DEmRNAs in the three pathways, specific transcriptional characteristics at each stage during floral induction and regulatory network involving co-expressed genes were investigated. The results showed that sucrose metabolism and auxin signal transduction may be crucial for the growth and maturity of autumn shoots in September and October (B1-B2 stage); starch and sucrose metabolic, circadian rhythms, and plant hormone signal transduction pathways participated in the regulation of floral bud physiological differentiation together in November and December (B3-B4 stage) and the crosstalk among three pathways was also found. Hub genes in the co-expression network and key DEmRNAs in three pathways were identified. The circadian rhythm genes FKF1 and GI were found to activate SOC1gene through the photoperiod core factor COL genes, and they were co-expressed with auxin, gibberellin, abscisic acid, ethylene signaling genes, and sucrose biosynthesis genes at B4 stage. A total of 12 hub-DElncRNAs had potential for positively affecting their distant target genes in three putative key pathways, predominantly in a co-transcriptional manner. A hypothetical model of regulatory pathways and key genes and lncRNAs during floral bud induction in longan was proposed finally. Our studies will provide valuable clues and information to help elucidate the potential molecular mechanisms of floral initiation in longan and woody fruit trees.

Cytokinin increases vegetative growth period by suppressing florigen expression in rice and maize

Increasing the vegetative growth period of crops can increase biomass and grain yield. In rice (Oryza sativa), the concentration of trans -zeatin, an active cytokinin, was high in the leaves during vegetative growth and decreased rapidly upon induction of florigen expression, suggesting that this hormone is involved in the regulation of the vegetative phase. To elucidate whether exogenous cytokinin application influences the length of the vegetative phase, we applied 6-benzylaminopurine (BAP) to rice plants at various developmental stages. Our treatment delayed flowering time by 8-9 days when compared with mock-treated rice plants, but only at the transition stage when the flowering signals were produced. Our observations also showed that flowering in the paddy field is delayed by thidiazuron, a stable chemical that mimics the effects of cytokinin. The transcript levels of florigen genes Heading date 3a (Hd3a) and Rice Flowering locus T1 (RFT1) were significantly reduced by the treatment, but the expression of Early heading date 1 (Ehd1), a gene found directly upstream of the florigen genes, was not altered. In maize (Zea mays), similarly, BAP treatment increased the vegetative phage by inhibiting the expression of ZCN8, an ortholog of Hd3a. We showed that cytokinin treatment induced the expression of two type-A response regulators (OsRR1 and OsRR2) which interacted with Ehd1, a type-B response regulator. We also observed that cytokinin did not affect flowering time in ehd1 knockout mutants. Our study indicates that cytokinin application increases the duration of the vegetative phase by delaying the expression of florigen genes in rice and maize by inhibiting Ehd1.

Engineering drought-tolerant apple by knocking down six GH3 genes and potential application of transgenic apple as a rootstock

Drought poses a major threat to apple fruit production and quality. Because of the apple's long juvenile phase, developing varieties with improved drought tolerance using biotechnology approaches is needed. Here, we used the RNAi approach to knock down six GH3 genes in the apple. Under prolonged drought stress, the MdGH3 RNAi plants performed better than wild-type plants and had stronger root systems, higher root-to-shoot ratio, greater hydraulic conductivity, increased photosynthetic capacity, and increased water use efficiency. Moreover, MdGH3 RNAi plants promoted the drought tolerance of the scion when they were used as rootstock, compared with wild-type and M9-T337 rootstocks. Scions grafted onto MdGH3 RNAi plants showed increased plant height, stem diameter, photosynthetic capacity, specific leaf weight, and water use efficiency. The use of MdGH3 RNAi plants as rootstocks can also increase the C/N ratio of the scion and achieve the same effect as the M9-T337 rootstock in promoting the flowering and fruiting of the scion. Notably, using MdGH3 RNAi plants as rootstocks did not reduce fruit weight and scion quality compared with using M9-T337 rootstock. Our research provides candidate genes and demonstrates a general approach that could be used to improve the drought tolerance of fruit trees without sacrificing the yield and quality of scion fruits.

Between Light and Shading: Morphological, Biochemical, and Metabolomics Insights Into the Influence of Blue Photoselective Shading on Vegetable Seedlings

High nursery densities reduce the seedling quality due to the competition for light. High light intensity, shading, and blue light depletion activate morphophysiological and metabolomic responses in plants, resulting in size modification to gain an advantage over neighboring plants. Our research aimed to unravel the effects of light intensity and quality on nursery seedlings at the morphological and biochemical levels. To this aim, the effect of black shading and blue photoselective shading nets were investigated in terms of morphometric, ionomic, and untargeted metabolomics signatures in Cucurbita pepo L., Citrullus lanatus L., Solanum lycopersicum L., and Solanum melongena L. seedlings. Plant height, diameter, sturdiness index, leaf area, specific leaf area, shoot/root ratio, and mineral content (by ion chromatography-IC) were evaluated. In C. pepo L and C. lanatus L., the blue net reduced the shoot/root and chlorophyll a/b ratios and increased stem diameter and total chlorophyll content. The black net increased plant height, stem diameter, and sturdiness index in Solanum lycopersicum L. and Solanum melongena L. At the same time, unshading conditions reduced leaf area, specific leaf area, shoot/root ratio, and total chlorophyll content. The blue net improved the sturdiness index and quality of C. pepo L. and C. lanatus L. Such impact on morphological parameters induced by the different shading conditions was corroborated by a significant modulation at the metabolomics level. Untargeted metabolomic phytochemical signatures of the selected plants, and the subsequent multivariate analysis coupled to pathway analysis, allowed highlighting a broad and diverse biochemical modulation. Metabolomics revealed that both primary and secondary metabolism were largely affected by the different shading conditions, regardless of the species considered. A common pattern arose to point at the activation of plant energy metabolism and lipid biosynthesis, together with a generalized down accumulation of several secondary metabolites, particularly phenylpropanoids. Our findings indicate an intriguing scientific interest in the effects of selective shading and its application to other species and different phenological stages.

MSI1 and HDA6 function interdependently to control flowering time via chromatin modifications

MULTICOPY SUPPRESSOR OF IRA1 (MSI1) is a conserved subunit of Polycomb Repressive Complex 2 (PRC2), which mediates gene silencing by histone H3 lysine 27 trimethylation (H3K27Me3). Here, we demonstrated that MSI1 interacts with the RPD3-like histone deacetylase HDA6 both in vitro and in vivo. MSI1 and HDA6 are involved in flowering and repress the expression of FLC, MAF4, and MAF5 by removing H3K9 acetylation but adding H3K27Me3. Chromatin immunoprecipitation analysis showed that HDA6 and MSI1 interdependently bind to the chromatin of FLC, MAF4, and MAF5. Furthermore, H3K9 deacetylation mediated by HDA6 is dependent on MSI1, while H3K27Me3 mediated by PRC2 containing MSI1 is also dependent on HDA6. Taken together, these data indicate that MSI1 and HDA6 act interdependently to repress the expression of FLC, MAF4, and MAF5 through histone modifications. Our findings reveal that the HDA6-MSI1 module mediates the interaction between histone H3 deacetylation and H3K27Me3 to repress gene expression involved in flowering time control.

Efficiency of graft-transmitted JcFT for floral induction in woody perennial species of the Jatropha genus depends on transport distance

FLOWERING LOCUS T (FT) promotes flowering by integrating six genetic pathways. In Arabidopsis, the FT protein is transported from leaves to shoot apices and induces flowering. However, contradictory conclusions about floral induction via graft-transmitted FT in trees were reported in previous studies. We obtained extremely early-flowering transgenic woody Jatropha curcas L. by overexpression of J. curcas FT using Arabidopsis thaliana SUCROSE TRANSPORTER 2 (SUC2) promoter (SUC2:JcFT) and non-flowering transgenic J. curcas by RNA interference (RNAi), which were used to investigate the function of graft-transmitted JcFT in floral induction in woody perennials. Scions from five wild-type species of the Jatropha genus and from JcFT-RNAi transgenic J. curcas were grafted onto SUC2:JcFT rootstocks. Most grafted plants produced flowers in 1-2 months, and the flowering percentage and frequency of various grafted plants decreased with increasing scion length. Consistently, FT protein abundance in scions also decreased with increasing distance from graft junctions to the buds. These findings suggest that FT proteins can be transmitted by grafting and can induce the floral transition in woody perennials, and the efficiency of graft-transmitted JcFT for floral induction depends on the scion length, which may help explain previous seemingly contradictory observations regarding floral induction via graft-transmitted FT in trees.

The term "caline" in plant developmental biology

In the 1930s, Frits Warmolt Went conducted a number of seminal studies on pea seedlings that had been germinated in the dark and assessed their growth when either the apical parts, cotyledons, or roots were cut off or grafted, to assess whether coplant growth factors assisted auxin in the development of these organs. Went assigned the term "calines" to all auxin-assisting substances, specifically rhizocaline, caulocaline, and phyllocaline in root, shoot (and axillary buds) and leaf development, respectively. Those experiments were based exclusively on growth assays, and no supplementary biochemical or physiological analyses were ever conducted, and additional proof was only provided by Went using pea or tomato. The lack of independent reproducibility by other groups, combined with the fact that the hormonal control of these developmental events in plants is now fairly well-studied event, even at the molecular level, suggests that these growth factors that Went observed 80 years ago either do not exist or are known by some other term in modern plant development. The terms related to "calines" should thus no longer be used in plant developmental biology.

Metabolomics Analysis of Litchi Leaves during Floral Induction Reveals Metabolic Improvement by Stem Girdling

Prolonged exposure to cold temperatures often results in a relatively low flowering rate in litchi (Litchi chinensis Sonn.) trees with younger leaves. This study aimed to verify the impact of stem girdling on litchi flowering by identifying and characterizing the induced metabolic changes. After a 60 day exposure to cold treatment at 15 °C/10 °C (12 h/12 h), the flowering rate of the girdled trees was 100%, while that of the non-girdled trees was 20%, indicating that girdling improved litchi flowering at its turning stage. The metabolic profiles of litchi leaves with and without stem girdling during floral induction were compared and 505 metabolites potentially associated with litchi flowering were detected. Most metabolites were involved in the metabolism of starch and sucrose, fatty acid, and phenylpyruvic acid. The metabolic pathways concerned with the biosynthesis of epinephrine, sucrose, and d-maltose were induced in leaves after girdling treatment. The level of galactitol, phenylpyruvic acid, acetyl-CoA, linoleic acid, alpha-linolenic acid, and 13-HPOT biosynthesis remained stable in the leaves from girdled trees but changed drastically in the leaves from non-girdled trees. In addition, 379 metabolites concerning flowering rate were characterized. Metabolism pathways of starch and sucrose, galactose, and linoleic acid are of great significance to the flowering of litchi. Linoleic acid exhibited the most significant variations between girdled trees and non-girdled trees with fold changes of up to 13.62. These results contribute to understanding the biological mechanism of litchi floral induction and the metabolic changes after stem girdling.

Dissection of floral transition by single-meristem transcriptomes at high temporal resolution

The vegetative-to-floral transition is a dramatic developmental change of the shoot apical meristem, promoted by the systemic florigen signal. However, poor molecular temporal resolution of this dynamic process has precluded characterization of how meristems respond to florigen induction. Here, we develop a technology that allows sensitive transcriptional profiling of individual shoot apical meristems. Computational ordering of hundreds of tomato samples reconstructed the floral transition process at fine temporal resolution and uncovered novel short-lived gene expression programs that are activated before flowering. These programs are annulled only when both florigen and a parallel signalling pathway are eliminated. Functional screening identified genes acting at the onset of pre-flowering programs that are involved in the regulation of meristem morphogenetic changes but dispensable for the timing of floral transition. Induced expression of these short-lived transition-state genes allowed us to determine their genetic hierarchies and to bypass the need for the main flowering pathways. Our findings illuminate how systemic and autonomous pathways are integrated to control a critical developmental switch.

The interplay of phloem-mobile signals in plant development and stress response

Plants integrate a variety of biotic and abiotic factors for optimal growth in their given environment. While some of these responses are local, others occur distally. Hence, communication of signals perceived in one organ to a second, distal part of the plant and the coordinated developmental response require an intricate signaling system. To do so, plants developed a bipartite vascular system that mediates the uptake of water, minerals, and nutrients from the soil; transports high-energy compounds and building blocks; and traffics essential developmental and stress signals. One component of the plant vasculature is the phloem. The development of highly sensitive mass spectrometry and molecular methods in the last decades has enabled us to explore the full complexity of the phloem content. As a result, our view of the phloem has evolved from a simple transport path of photoassimilates to a major highway for pathogens, hormones and developmental signals. Understanding phloem transport is essential to comprehend the coordination of environmental inputs with plant development and, thus, ensure food security. This review discusses recent developments in its role in long-distance signaling and highlights the role of some of the signaling molecules. What emerges is an image of signaling paths that do not just involve single molecules but rather, quite frequently an interplay of several distinct molecular classes, many of which appear to be transported and acting in concert.

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.

Molecular characterization of a soybean FT homologue, GmFT7

Soybean (Glycine max) is a vital oilseed legume crop that provides protein and oil for humans and feedstock for animals. Flowering is a prerequisite for seed production. Floral transition, from vegetative to reproductive stage, in a plant, is regulated by environmental (light, temperature) and endogenous factors. In Arabidopsis, Flowering Locus T (FT) protein is shown to be a mobile signal that moves from leaf to shoot apical meristem to induce flowering. However, FTs role in soybean is not fully resolved due to the presence of multiple (ten) homologs in the genome. Two of the ten FT homologs (GmFT2a and GmFT5a) have a role in the floral transition while GmFT1a and GmFT4 suppress soybean flowering. Recent deep sequencing data revealed that six FT homologs are expressed in shoot apical meristem and leaves during floral transition. One FT homolog, GmFT7 showed strong expression during soybean floral transition. Though bioinformatic analyses revealed that GmFT7 had high similarity with GmFT2a, ectopic GmFT7 expression in Arabidopsis could not promote flowering or rescue the late-flowering phenotype of Arabidopsis ft-10 mutant.

A suppressor of axillary meristem maturation promotes longevity in flowering plants

Post-embryonic development and longevity of flowering plants are, for a large part, determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. The genes that are associated with AM maturation and underlie the differences between monocarpic (reproduce once and die) annual and the longer-lived polycarpic (reproduce more than once) perennial plants are still largely unknown. Here we identify a new role for the Arabidopsis AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15) gene as a suppressor of AM maturation. Loss of AHL15 function accelerates AM maturation, whereas ectopic expression of AHL15 suppresses AM maturation and promotes longevity in monocarpic Arabidopsis and tobacco. Accordingly, in Arabidopsis grown under longevity-promoting short-day conditions, or in polycarpic Arabidopsis lyrata, expression of AHL15 is upregulated in AMs. Together, our results indicate that AHL15 and other AHL clade-A genes play an important role, directly downstream of flowering genes (SOC1, FUL) and upstream of the flowering-promoting hormone gibberellic acid, in suppressing AM maturation and extending the plant's lifespan.

Scion control of miRNA abundance and tree maturity in grafted avocado

BACKGROUND

Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown.

RESULTS

Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1.

CONCLUSION

Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.

Scion control of miRNA abundance and tree maturity in grafted avocado

BACKGROUND

Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown.

RESULTS

Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1.

CONCLUSION

Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.

Stem growth characteristics of high yielding Miscanthus correlate with yield, development and intraspecific competition within plots

High yielding perennial grasses are utilized as biomass for the bioeconomy and to displace fossil fuels. Many such grasses, including Miscanthus, are largely undomesticated. The main Miscanthus crop is a naturally occurring hydrid M. × giganteus (Mxg). All above ground biomass from Miscanthus is harvested. Stem traits correlate strongly with yield and therefore understanding the seasonal progression of stem growth should identify routes for improved yield. If such studies utilized high yielding commercial genotypes growing in plots the conclusions are likely to be more commercially relevant. Stem elongation was measured from five high yielding genotypes, 10 plants per plot from 20 plots in a replicated field trial over 4 years. Richards growth function produced an accurate fit to stem elongation. Differentials, double differentials and integrals of the parameterized function produced six growth characteristics, describing growth rate, timing and duration of the logarithmic growth phase and area under the growth curve. Maximum growth rate was correlated with yield and compensatory interactions were identified, for example plants with higher maximal growth rates had shorter durations of logarithmic growth. Plant position within plots of lower yielding genotypes did not affect growth characteristics but had a significant effect on late season growth characteristics in higher yielding genotypes. Two high yielding genotypes were compared over 3 years and growth parameterized using four different factors. The inverse correlation between maximum growth rate and duration of logarithmic growth was consistent across years and factors in both genotypes except when parameterized using temperature and only in Mxg. This suggested that different limitations to growth were exerted on the two genotypes which may help explain the exceptional performance of the Mxg genotype. We discuss the implications of the identified complex interactions in growth characteristics for approaches to maximize seasonal yield in perennial biomass crops.

De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.

Genetic interactions reveal the antagonistic roles of FT/TSF and TFL1 in the determination of inflorescence meristem identity in Arabidopsis

During the transition to the reproductive phase, the shoot apical meristem switches from the developmental program that generates vegetative organs to instead produce flowers. In this study, we examined the genetic interactions of FLOWERING LOCUS T (FT)/TWIN SISTER OF FT (TSF) and TERMINAL FLOWER 1 (TFL1) in the determination of inflorescence meristem identity in Arabidopsis thaliana. The ft-10 tsf-1 mutants produced a compact inflorescence surrounded by serrated leaves (hyper-vegetative shoot) at the early bolting stage, as did plants overexpressing TFL1. Plants overexpressing FT or TSF (or both FT and TFL1) generated a terminal flower, as did tfl1-20 mutants. The terminal flower formed in tfl1-20 mutants converted to a hyper-vegetative shoot in ft-10 tsf-1 mutants. Grafting ft-10 tsf-1 or ft-10 tsf-1 tfl1-20 mutant scions to 35S::FT rootstock plants produced a normal inflorescence and a terminal flower in the scion plants, respectively, although both scions showed similar early flowering. Misexpression of FT in the vasculature and in the shoot apex in wild-type plants generated a normal inflorescence and a terminal flower, respectively. By contrast, in ft-10 tsf-1 mutants the vasculature-specific misexpression of FT converted the hyper-vegetative shoot to a normal inflorescence, and in the ft-10 tsf-1 tfl1-20 mutants converted the shoot to a terminal flower. TFL1 levels did not affect the inflorescence morphology caused by FT/TSF overexpression at the early bolting stage. Taking these results together, we proposed that FT/TSF and TFL1 play antagonistic roles in the determination of inflorescence meristem identity, and that FT/TSF are more important than TFL1 in this process.

The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development

Florigen, a proteinaceous hormone, functions as a universal long-range promoter of flowering and concurrently as a generic growth-attenuating hormone across leaf and stem meristems. In flowering plants, the transition from the vegetative phase to the reproductive phase entails the orchestration of new growth coordinates and a global redistribution of resources, signals, and mechanical loads among organs. However, the ultimate cellular processes governing the adaptation of the shoot system to reproduction remain unknown. We hypothesized that if the mechanism for floral induction is universal, then the cellular metabolic mechanisms underlying the conditioning of the shoot system for reproduction would also be universal and may be best regulated by florigen itself. To understand the cellular basis for the vegetative functions of florigen, we explored the radial expansion of tomato stems. RNA-Seq and complementary genetic and histological studies revealed that florigen of endogenous, mobile, or induced origins accelerates the transcription network navigating secondary cell wall biogenesis as a unit, promoting vascular maturation and thereby adapting the shoot system to the developmental needs of the ensuing reproductive phase it had originally set into motion. We then demonstrated that a remarkably stable and broadly distributed florigen promotes MADS and MIF genes, which in turn regulate the rate of vascular maturation and radial expansion of stems irrespective of flowering or florigen level. The dual acceleration of flowering and vascular maturation by florigen provides a paradigm for coordinated regulation of independent global developmental programs.

Plant Physiology: Unveiling the Dark Side of Phloem Translocation

Sugars and other macromolecules arrive in heterotrophic plant tissues through the phloem, a long-distance transport system. Owing to a recent study, we now have a better understanding of how these molecules exit the phloem at their final destinations.

Maturity2, a novel regulator of flowering time in Sorghum bicolor, increases expression of SbPRR37 and SbCO in long days delaying flowering

Sorghum bicolor is a drought-resilient facultative short-day C4 grass that is grown for grain, forage, and biomass. Adaptation of sorghum for grain production in temperate regions resulted in the selection of mutations in Maturity loci (Ma1 -Ma6) that reduced photoperiod sensitivity and resulted in earlier flowering in long days. Prior studies identified the genes associated with Ma1 (PRR37), Ma3 (PHYB), Ma5 (PHYC) and Ma6 (GHD7) and characterized their role in the flowering time regulatory pathway. The current study focused on understanding the function and identity of Ma2. Ma2 delayed flowering in long days by selectively enhancing the expression of SbPRR37 (Ma1) and SbCO, genes that co-repress the expression of SbCN12, a source of florigen. Genetic analysis identified epistatic interactions between Ma2 and Ma4 and located QTL corresponding to Ma2 on SBI02 and Ma4 on SBI10. Positional cloning and whole genome sequencing identified a candidate gene for Ma2, Sobic.002G302700, which encodes a SET and MYND (SYMD) domain lysine methyltransferase. Eight sorghum genotypes previously identified as recessive for Ma2 contained the mutated version of Sobic.002G302700 present in 80M (ma2) and one additional putative recessive ma2 allele was identified in diverse sorghum accessions.

RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines

BACKGROUND

Gibberellins (GAs) and their regulator DELLA are involved in many aspects of plant growth and development and most of our current knowledge in the DELLA-facilitated GA signaling was obtained from the studies of annual species. To understand GA-DELLA signaling in perennial species, we created ten GA-insensitive transgenic grapevines carrying a DELLA mutant allele (Vvgai1) in the background of Vitis vinifera 'Thompson Seedless' and conducted comprehensive analysis of their RNA expression profiles in the shoot, leaf and root tissues.

RESULTS

The transgenic lines showed varying degrees of dwarf stature and other typical DELLA mutant phenotypes tightly correlated with the levels of Vvgai1 expression. A large number of differentially expressed genes (DEGs) were identified in the shoot, leaf and root tissues of the transgenic lines and these DEGs were involved in diverse biological processes; many of the DEGs showed strong tissue specificity and about 30% them carried a DELLA motif. We further discovered unexpected expression patterns of several key flowering induction genes VvCO, VvCOL1 and VvTFL1.

CONCLUSIONS

Our results not only confirmed many previous DELLA study findings in annual species, but also revealed new DELLA targets and responses in grapevine, including the roles of homeodomain transcription factors as potential co-regulators with DELLA in controlling the development of grapevine which uniquely possess both vegetative and reproductive meristems at the same time. The contrasting responses of some key flowering induction pathway genes provides new insights into the divergence of GA-DELLA regulations between annual and perennial species in GA-DELLA signaling.

Comprehensive analysis of the longan transcriptome reveals distinct regulatory programs during the floral transition

Background

Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical regions of Southeast Asia and Australia. Among the factors affecting D. longan fruit yield, the difficulty and instability of blossoming is one of the most challenging issues. Perpetual flowering (PF) is a crucial trait for fruit trees and is directly linked to production potential. Therefore, studying the molecular regulatory mechanism of longan PF traits is crucial for understanding and solving problems related to flowering. In this study, comparative transcriptome analysis was performed using two longan cultivars that display opposite flowering phenotypes during floral induction.

Results

We obtained 853.72 M clean reads comprising 125.08 Gb. After comparing these data with the longan genome, 27,266 known genes and 1913 new genes were detected. Significant differences in gene expression were observed between the two genotypes, with 6150 and 6202 differentially expressed genes (DEGs) for ‘SJ’ and ‘SX’, respectively. The transcriptional landscape of floral transition at the early stage was very different in these two longan genotypes with respect to key hormones, circadian rhythm, sugar metabolism, and transcription factors. Almost all flowering-related DEGs identified are involved in photoperiod and circadian clock pathways, such as CONSTANS-like (COL), two-component response regulator-like (APRRs), gigantea (GI), and early flowering (EFL). In addition, the leafy (LFY) gene, which is the central floral meristem identity gene, may inhibit PF formation in ‘SJ’.

Conclusion

This study provides a platform for understanding the molecular mechanisms responsible for changes between PF and seasonal flowering (SF) longan genotypes and may benefit studies on PF trait mechanisms of evergreen fruit trees.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5461-3) contains supplementary material, which is available to authorized users.

Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize

Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.

Transcription profiles reveal the regulatory mechanisms of spur bud changes and flower induction in response to shoot bending in apple (Malus domestica Borkh.)

Shoot bending, as an effective agronomic measure, has been widely used to promote flowering in 'Fuji' apple trees. Here, we examined the transcriptional responses of genes in 'Fuji' apple buds at different flowering stages under a shoot-bending treatment using RNA sequencing. A complex genetic crosstalk-regulated network, involving abscisic acid-related genes, starch metabolism and circadian rhythm-related genes, as well as stress response-related genes, was up-regulated by shoot bending, in which were contrbuted to apple flower bud formation in response to shoot-bending conditions. Flower induction plays an important role in the apple tree life cycle, but young trees produce fewer and inferior flower buds. Shoot bending, as an effective agronomic measure, has been widely used to promote flowering in 'Fuji' apple trees. However, little is known about the gene expression network patterns and molecular regulatory mechanisms caused by shoot bending during the induced flowering. Here, we examined the transcriptional responses of genes in 'Fuji' apple buds at different flowering stages under a shoot-bending treatment using RNA sequencing. A steady up-regulation of carbon metabolism-related genes led to relatively high levels of sucrose in early induced flowering stages and starch accumulation during shoot bending. Additionally, global gene expression profiling determined that cytokinin, indole-3-acetic acid, gibberellin synthesis and signalling-related genes were significantly regulated by shoot bending, contributing to cell division and differentiation, bud growth and flower induction. A complex genetic crosstalk-regulated network, involving abscisic acid-related genes, starch metabolism- and circadian rhythm-related genes, as well as stress response-related genes, was up-regulated by shoot bending. Additionally, some transcription factor family genes that were involved in sugar, abscisic acid and stress response signalling were significantly induced by shoot bending. These important flowering genes, which were mainly involved in photoperiod, age and autonomous pathways, were up-regulated by shoot bending. Thus, a complex genetic network of regulatory mechanisms involved in sugar, hormone and stress response signalling pathways may mediate the induction of apple tree flowering in response to shoot-bending conditions.

Comparative RNA-sequencing-based transcriptome profiling of buds from profusely flowering 'Qinguan' and weakly flowering 'Nagafu no. 2' apple varieties reveals novel insights into the regulatory mechanisms underlying floral induction

BACKGROUND

Floral induction is an important stage in the apple tree life cycle. In 'Nagafu No. 2', which was derived from a 'Fuji' bud sport, flower bud formation is associated with serious problems, such as fewer and inferior flower buds, a long juvenile phase, and an alternate bearing phenotype. Moreover, the molecular regulatory mechanisms underlying apple floral induction remain unknown. To characterize these mechanisms, we compared the RNA-sequencing-based transcriptome profiles of buds during floral induction in profusely flowering 'Qinguan' and weakly flowering 'Nagafu No. 2' apple varieties.

RESULTS

Genes differentially expressed between the buds of the two varieties were mainly related to carbohydrate, fatty acid, and lipid pathways. Additionally, the steady up-regulated expression of genes related to the fatty acid and lipid pathways and the down-regulated expression of starch synthesis-related genes in the carbon metabolic pathway of 'Qinguan' relative to 'Nagafu No. 2' were observed to contribute to the higher flowering rate of 'Qinguan'. Additionally, global gene expression profiling revealed that genes related to cytokinin, indole-3-acetic acid, and gibberellin synthesis, signalling, and responses (i.e., factors contributing to cell division and differentiation and bud growth) were significantly differentially expressed between the two varieties. The up-regulated expression of genes involved in abscisic acid and salicylic acid biosynthesis via shikimate pathways as well as jasmonic acid production through fatty acid pathways in 'Qinguan' buds were also revealed to contribute to the floral induction and relatively high flowering rate of this variety. The differential expression of transcription factor genes (i.e., SPL, bZIP, IDD, and MYB genes) involved in multiple biological processes was also observed to play key roles in floral induction. Finally, important flowering genes (i.e., FT, FD, and AFL) were significantly more highly expressed in 'Qinguan' buds than in 'Nagafu No. 2' buds during floral induction.

CONCLUSIONS

A complex genetic network of regulatory mechanisms involving carbohydrate, fatty acid, lipid, and hormone pathways may mediate the induction of apple tree flowering.

Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea

Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Longan is an important fruit tree in the subtropical region of Southeast Asia and Australia. However, its blooming and its yield are susceptible to stresses such as droughts, high salinity, and high and low temperature. To date, the molecular mechanisms of abiotic stress tolerance and flower induction in longan have not been elucidated. WRKY transcription factors (TFs), which have been studied in various plant species, play important regulatory roles in plant growth, development, and responses to stresses. However, there is no report about WRKYs in longan. In this study, we identified 55 WRKY genes with the conserved WRKY domain and zinc finger motif in the longan genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the longan WRKY (DlWRKY) family was classified into three major groups (I–III) and five subgroups (IIa–IIe) in group II. Tissue expression analysis showed that 25 DlWRKYs were highly expressed in almost all organs, suggesting that these genes may be important for plant growth and organ development in longan. Comparative RNA-seq and qRT-PCR-based gene expression analysis revealed that 18 DlWRKY genes showed a specific expression during three stages of flower induction in “Sijimi” (“SJ”), which exhibited the “perpetual flowering” (PF) habit, indicating that these 18 DlWRKY genes may be involved in the flower induction and the genetic control of the perpetual flowering trait in longan. Furthermore, the RT-qPCR analysis illustrated the significant variation of 27, 18, 15, 17, 27, and 23 DlWRKY genes under SA (Salicylic acid), MeJA (Methyl Jasmonate), heat, cold, drought, or high salinity treatment, respectively, implicating that they might be stress- or hormone-responsive genes. In summary, we systematically and comprehensively analyzed the structure, evolution, and expression pattern of the DlWRKY genes. The results presented here increase our understanding of the WRKY family in fruit trees and provide a basis for the further elucidation of the biological function of DlWRKY genes in longan.

The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses

Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up- or down-regualted in the cultivar “Sijimi” (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were up- or down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan.

Improved water use efficiency and shorter life cycle of Nicotiana tabacum due to modification of guard and vascular companion cells

Severe droughts are predicted for the twenty-first century, which contrast with the increased demand for plant materials. Thus, to sustain future generations, a great challenge is to improve crop yield and water use efficiency (WUE), which is the carbon gained per water lost. Here, expression of maize NADP-malic enzyme (NADP-ME) in the guard and vascular companion cells of Nicotiana tabacum results in enhanced WUE, earlier flowering and shorter life cycle. Transgenic lines exhibit reduced stomatal aperture than wild-type (WT). Nevertheless, an increased net CO2 fixation rate is observed, which results in less water consumption and more biomass production per water used. Transgenic lines export sugars to the phloem at higher rate than WT, which leads to higher sugars levels in phloem exudates and veins. Leaf quantitative proteomic profiling revealed drastic differences in proteins related to cell cycle, flowering, hormone signaling and carbon metabolism between transgenic lines and WT. We propose that the increased sugar export from leaves in the transgenic lines alleviates sugar negative feedback on photosynthesis and thus, stomatal closure takes place without a penalty in CO2 assimilation rate. This results in improved WUE and accelerated overall life cycle, key traits for plant productivity in the near future world.

Light signalling-induced regulation of nutrient acquisition and utilisation in plants

Light is the foremost regulator of plant growth and development, and the critical role of light signalling in the promotion of nutrient uptake and utilisation was clarified in recent decades. Recent studies with Arabidopsis demonstrated the molecular mechanisms underlying such promotive effects and uncovered the pivotal role of the transcription factor ELONGATED HYPOCOTYL5 (HY5) whose activity is under the control of multiple photoreceptors. Together with a recent finding that phytochrome B, one of photoreceptors, is activated in subterranean plant parts, the discovery that HY5 directly promotes the transcription of genes involved in nutrient uptake and utilisation, including several nitrogen and sulphur assimilation-related genes, expands our understanding of the ways in which light signalling effectively and co-ordinately modulates uptake and utilisation of multiple nutrients in plants. This review presents a summary of the current knowledge regarding light signalling-induced regulation of nutrient uptake and utilisation.

Transcriptomics analysis of the flowering regulatory genes involved in the herbicide resistance of Asia minor bluegrass (Polypogon fugax)

Background

Asia minor bluegrass (Polypogon fugax, P. fugax), a weed that is both distributed across China and associated with winter crops, has evolved resistance to acetyl-CoA carboxylase (ACCase) herbicides, but the resistance mechanism remains unclear. The goal of this study was to analyze the transcriptome between resistant and sensitive populations of P. fugax at the flowering stage.

Results

Populations resistant and susceptible to clodinafop-propargyl showed distinct transcriptome profiles. A total of 206,041 unigenes were identified; 165,901 unique sequences were annotated using BLASTX alignment databases. Among them, 5904 unigenes were classified into 58 transcription factor families. Nine families were related to the regulation of plant growth and development and to stress responses. Twelve unigenes were differentially expressed between the clodinafop-propargyl-sensitive and clodinafop-propargyl-resistant populations at the early flowering stage; among those unigenes, three belonged to the ABI3VP1, BHLH, and GRAS families, while the remaining nine belonged to the MADS family. Compared with the clodinafop-propargyl-sensitive plants, the resistant plants exhibited different expression pattern of these 12 unigenes.

Conclusion

This study identified differentially expressed unigenes related to ACCase-resistant P. fugax and thus provides a genomic resource for understanding the molecular basis of early flowering.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4324-z) contains supplementary material, which is available to authorized users.

Variation in shade-induced flowering in Arabidopsis thaliana results from FLOWERING LOCUS T allelic variation

Plants have evolved developmental mechanisms to ensure reproduction when in sub-optimal local environments. The shade-avoidance syndrome is one such mechanism that causes plants to elongate and accelerate flowering. Plants sense shade via the decreased red:far-red (R:FR) ratio that occurs in shade. We explored natural variation in flowering behavior caused by a decrease in the R:FR ratio of Arabidopsis thaliana accessions. A survey of accessions revealed that most exhibit a vigorous rapid-flowering response in a FR-enriched environment. However, a subset of accessions appeared to be compromised in the accelerated-flowering component of the shade-avoidance response. The genetic basis of the muted response to FR enrichment was studied in three accessions (Fl-1, Hau-0, and Mir-0). For all three accessions, the reduced FR flowering-time effect mapped to the FLOWERING LOCUS T (FT) region, and the FT alleles from these accessions are expressed at a lower level in FR-enriched light compared to alleles from accessions that respond robustly to FR enrichment. In the Mir-0 accession, a second genomic region, which includes CONSTANTS (CO), also influenced flowering in FR-enriched conditions. We have demonstrated that variation in the degree of precocious flowering in shaded conditions (low R:FR ratio) results from allelic variation at FT.

Identification of TPS family members in apple (Malus x domestica Borkh.) and the effect of sucrose sprays on TPS expression and floral induction

Trehalose (α-D-glucopyranosyl α-D-glucopyranoside) is a non-reducing disaccharide that serves as a carbon source and stress protectant in apple trees. Trehalose-6-phosphate (T6P) is the biosynthetic precursor of trehalose. It functions as a crucial signaling molecule involved in the regulation of floral induction, and is closely related to sucrose. Trehalose-6-phosphate synthase (TPS) family members are pivotal components of the T6P biosynthetic pathway. The present study identified 13 apple TPS family members and characterized their expression patterns in different tissues and in response to exogenous application of sucrose during floral induction. 'Fuji' apple trees were sprayed with sucrose prior to the onset of floral induction. Bud growth, flowering rate, and endogenous sugar levels were then monitored. The expression of genes associated with sucrose metabolism and flowering were also characterized by RT-quantitative PCR. Results revealed that sucrose applications significantly improved flower production and increased bud size and fresh weight, as well as the sucrose content in buds and leaves. Furthermore, the expression of MdTPS1, 2, 4, 10, and 11 was rapidly and significantly up-regulated in response to the sucrose treatments. In addition, the expression levels of flowering-related genes (e.g., SPL genes, FT1, and AP1) also increased in response to the sucrose sprays. In summary, apple TPS family members were identified that may influence the regulation of floral induction and other responses to sucrose. The relationship between sucrose and T6P or TPS during the regulation of floral induction in apple trees is discussed.

Spatial patterns and broad-scale weather cues of beech mast seeding in Europe

Mast seeding is a crucial population process in many tree species, but its spatio-temporal patterns and drivers at the continental scale remain unknown . Using a large dataset (8000 masting observations across Europe for years 1950-2014) we analysed the spatial pattern of masting across the entire geographical range of European beech, how it is influenced by precipitation, temperature and drought, and the temporal and spatial stability of masting-weather correlations. Beech masting exhibited a general distance-dependent synchronicity and a pattern structured in three broad geographical groups consistent with continental climate regimes. Spearman's correlations and logistic regression revealed a general pattern of beech masting correlating negatively with temperature in the summer 2 yr before masting, and positively with summer temperature 1 yr before masting (i.e. 2T model). The temperature difference between the two previous summers (DeltaT model) was also a good predictor. Moving correlation analysis applied to the longest eight chronologies (74-114 yr) revealed stable correlations between temperature and masting, confirming consistency in weather cues across space and time. These results confirm widespread dependency of masting on temperature and lend robustness to the attempts to reconstruct and predict mast years using temperature data.

Functional Characterization of a Putative Glycine max ELF4 in Transgenic Arabidopsis and Its Role during Flowering Control

Flowering is an important trait in major crops like soybean due to its direct relation to grain production. The circadian clock mediates the perception of seasonal changes in day length and temperature to modulate flowering time. The circadian clock gene EARLY FLOWERING 4 (ELF4) was identified in Arabidopsis thaliana and is believed to play a key role in the integration of photoperiod, circadian regulation, and flowering. The molecular circuitry that comprises the circadian clock and flowering control in soybeans is just beginning to be understood. To date, insufficient information regarding the soybean negative flowering regulators exist, and the biological function of the soybean ELF4 (GmELF4) remains unknown. Here, we investigate the ELF4 family members in soybean and functionally characterize a GmELF4 homologous gene. The constitutive overexpression of GmELF4 delayed flowering in Arabidopsis, showing the ELF4 functional conservation among plants as part of the flowering control machinery. We also show that GmELF4 alters the expression of Arabidopsis key flowering time genes (AtCO and AtFT), and this down-regulation is the likely cause of flowering delay phenotypes. Furthermore, we identified the GmELF4 network genes to infer the participation of GmELF4 in soybeans. The data generated in this study provide original insights for comprehending the role of the soybean circadian clock ELF4 gene as a negative flowering controller.

The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities

FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) proteins share highly conserved amino acid residues but they play opposite regulatory roles in promoting and repressing the flowering response, respectively. Previous substitution models and functional analysis have identified several key amino acid residues which are critical for the promotion of flowering. However, the precise relationship between naturally occurring FT/TFL1 homologs and the mechanism of their role in flowering is still unclear. In this study, FT/TFL1 homologs from eight Rosaceae species, namely, Spiraea cantoniensis, Pyracantha fortuneana, Photinia serrulata, Fragaria ananassa, Rosa hybrida, Prunus mume, Prunus persica and Prunus yedoensis, were isolated. Three of these homologs were further characterized by functional analyses involving site-directed mutagenesis. The results showed that these FT/TFL1 homologs might have diverse functions despite sharing a high similarity of sequences or crystal structures. Functional analyses were conducted for the key FT amino acids, Tyr-85 and Gln-140. It revealed that TFL1 homologs cannot promote flowering simply by substitution with key FT amino acid residues. Mutations of the IYN triplet motif within segment C of exon 4 can prevent the FT homolog from promoting the flowering. Furthermore, physical interaction of FT homologous or mutated proteins with the transcription factor FD, together with their lipid-binding properties analysis, showed that it was not sufficient to trigger flowering. Thus, our findings revealed that the divergence of flowering time modulating by FT/TFL1 homologs is independent to interaction and binding activities.

Mechanisms of mast seeding: resources, weather, cues, and selection

546 I. 546 II. 547 III. 548 IV. 552 V. 554 VI. 556 VII. 558 VIII. 558 IX. 559 559 References 559 SUMMARY: Mast seeding is a widespread and widely studied phenomenon. However, the physiological mechanisms that mediate masting events and link them to weather and plant resources are still debated. Here, we explore how masting is affected by plant resource budgets, fruit maturation success, and hormonal coordination of cues including weather and resources. There is little empirical support for the commonly stated hypothesis that plants store carbohydrates over several years to expend in a high-seed year. Plants can switch carbohydrates away from growth in high-seed years, and seed crops are more probably limited by nitrogen or phosphorus. Resources are clearly involved in the proximate mechanisms driving masting, but resource budget (RB) models cannot create masting in the absence of selection because some underlying selective benefit is required to set the level of a 'full' seed crop at greater than the annual resource increment. Economies of scale (EOSs) provide the ultimate factor selecting for masting, but EOSs probably always interact with resources, which modify the relationship between weather cues and reproduction. Thus, RB and EOS models are not alternative explanations for masting - both are required. Experiments manipulating processes that affect mast seeding will help clarify the physiological mechanisms that underlie mast seeding.