Physiological differences between bud breaking and flowering after dormancy completion revealed by DAM and FT/TFL1 expression in Japanese pear (Pyrus pyrifolia)

Molecular Mechanisms of Seasonal Gene Expression in Trees

In trees, the annual cycling of active and dormant states in buds is closely regulated by environmental factors, which are of primary significance to their productivity and survival. It has been found that the parallel or convergent evolution of molecular pathways that respond to day length or temperature can lead to the establishment of conserved periodic gene expression patterns. In recent years, it has been shown in many woody plants that change in annual rhythmic patterns of gene expression may underpin the adaptive evolution in forest trees. In this review, we summarize the progress on the molecular mechanisms of seasonal regulation on the processes of shoot growth, bud dormancy, and bud break in response to day length and temperature factors. We focus on seasonal expression patterns of genes involved in dormancy and their associated epigenetic modifications; the seasonal changes in the extent of modifications, such as DNA methylation, histone acetylation, and histone methylation, at dormancy-associated loci have been revealed for their actions on gene regulation. In addition, we provide an outlook on the direction of research on the annual cycle of tree growth under climate change.

Effects of low temperature on flowering and the expression of related genes in Loropetalum chinense var. rubrum

INTRODUCTION

Loropetalum chinense var. rubrum blooms 2-3 times a year, among which the autumn flowering period has great potential for exploitation, but the number of flowers in the autumn flowering period is much smaller than that in the spring flowering period.

METHODS

Using 'Hei Zhenzhu' and 'Xiangnong Xiangyun' as experimental materials, the winter growth environment of L. chinense var. rubrum in Changsha, Hunan Province was simulated by setting a low temperature of 6-10°C in an artificial climate chamber to investigate the effect of winter low temperature on the flowering traits and related gene expression of L. chinense var. rubrum.

RESULTS

The results showed that after 45 days of low temperature culture and a subsequent period of 25°C greenhouse culture, flower buds and flowers started to appear on days 24 and 33 of 25°C greenhouse culture for 'Hei Zhenzhu', and flower buds and flowers started to appear on days 21 and 33 of 25°C greenhouse culture for 'Xiangnong Xiangyun'. The absolute growth rate of buds showed a 'Up-Down' pattern during the 7-28 days of low temperature culture; the chlorophyll fluorescence decay rate (Rfd) of both materials showed a 'Down-Up-Down' pattern during this period. The non-photochemical quenching coefficient (NPQ) showed the same trend as Rfd, and the photochemical quenching coefficient (QP) fluctuated above and below 0.05. The expression of AP1 and FT similar genes of L. chinense var. rubrum gradually increased after the beginning of low temperature culture, reaching the highest expression on day 14 and day 28, respectively, and the expression of both in the experimental group was higher than that in the control group. The expressions of FLC, SVP and TFL1 similar genes all decreased gradually with low temperature culture, among which the expressions of FLC similar genes and TFL1 similar genes in the experimental group were extremely significantly lower than those in the control group; in the experimental group, the expressions of GA3 similar genes were all extremely significantly higher than those in the control group, and the expressions all increased with the increase of low temperature culture time.

DISCUSSION

We found that the high expression of gibberellin genes may play an important role in the process of low temperature promotion of L. chinense var. rubrum flowering, and in the future, it may be possible to regulate L. chinense var. rubrum flowering by simply spraying exogenous gibberellin instead of the promotion effect of low temperature.

How Is Global Warming Affecting Fruit Tree Blooming? "Flowering (Dormancy) Disorder" in Japanese Pear (Pyrus pyrifolia) as a Case Study

Recent climate change has resulted in warmer temperatures. Warmer temperatures from autumn to spring has negatively affected dormancy progression, cold (de)acclimation, and cold tolerance in various temperate fruit trees. In Japan, a physiological disorder known as flowering disorder, which is an erratic flowering and bud break disorder, has recently emerged as a serious problem in the production of the pome fruit tree, Japanese (Asian) pear (Pyrus pyrifolia Nakai). Due to global warming, the annual temperature in Japan has risen markedly since the 1990s. Surveys of flowering disorder in field-grown and greenhouse-grown Japanese pear trees over several years have indicated that flowering disorder occurs in warmer years and cultivation conditions, and the risk of flowering disorder occurrence is higher at lower latitudes than at higher latitudes. Susceptibility to flowering disorder is linked to changes in the transcript levels of putative dormancy/flowering regulators such as DORMANCY-ASSOCIATED MADS-box (DAM) and FLOWERING LOCUS T (FT). On the basis of published studies, we conclude that autumn-winter warm temperatures cause flowering disorder through affecting cold acclimation, dormancy progression, and floral bud maturation. Additionally, warm conditions also decrease carbohydrate accumulation in shoots, leading to reduced tree vigor. We propose that all these physiological and metabolic changes due to the lack of chilling during the dormancy phase interact to cause flowering disorder in the spring. We also propose that the process of chilling exposure rather than the total amount of chilling may be important for the precise control of dormancy progression and robust blooming, which in turn suggests the necessity of re-evaluation of the characteristics of cultivar-dependent chilling requirement trait. A full understanding of the molecular and metabolic regulatory mechanisms of both dormancy completion (floral bud maturation) and dormancy break (release from the repression of bud break) will help to clarify the physiological basis of dormancy-related physiological disorder and also provide useful strategies to mitigate or overcome it under global warming.

Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume

MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.

Alternative splicing of the dormancy-associated MADS-box transcription factor gene PpDAM1 is associated with flower bud dormancy in 'Dangshansu' pear (Pyrus pyrifolia white pear group)

Alternative splicing (AS) plays a crucial role in plant growth, development and response to various environmental changes. However, whether alternative splicing of MADS-box transcription factors contributes to the flower bud dormancy process in fruit trees still remains unknown. In this work, the AS profile of genes in the dormant flower buds of 'Dangshansu' pear tree were examined. A total number of 3661 alternatively spliced genes were identified, and three mRNA isoforms of the dormancy associated MADS box (DAM) gene, PpDAM1, derived by alternative splicing, designated as PpDAM1.1, PpDAM1.2 and PpDAM1.3, were characterized. Bimolecular fluorescence complementation (BiFC) analysis indicated that AS of PpDAM1 didn't affect the nucleus localization and homo-/heterodimerization of PpDAM1.1, PpDAM1.2 and PpDAM1.3 proteins, but disturbed the translocation of PpDAM1.1/PpDAM1.1, PpDAM1.3/PpDAM1.3, PpDAM1.1/PpDAM1.3, and PpDAM1.2/PpDAM1.3 dimers to the nucleus. Constitutive expression of PpDAM1.2, but not PpDAM1.1 and PpDAM1.3, in Arabidopsis retarded the growth and development of transgenic plants. Further comparative expression analyses of PpDAM1.1, PpDAM1.2 and PpDAM1.3 in the flower buds of 'Dangshansu' and a less dormant pear cultivar, 'Cuiguan', exhibited that the expression of all the three isoforms in 'Dangshansu' were significantly higher than in 'Cuiguan', especially PpDAM1.2, which showed a predominantly higher expression than PpDAM1.1 and PpDAM1.3 in both cultivars. Our results suggest that alternative splicing of PpDAM1 could play a crucial role in pear flower bud dormancy process.

Male meiosis in sweet cherry is constrained by the chilling and forcing phases of dormancy

Male meiosis in temperate fruit trees occurs in the anthers once a year, synchronized with the seasons. The alternation of dormant and growth cycles determines the optimum moment for the male gametophyte formation, a process sensitive to both cold and warm temperatures. This ensures pollen viability and subsequent reproduction success that guarantee fruit production. In this work, we explore how male meiosis is framed by seasonality in sweet cherry. For this purpose, the dormant phases, male meiosis and blooming dates were established in four cultivars with different flowering dates and chilling requirements over 7 years. The chilling and heat requirements for each cultivar were empirically estimated, and chilling and heat temperatures were quantified according to the Dynamic and Growing Degree Hours (GDH) models, respectively. Endodormancy was overcome approximately a fortnight earlier during the colder winters than during the milder winters. Against our initial hypothesis, these differences were not clearly reflected in the time of male meiosis. The period between chilling fulfillment and meiosis lasted several weeks, during which a high amount of GDH accumulated. Results showed that male meiosis is conditioned by endodormancy but especially by warm temperatures, during the forcing period. This differs from what has been described in other related species and creates a framework for further studies to understand the strategies of synchronizing dormancy with seasons.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

BACKGROUND

Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees.

RESULTS

To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume.

CONCLUSIONS

We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

VvDAM-SVPs genes are regulated by FLOWERING LOCUS T (VvFT) and not by ABA/low temperature-induced VvCBFs transcription factors in grapevine buds

In deciduous fruit trees in which dormancy is induced by low temperatures, the expression of DORMACY-ASSOCIATED MADS-BOX genes (DAM) is regulated by CBF/DREB1 transcription factors. In Vitis vinifera, in which dormancy is induced by the photoperiod, VvDAM-SVPs gene expression is regulated by FLOWERING LOCUS T (VvFT). Using the sequences of the six peach (Prunus persica) DORMACY-ASSOCIATED MADS-box genes (DAM) as query, eight putative DAM genes belonging to the family of MADS-box transcription factors and related to the Arabidopsis floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS LIKE 24 (AGL24) were identified in the V. vinifera genome. Among these, five belong to the subfamily SVP-like genes which have been associated with the regulation of flowering and dormancy in annual and perennial plants, respectively. It has been proposed that they play a direct role in the induction and maintenance of endodormancy (ED) through the regulation of the FLOWERING LOCUS T (FT) gene. In the present study, it is demonstrated that in V. vinifera: (1) VvDAM-SVPs genes are not regulated by ABA/low temperature-induced VvCBFs transcription factors as described for other species of deciduous fruit trees. (2) A contrasting expression pattern between VvDAM3-SVP and VvFT was found under different experimental conditions related to the entry and exit of grapevine buds from ED. (3) Overexpression of VvFT in somatic grapevine embryos (SGE) repressed the expression of VvDAM3-SVP and VvDAM4-SVP. Taken together, the results suggest that VvDAM3-SVP could be associated with ED in grapevine buds, and that its expression could be regulated by VvFT.

Integrated transcriptome and proteome analysis provides insight into chilling-induced dormancy breaking in Chimonanthus praecox

Chilling has a critical role in the growth and development of perennial plants. The chilling requirement (CR) for dormancy breaking largely depends on the species. However, global warming is expected to negatively affect chilling accumulation and dormancy release in a wide range of perennial plants. Here, we used Chimonanthus praecox as a model to investigate the CR for dormancy breaking under natural and artificial conditions. We determined the minimum CR (570 chill units, CU) needed for chilling-induced dormancy breaking and analyzed the transcriptomes and proteomes of flowering and non-flowering flower buds (FBs, anther and ovary differentiation completed) with different CRs. The concentrations of ABA and GA3 in the FBs were also determined using HPLC. The results indicate that chilling induced an upregulation of ABA levels and significant downregulation of SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS T (FT) homologs at the transcript level in FBs when the accumulated CR reached 570 CU (IB570) compared to FBs in November (FB.Nov, CK) and nF16 (non-flowering FBs after treatment at 16 °C for -300 CU), which suggested that dormancy breaking of FBs could be regulated by the ABA-mediated SVP-FT module. Overexpression in Arabidopsis was used to confirm the function of candidate genes, and early flowering was induced in 35S::CpFT1 transgenic lines. Our data provide insight into the minimum CR (570 CU) needed for chilling-induced dormancy breaking and its underlying regulatory mechanism in C. praecox, which provides a new tool for the artificial regulation of flowering time and a rich gene resource for controlling chilling-induced blooming.

Genome-Wide Identification of Epigenetic Regulators in Quercus suber L

Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.

Comparative study of DAM, Dof, and WRKY gene families in fourteen species and their expression in Vitis vinifera

Bud dormancy is one of the most important defensive mechanisms through which plants resist cold stress during harsh winter weather. DAM, Dof, and WRKY have been reported to be involved in many biological processes, including bud dormancy. In the present study, grapevine (Vitis vinifera) and other thirteen plants (six woody plants and seven herbaceous plants) were analyzed for the quantity, sequence structure, and evolution patterns of their DAM, Dof, and WRKY gene family members. Moreover, the expression of VvDAM, VvDof, and VvWRKY genes was also investigated. Thus, 51 DAM, 1,205 WRKY, and 489 Dof genes were isolated from selected genomes, while 5 DAM, 114 WRKY, and 50 Dof duplicate gene pairs were identified in 10 genomes. Moreover, WGD and segmental duplication events were associated with the majority of the expansions of Dof and WRKY gene families. The VvDAM, VvDof, and VvWRKY genes significantly differentially expressed throughout bud dormancy outnumbered those significantly differentially expressed throughout fruit development or under abiotic stresses. Interestingly, multiple stress responsive genes were identified, such as VvDAM (VIT_00s0313g00070), two VvDof genes (VIT_18s0001g11310 and VIT_02s0025g02250), and two VvWRKY genes (VIT_07s0031g01710 and VIT_11s0052g00450). These data provide candidate genes for molecular biology research investigating bud dormancy and responses to abiotic stresses (namely salt, drought, copper, and waterlogging).

The Role of EjSVPs in Flower Initiation in Eriobotrya japonica

Flowering plants have evolved different flowering habits to sustain long-term reproduction. Most woody trees experience dormancy and then bloom in the warm spring, but loquat blooms in the cold autumn and winter. To explore its mechanism of flowering regulation, we cloned two SHORT VEGETATIVE PHASE (SVP) homologous genes from 'Jiefanzhong' loquat (Eriobotrya japonica Lindl.), namely, EjSVP1 and EjSVP2. Sequence analysis revealed that the EjSVPs were typical MADS-box transcription factors and exhibited a close genetic relationship with other plant SVP/DORMANCY-ASSOCIATED MADS-BOX (DAM) proteins. The temporal and spatial expression patterns showed that EjSVP1 and EjSVP2 were mainly expressed in the shoot apical meristem (SAM) after the initiation of flowering; after reaching their highest level, they gradually decreased with the development of the flower until they could not be detected. EjSVP1 expression levels were relatively high in young tissues, and EjSVP2 expression levels were relatively high in young to mature transformed tissues. Interestingly, EjSVP2 showed relatively high expression levels in various flower tissues. We analyzed the EjSVP promoter regions and found that they did not contain the C-repeat/dehydration-responsive element. Finally, we overexpressed the EjSVPs in wild-type Arabidopsis thaliana Col-0 and found no significant changes in the number of rosette leaves of Arabidopsis thaliana; however, overexpression of EjSVP2 affected the formation of Arabidopsis thaliana flower organs. In conclusion, EjSVPs were found to play an active role in the development of loquat flowering. These findings may provide a reference for exploring the regulation mechanisms of loquat flowering and the dormancy mechanisms of other plants.

Overexpression of Prunus DAM6 inhibits growth, represses bud break competency of dormant buds and delays bud outgrowth in apple plants

Most deciduous fruit trees cultivated in the temperate zone require a genotype-dependent amounts of chilling exposure for dormancy release and bud break. In Japanese apricot (Prunus mume), DORMANCY-ASSOCIATED MADS-box 6 (PmDAM6) may influence chilling-mediated dormancy release and bud break. In this study, we attempted to elucidate the biological functions of PmDAM6 related to dormancy regulation by analyzing PmDAM6-overexpressing transgenic apple (Malus spp.). We generated 35S:PmDAM6 lines and chemically inducible overexpression lines, 35S:PmDAM6-GR. In both overexpression lines, shoot growth was inhibited and early bud set was observed. In addition, PmDAM6 expression repressed bud break competency during dormancy and delayed bud break. Moreover, PmDAM6 expression increased abscisic acid levels and decreased cytokinins contents during the late dormancy and bud break stages in both 35S:PmDAM6 and 35S:PmDAM6-GR. Our analysis also suggested that abscisic acid levels increased during dormancy but subsequently decreased during dormancy release whereas cytokinins contents increased during the bud break stage in dormant Japanese apricot buds. We previously revealed that PmDAM6 expression is continuously down-regulated during dormancy release toward bud break in Japanese apricot. The PmDAM6 expression pattern was concurrent with a decrease and increase in the abscisic acid and cytokinins contents, respectively, in dormant Japanese apricot buds. Therefore, we hypothesize that PmDAM6 represses the bud break competency during dormancy and bud break stages in Japanese apricot by modulating abscisic acid and cytokinins accumulation in dormant buds.

Comparative phenology of dormant Japanese pear (Pyrus pyrifolia) flower buds: a possible cause of 'flowering disorder'

Mild winters influenced by global warming have increased the incidence of erratic flowering ('flowering disorder') in Japanese pear (Pyrus pyrifolia Nakai) trees in Japan. To discover how, when and what kind of disorder/damage occur in pear flower buds, we observed axillary flower buds of two cultivars, 'Kosui' (a mid-chill cultivar) and 'Niitaka' (a high-chill cultivar), grown at five locations. We focused on the phenology from autumn 2015 to spring 2016, when temperatures were higher than for average years, especially from September to January, and large fluctuations occurred due to El Niño. During the blooming season in the spring of 2016, both the percentage of blooming flower buds and the number of florets per flower bud decreased in trees located at lower latitudes (with lower chilling accumulation) with a more severe problem in 'Niitaka' than in 'Kosui'. As shown by forcing excised shoots, the onset and release of endodormancy occurred earlier in 'Kosui' than 'Niitaka' and occurred earlier in trees growing at higher latitudes than at lower latitudes (warmer regions). The freezing tolerance of flower buds, measured as the lethal temperature for 50% survival (LT50), was similar for the cultivars beginning in autumn and reached maximum levels, LT50 values of less than -12 °C, between late-December and mid-January in both cultivars, except for those in Kagoshima (the lowest latitude), where the maximum LT50 was only -5 °C throughout the season. We propose that warmer autumn-winter temperatures may prevent the acquisition of freezing tolerance, disturb endodormancy progression and disrupt floral organ development, thereby causing flowering disorder in pear trees. The risk of occurrence of flowering disorder in pear may be higher in high-chill cultivars than in low- or mid-chill cultivars and at lower latitudes compared with higher latitudes.

I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees

Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.

Small RNAs, emerging regulators critical for the development of horticultural traits

Small RNAs (sRNAs) have been recently recognized as key genetic and epigenetic regulators in various organisms, ranging from the modification of DNA and histone methylations to the modulation of the abundance of coding or non-coding RNAs. In plants, major regulatory sRNAs are classified as respective microRNA (miRNA) and small interfering RNA (siRNA) species, with the former primarily engaging in posttranscriptional regulation while the latter in transcriptional one. Many of these characterized sRNAs are involved in regulation of diverse biological programs, processes, and pathways in response to developmental cues, environmental signals/stresses, pathogen infection, and pest attacks. Recently, sRNAs-mediated regulations have also been extensively investigated in horticultural plants, with many novel mechanisms unveiled, which display far more mechanistic complexity and unique regulatory features compared to those studied in model species. Here, we review the recent progress of sRNA research in horticultural plants, with emphasis on mechanistic aspects as well as their relevance to trait regulation. Given that major and pioneered sRNA research has been carried out in the model and other plants, we also discuss ongoing sRNA research on these plants. Because miRNAs and phased siRNAs (phasiRNAs) are the most studied sRNA regulators, this review focuses on their biogenesis, conservation, function, and targeted genes and traits as well as the mechanistic relation between them, aiming at providing readers comprehensive information instrumental for future sRNA research in horticulture crops.

Repression of TERMINAL FLOWER1 primarily mediates floral induction in pear (Pyrus pyrifolia Nakai) concomitant with change in gene expression of plant hormone-related genes and transcription factors

Floral induction is an important event in the annual growth cycle of perennial fruit trees. For pear, this event directly affects fruit production in the following year. The flower buds in many species are induced by FLOWERING LOCUS T (FT), whose effect is repressed by the meristem-expressed gene TERMINAL FLOWER1 (TFL1). In this study, we investigated the functions of pear FT and TFL1 genes during floral development. Expression of pear FTs (PpFT1a and PpFT2a) in reproductive meristems was not obviously induced prior to floral initiation, while expression of TFL1s (PpTFL1-1a and PpTFL1-2a) rapidly decreased. The induction of the productive meristem identity MADS-box gene AP1 after repression of PpTFL1s suggested a primary role for PpTFL1 in floral induction. RNA-seq analysis suggested that plant hormone-related genes and several transcription factors that were coexpressed with PpTFL1 were potentially involved in the PpTFL1-mediated floral induction. Our data indicate the essential function of TFL1 in pear floral induction and add another species in the family Rosaceae in addition to strawberry and rose that shows a role for TFL1 in floral induction.

Chilling Affects Phytohormone and Post-Embryonic Development Pathways during Bud Break and Fruit Set in Apple (Malus domestica Borkh.)

The availability of sufficient chilling during bud dormancy plays an important role in the subsequent yield and quality of apple fruit, whereas, insufficient chilling availability negatively impacts the apple production. The transcriptome profiling during bud dormancy release and initial fruit set under low and high chill conditions was performed using RNA-seq. The comparative high number of differentially expressed genes during bud break and fruit set under high chill condition indicates that chilling availability was associated with transcriptional reorganization. The comparative analysis reveals the differential expression of genes involved in phytohormone metabolism, particularly for Abscisic acid, gibberellic acid, ethylene, auxin and cytokinin. The expression of Dormancy Associated MADS-box, Flowering Locus C-like, Flowering Locus T-like and Terminal Flower 1-like genes was found to be modulated under differential chilling. The co-expression network analysis indentified two high chill specific modules that were found to be enriched for "post-embryonic development" GO terms. The network analysis also identified hub genes including Early flowering 7, RAF10, ZEP4 and F-box, which may be involved in regulating chilling-mediated dormancy release and fruit set. The results of transcriptome and co-expression network analysis indicate that chilling availability majorly regulates phytohormone-related pathways and post-embryonic development during bud break.

Small RNA-Sequencing Links Physiological Changes and RdDM Process to Vegetative-to-Floral Transition in Apple

Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined. Here, we performed Illumina sequencing of sRNA libraries prepared from vegetative and floral bud during flower induction of the apple trees. A large number of sRNAs exemplified by 33 previously annotated miRNAs and six novel members display significant differential expression (DE) patterns. Notably, most of these DE-miRNAs in floral transition displayed opposite expression changes in reported phase transition in apple trees. Bioinformatics analysis suggests most of the DE-miRNAs targeted transcripts involved in SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene regulation, stress responses, and auxin and gibberellin (GA) pathways, with further suggestion that there is an inherent link between physiological stress response and metabolism reprogramming during floral transition. We also observed significant changes in 24 nucleotide (nt) sRNAs that are hallmarks for RNA-dependent DNA methylation (RdDM) pathway, suggestive of the correlation between epigenetic modifications and the floral transition. The study not only provides new insight into our understanding of fundamental mechanism of poorly studied floral transition in apple and other woody plants, but also presents important sRNA resource for future in-depth research in the apple flowering physiology.