BRANCHED1 promotes axillary bud dormancy in response to shade in Arabidopsis

Shade signals activate distinct molecular mechanisms that induce dormancy and inhibit flowering in vegetative axillary buds of sorghum

Shoot branches grow from axillary buds and play a crucial role in shaping shoot architecture and determining crop yield. Shade signals inactivate phytochrome B (phyB) and induce bud dormancy, thereby inhibiting shoot branching. Prior transcriptome profiling of axillary bud dormancy in a phyB-deficient mutant (58M, phyB-1) and bud outgrowth in wild-type (100M, PHYB) sorghum genotypes identified differential expression of genes associated with flowering, plant hormones, and sugars, including SbCN2, SbNCED3, SbCKX1, SbACO1, SbGA2ox1, and SbCwINVs. This study examined the expression of these genes during bud dormancy induced by shade and defoliation in 100M sorghum. The aim was to elucidate the molecular mechanisms activated by shade in axillary buds by comparing them with those activated by defoliation. The expression of marker genes for sugar levels suggests shade and defoliation reduce the sugar supply to the buds and induce bud dormancy. Intriguingly, both shade signals and defoliation downregulated SbNCED3, suggesting that ABA might not play a role in promoting axillary bud dormancy in sorghum. Whereas the cytokinin (CK) degrading gene SbCKX1 was upregulated solely by shade signals in the buds, the CK inducible genes SbCGA1 and SbCwINVs were downregulated during both shade- and defoliation-induced bud dormancy. This indicates a decrease in CK levels in the dormant buds. Shade signals dramatically upregulated SbCN2, an ortholog of the Arabidopsis TFL1 known for inhibiting flowering, whereas defoliation did not increase SbCN2 expression in the buds. Removing shade temporarily downregulated SbCN2 in dormant buds, further indicating its expression is not always correlated with bud dormancy. Because shade signals also trigger a systemic early flowering signal, SbCN2 might be activated to protect the buds from transitioning to flowering before growing into branches. In conclusion, this study demonstrates that shade signals activate two distinct molecular mechanisms in sorghum buds: one induces dormancy by reducing CK and sugars, whereas the other inhibits flowering by activating SbCN2. Given the agricultural significance of TFL1-like genes, the rapid regulation of SbCN2 by light signals in axillary buds revealed in this study warrants further investigation to explore its potential in crop improvement strategies.

Class I TCP transcription factors TCP14 and TCP15 promote axillary branching in Arabidopsis by counteracting the action of Class II TCP BRANCHED1

Shoot branching is determined by a balance between factors that promote axillary bud dormancy and factors that release buds from the quiescent state. The TCP family of transcription factors is classified into two classes, Class I and Class II, which usually play different roles. While the role of the Class II TCP BRANCHED1 (BRC1) in suppressing axillary bud development in Arabidopsis thaliana has been widely explored, the function of Class I TCPs in this process remains unknown. We analyzed the role of Class I TCP14 and TCP15 in axillary branch development in Arabidopsis through a series of genetic and molecular studies. In contrast to the increased branch number shown by brc1 mutants, tcp14 tcp15 plants exhibit a reduced number of branches compared with wild-type. Our findings provide evidence that TCP14 and TCP15 act by counteracting BRC1 function through two distinct mechanisms. First, they indirectly reduce BRC1 expression levels. Additionally, TCP15 directly interacts with BRC1 decoying it from chromatin and thereby preventing the transcriptional activation of a set of BRC1-dependent genes. We describe a molecular mechanism by which Class I TCPs physically antagonize the action of the Class II TCP BRC1, aligning with their opposite roles in axillary bud development.

Transcription factors HB21/40/53 trigger inflorescence arrest through abscisic acid accumulation at the end of flowering

Flowers, and hence, fruits and seeds, are produced by the activity of the inflorescence meristem after the floral transition. In plants with indeterminate inflorescences, the final number of flowers produced by the inflorescence meristem is determined by the length of the flowering period, which ends with inflorescence arrest. Inflorescence arrest depends on many different factors, such as the presence of seeds, the influence of the environment, or endogenous factors such as phytohormone levels and age, which modulate inflorescence meristem activity. The FRUITFULL-APETALA2 (FUL-AP2) pathway plays a major role in regulating the end of flowering, likely integrating both endogenous cues and those related to seed formation. Among AP2 targets, HOMEOBOX PROTEIN21 (HB21) has been identified as a putative mediator of AP2 function in the control of inflorescence arrest. HB21 is a homeodomain leucine zipper transcription factor involved in establishing axillary bud dormancy. Here, we characterized the role of HB21 in the control of the inflorescence arrest at the end of flowering in Arabidopsis (Arabidopsis thaliana). HB21, together with HB40 and HB53, are upregulated in the inflorescence apex at the end of flowering, promoting floral bud arrest. We also show that abscisic acid (ABA) accumulation occurs in the inflorescence apex in an HB-dependent manner. Our work suggests a physiological role of ABA in floral bud arrest at the end of flowering, pointing to ABA as a regulator of inflorescence arrest downstream of the HB21/40/53 genes.

Genome-wide transcript expression analysis reveals major chickpea and lentil genes associated with plant branching

The search for elite cultivars with better architecture has been a demand by farmers of the chickpea and lentil crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. Herein, this work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested. A total of 1,624 and 2,512 transcripts were identified as differentially expressed among different tissues and contrasting cultivars of chickpea and lentil, respectively. Several gene categories were significantly modulated such as cell cycle, DNA transcription, energy metabolism, hormonal biosynthesis and signaling, proteolysis, and vegetative development between apical and axillary tissues and contrasting cultivars of chickpea and lentil. Based on differential expression and branching-associated biological function, ten chickpea genes and seven lentil genes were considered the main players involved in differentially regulating the plant branching between contrasting cultivars. These collective data putatively revealed the general mechanism and high-effect genes associated with the regulation of branching in chickpea and lentil, which are potential targets for manipulation through genome editing and transgenesis aiming to improve plant architecture.

The activation of Arabidopsis axillary buds involves a switch from slow to rapid committed outgrowth regulated by auxin and strigolactone

Arabidopsis thaliana (Arabidopsis) shoot architecture is largely determined by the pattern of axillary buds that grow into lateral branches, the regulation of which requires integrating both local and systemic signals. Nodal explants - stem explants each bearing one leaf and its associated axillary bud - are a simplified system to understand the regulation of bud activation. To explore signal integration in bud activation, we characterised the growth dynamics of buds in nodal explants in key mutants and under different treatments. We observed that isolated axillary buds activate in two genetically and physiologically separable phases: a slow-growing lag phase, followed by a switch to rapid outgrowth. Modifying BRANCHED1 expression or the properties of the auxin transport network, including via strigolactone application, changed the length of the lag phase. While most interventions affected only the length of the lag phase, strigolactone treatment and a second bud also affected the rapid growth phase. Our results are consistent with the hypothesis that the slow-growing lag phase corresponds to the time during which buds establish canalised auxin transport out of the bud, after which they enter a rapid growth phase. Our work also hints at a role for auxin transport in influencing the maximum growth rate of branches.

The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem

Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.

Quantifying differences in plant architectural development between hybrid potato (Solanum tuberosum) plants grown from two types of propagules

BACKGROUND AND AIMS

Plants can propagate generatively and vegetatively. The type of propagation and the resulting propagule can influence the growth of the plants, such as plant architectural development and pattern of biomass allocation. Potato is a species that can reproduce through both types of propagation: through true botanical seeds and seed tubers. The consequences of propagule type on the plant architectural development and biomass partitioning in potatoes are not well known. We quantified architectural differences between plants grown from these two types of propagules from the same genotype, explicitly analysing branching dynamics above and below ground, and related these differences to biomass allocation patterns.

METHODS

A greenhouse experiment was conducted, using potato plants of the same genotype but grown from two types of propagules: true seeds and seed tubers from a plant grown from true seed (seedling tuber). Architectural traits and biomass allocation to different organs were quantified at four developmental stages. Differences between true-seed-grown and seedling-tuber-grown plants were compared at the whole-plant level and at the level of individual stems and branches, including their number, size and location on the plant.

KEY RESULTS

A more branched and compact architecture was produced in true-seed-grown plants compared with seedling-tuber-grown plants. The architectural differences between plants grown from true seeds and seedling tubers appeared gradually and were attributed mainly to the divergent temporal-spatial distribution of lateral branches above and below ground on the main axis. The continual production of branches in true-seed-grown plants indicated their indeterminate growth habit, which was also reflected in a slower shift of biomass allocation from above- to below-ground branches, whereas the opposite trend was found in seedling-tuber-grown plants.

CONCLUSIONS

In true-seed-grown plants, lateral branching was stronger and determined whole-plant architecture and plant function with regard to light interception and biomass production, compared with seedling-tuber-grown plants. This different role of branching indicates that a difference in preference between clonal and sexual reproduction might exist. The divergent branching behaviours in true-seed-grown and seedling-tuber-grown plants might be regulated by the different intensity of apical dominance, which suggests that the control of branching can depend on the propagule type.

Physiological and Proteomic Analyses of mtn1 Mutant Reveal Key Players in Centipedegrass Tiller Development

Tillering directly determines the seed production and propagation capacity of clonal plants. However, the molecular mechanisms involved in the tiller development of clonal plants are still not fully understood. In this study, we conducted a proteome comparison between the tiller buds and stem node of a multiple-tiller mutant mtn1 (more tillering number 1) and a wild type of centipedegrass. The results showed significant increases of 29.03% and 27.89% in the first and secondary tiller numbers, respectively, in the mtn1 mutant compared to the wild type. The photosynthetic rate increased by 31.44%, while the starch, soluble sugar, and sucrose contents in the tiller buds and stem node showed increases of 13.79%, 39.10%, 97.64%, 37.97%, 55.64%, and 7.68%, respectively, compared to the wild type. Two groups comprising 438 and 589 protein species, respectively, were differentially accumulated in the tiller buds and stem node in the mtn1 mutant. Consistent with the physiological characteristics, sucrose and starch metabolism as well as plant hormone signaling were found to be enriched with differentially abundant proteins (DAPs) in the mtn1 mutant. These results revealed that sugars and plant hormones may play important regulatory roles in the tiller development in centipedegrass. These results expanded our understanding of tiller development in clonal plants.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Striking a growth-defense balance: Stress regulators that function in maize development

Maize (Zea mays) cultivation is strongly affected by both abiotic and biotic stress, leading to reduced growth and productivity. It has recently become clear that regulators of plant stress responses, including the phytohormones abscisic acid (ABA), ethylene (ET), and jasmonic acid (JA), together with reactive oxygen species (ROS), shape plant growth and development. Beyond their well established functions in stress responses, these molecules play crucial roles in balancing growth and defense, which must be finely tuned to achieve high yields in crops while maintaining some level of defense. In this review, we provide an in-depth analysis of recent research on the developmental functions of stress regulators, focusing specifically on maize. By unraveling the contributions of these regulators to maize development, we present new avenues for enhancing maize cultivation and growth while highlighting the potential risks associated with manipulating stress regulators to enhance grain yields in the face of environmental challenges.

A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1

The Arabidopsis thaliana transcription factor BRANCHED1 (BRC1) plays a pivotal role in the control of shoot branching as it integrates environmental and endogenous signals that influence axillary bud growth. Despite its remarkable activity as a growth inhibitor, the mechanisms by which BRC1 promotes bud dormancy are largely unknown. We determined the genome-wide BRC1 binding sites in vivo and combined these with transcriptomic data and gene co-expression analyses to identify bona fide BRC1 direct targets. Next, we integrated multi-omics data to infer the BRC1 gene regulatory network (GRN) and used graph theory techniques to find network motifs that control the GRN dynamics. We generated an open online tool to interrogate this network. A group of BRC1 target genes encoding transcription factors (BTFs) orchestrate this intricate transcriptional network enriched in abscisic acid-related components. Promoter::β-GLUCURONIDASE transgenic lines confirmed that BTFs are expressed in axillary buds. Transient co-expression assays and studies in planta using mutant lines validated the role of BTFs in modulating the GRN and promoting bud dormancy. This knowledge provides access to the developmental mechanisms that regulate shoot branching and helps identify candidate genes to use as tools to adapt plant architecture and crop production to ever-changing environmental conditions.

Far-red light inhibits lateral bud growth mainly through enhancing apical dominance independently of strigolactone synthesis in tomato

The ratio of red light to far-red light (R:FR) is perceived by light receptors and consequently regulates plant architecture. Regulation of shoot branching by R:FR ratio involves plant hormones. However, the roles of strigolactone (SL), the key shoot branching hormone and the interplay of different hormones in the light regulation of shoot branching in tomato (Solanum lycopersicum) are elusive. Here, we found that defects in SL synthesis genes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) and CCD8 in tomato resulted in more lateral bud growth but failed to reverse the FR inhibition of lateral bud growth, which was associated with increased auxin synthesis and decreased synthesis of cytokinin (CK) and brassinosteroid (BR). Treatment of auxin also inhibited shoot branching in ccd mutants. However, CK released the FR inhibition of lateral bud growth in ccd mutants, concomitant with the upregulation of BR synthesis genes. Furthermore, plants that overexpressed BR synthesis gene showed more lateral bud growth and the shoot branching was less sensitive to the low R:FR ratio. The results indicate that SL synthesis is dispensable for light regulation of shoot branching in tomato. Auxin mediates the response to R:FR ratio to regulate shoot branching by suppressing CK and BR synthesis.

How do brassinosteroids fit in bud outgrowth models?

A network of plant hormonal signals coordinates plant branching. Brassinosteroids are important in this network, acting as repressors of the strigolactone pathway and TEOSINTE BRANCHED1 .

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.

Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching

Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions.

Improving citrus bud grafting efficiency

Commercial citrus trees are composed of a scion grafted onto a rootstock. Because grafting is one of the most expensive methods of plant propagation, grafting efficiency is of large practical importance. The purpose of this study was to improve citrus bud-grafting efficiency. The effects of six factors that included BA, Tween-20, DMSO, type of solvent (water or EtOH), cardinal orientation of grafted bud, and type of supplemental light (LED, metal halide, none) on forty-four bud-grafting measures were determined using a multifactor design of experiment approach. Four measures useful for identifying treatments of practical value included the number of rootstock axial buds that formed shoots, the percentage of grafted buds that formed shoots, the length of the longest shoot formed from the grafted buds, and the total leaf area of the grafted bud shoots. The factors that most affected these responses were no supplemental light to minimize the number of shoots from rootstock axial buds, a south orientation and 5 mM BA to maximize the percentage of grafted buds that formed shoots, a north orientation and 5 mM BA to maximize the length of the longest grafted bud shoot, and 5 mM BA to maximize the leaf area of the grafted bud shoots.

Tapping into the plasticity of plant architecture for increased stress resilience

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.

Comparative transcriptome analysis of genes involved in paradormant bud release response in 'Summer Black' grape

Grapevines possess a hierarchy of buds, and the fruitful winter bud forms the foundation of the two-crop-a-year cultivation system, yielding biannual harvests. Throughout its developmental stages, the winter bud sequentially undergoes paradormancy, endodormancy, and ecodormancy to ensure survival in challenging environmental conditions. Releasing the endodormancy of winter bud results in the first crop yield, while breaking the paradormancy of winter bud allows for the second crop harvest. Hydrogen cyanamide serves as an agent to break endodormancy, which counteracting the inhibitory effects of ABA, while H2O2 and ethylene function as signaling molecules in the process of endodormancy release. In the context of breaking paradormancy, common agronomic practices include short pruning and hydrogen cyanamide treatment. However, the mechanism of hydrogen cyanamide contributes to this process remains unknown. This study confirms that hydrogen cyanamide treatment significantly improved both the speed and uniformity of bud sprouting, while short pruning proved to be an effective method for releasing paradormancy until August. This observation highlights the role of apical dominance as a primary inhibitory factor in suppressing the sprouting of paradormant winter bud. Comparative transcriptome analysis revealed that the sixth node winter bud convert to apical tissue following short pruning and established a polar auxin transport canal through the upregulated expression of VvPIN3 and VvTIR1. Moreover, short pruning induced the generation of reactive oxygen species, and wounding, ethylene, and H2O2 collectively acted as stimulating signals and amplified effects through the MAPK cascade. In contrast, hydrogen cyanamide treatment directly disrupted mitochondrial function, resulting in ROS production and an extended efficacy of the growth hormone signaling pathway induction.

Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules

Abnormal high temperature (HT) caused by global warming threatens plant survival and food security, but the effects of HT on plant organ identity are elusive. Here, we show that Class II TEOSINTE BRANCHED 1/CYCLOIDEA/ PCF (TCP) transcription factors redundantly protect ovule identity under HT. The duodecuple tcp2/3/4/5/10/13/17/24/1/12/18/16 (tcpDUO) mutant displays HT-induced ovule conversion into carpelloid structures. Expression of TCP4 in tcpDUO complements the ovule identity conversion. TCP4 interacts with AGAMOUS (AG), SEPALLATA3 (SEP3), and the homeodomain transcription factor BELL1 (BEL1) to strengthen the association of BEL1 with AG-SEP3. The tcpDUO mutant synergistically interacts with bel1 and the ovule identity gene seedstick (STK) mutant stk in tcpDUO bel1 and tcpDUO stk. Our findings reveal the critical roles of Class II TCPs in maintaining ovule identity under HT and shed light on the molecular mechanisms by which ovule identity is determined by the integration of internal factors and environmental temperature.

Bridging pathways: SBP15 regulates GOBLET in modulating tomato axillary bud outgrowth

This article comments on:

Barrera-Rojas CH, Vicente MH, Brito DAP, Silva EM,Muñoz Lopez A, Ferigolo LF, Carmo RM, Silva CMS, Silva GFF, Correa JPO, Notini MM, Freschi L, Cubas P, Nogueira FTS. 2023. Tomato miR156-targeted SlSBP15 represses shoot branching by modulating hormone dynamics and interacting with GOBLET and BRANCHED1b. Journal of Experimental Botany 74, 5124–5139.

Jujube witches' broom phytoplasmas inhibit ZjBRC1-mediated abscisic acid metabolism to induce shoot proliferation

Jujube witches' broom (JWB) phytoplasmas parasitize the sieve tubes of diseased phloem and cause an excessive proliferation of axillary shoots from dormant lateral buds to favour their transmission. In previous research, two JWB effectors, SJP1 and SJP2, were identified to induce lateral bud outgrowth by disrupting ZjBRC1-mediated auxin flux. However, the pathogenesis of JWB disease remains largely unknown. Here, tissue-specific transcriptional reprogramming was examined to gain insight into the genetic mechanisms acting inside jujube lateral buds under JWB phytoplasma infection. JWB phytoplasmas modulated a series of plant signalling networks involved in lateral bud development and defence, including auxin, abscisic acid (ABA), ethylene, jasmonic acid, and salicylic acid. JWB-induced bud outgrowth was accompanied by downregulation of ABA synthesis within lateral buds. ABA application rescued the bushy appearances of transgenic Arabidopsis overexpressing SJP1 and SJP2 in Col-0 and ZjBRC1 in the brc1-2 mutant. Furthermore, the expression of ZjBRC1 and ABA-related genes ZjHB40 and ZjNCED3 was negatively correlated with lateral main bud outgrowth in decapitated healthy jujube. Molecular evidence showed that ZjBRC1 interacted with ZjBRC2 via its N-terminus to activate ZjHB40 and ZjNCED3 expression and ABA accumulation in transgenic jujube calli. In addition, ZjBRC1 widely regulated differentially expressed genes related to ABA homeostasis and ABA signalling, especially by binding to and suppressing ABA receptors. Therefore, these results suggest that JWB phytoplasmas hijack the ZjBRC1-mediated ABA pathways to stimulate lateral bud outgrowth and expansion, providing a strategy to engineer plants resistant to JWB phytoplasma disease and regulate woody plant architecture to promote crop yield and quality.

Strigolactones positively regulate Verticillium wilt resistance in cotton via crosstalk with other hormones

Verticillium wilt caused by Verticillium dahliae is a serious vascular disease in cotton (Gossypium spp.). V. dahliae induces the expression of the CAROTENOID CLEAVAGE DIOXYGENASE 7 (GauCCD7) gene involved in strigolactone (SL) biosynthesis in Gossypium australe, suggesting a role for SLs in Verticillium wilt resistance. We found that the SL analog rac-GR24 enhanced while the SL biosynthesis inhibitor TIS108 decreased cotton resistance to Verticillium wilt. Knock-down of GbCCD7 and GbCCD8b genes in island cotton (Gossypium barbadense) decreased resistance, whereas overexpression of GbCCD8b in upland cotton (Gossypium hirsutum) increased resistance to Verticillium wilt. Additionally, Arabidopsis (Arabidopsis thaliana) SL mutants defective in CCD7 and CCD8 putative orthologs were susceptible, whereas both Arabidopsis GbCCD7- and GbCCD8b-overexpressing plants were more resistant to Verticillium wilt than wild-type (WT) plants. Transcriptome analyses showed that several genes related to the jasmonic acid (JA)- and abscisic acid (ABA)-signaling pathways, such as MYELOCYTOMATOSIS 2 (GbMYC2) and ABA-INSENSITIVE 5, respectively, were upregulated in the roots of WT cotton plants in responses to rac-GR24 and V. dahliae infection but downregulated in the roots of both GbCCD7- and GbCCD8b-silenced cotton plants. Furthermore, GbMYC2 suppressed the expression of GbCCD7 and GbCCD8b by binding to their promoters, which might regulate the homeostasis of SLs in cotton through a negative feedback loop. We also found that GbCCD7- and GbCCD8b-silenced cotton plants were impaired in V. dahliae-induced reactive oxygen species (ROS) accumulation. Taken together, our results suggest that SLs positively regulate cotton resistance to Verticillium wilt through crosstalk with the JA- and ABA-signaling pathways and by inducing ROS accumulation.

Shade-Induced Leaf Senescence in Plants

Leaf senescence is a vital developmental process that involves the orderly breakdown of macromolecules to transfer nutrients from mature leaves to emerging and reproductive organs. This process is essential for a plant's overall fitness. Multiple internal and external factors, such as leaf age, plant hormones, stresses, and light environment, regulate the onset and progression of leaf senescence. When plants grow close to each other or are shaded, it results in significant alterations in light quantity and quality, such as a decrease in photosynthetically active radiation (PAR), a drop in red/far-red light ratios, and a reduction in blue light fluence rate, which triggers premature leaf senescence. Recently, studies have identified various components involved in light, phytohormone, and other signaling pathways that regulate the leaf senescence process in response to shade. This review summarizes the current knowledge on the molecular mechanisms that control leaf senescence induced by shade.

Shade avoidance syndrome in soybean and ideotype toward shade tolerance

The shade avoidance syndrome (SAS) in soybean can have destructive effects on yield, as essential carbon resources reserved for yield are diverted to the petiole and stem for exaggerated elongation, resulting in lodging and susceptibility to disease. Despite numerous attempts to reduce the unfavorable impacts of SAS for the development of cultivars suitable for high-density planting or intercropping, the genetic bases and fundamental mechanisms of SAS remain largely unclear. The extensive research conducted in the model plant Arabidopsis provides a framework for understanding the SAS in soybean. Nevertheless, recent investigations suggest that the knowledge obtained from model Arabidopsis may not be applicable to all processes in soybean. Consequently, further efforts are required to identify the genetic regulators of SAS in soybean for molecular breeding of high-yield cultivars suitable for density farming. In this review, we present an overview of the recent developments in SAS studies in soybean and suggest an ideal planting architecture for shade-tolerant soybean intended for high-yield breeding.

Agave REVEILLE1 regulates the onset and release of seasonal dormancy in Populus

Deciduous woody plants like poplar (Populus spp.) have seasonal bud dormancy. It has been challenging to simultaneously delay the onset of bud dormancy in the fall and advance bud break in the spring, as bud dormancy, and bud break were thought to be controlled by different genetic factors. Here, we demonstrate that heterologous expression of the REVEILLE1 gene (named AaRVE1) from Agave (Agave americana) not only delays the onset of bud dormancy but also accelerates bud break in poplar in field trials. AaRVE1 heterologous expression increases poplar biomass yield by 166% in the greenhouse. Furthermore, we reveal that heterologous expression of AaRVE1 increases cytokinin contents, represses multiple dormancy-related genes, and up-regulates bud break-related genes, and that AaRVE1 functions as a transcriptional repressor and regulates the activity of the DORMANCY-ASSOCIATED PROTEIN 1 (DRM1) promoter. Our findings demonstrate that AaRVE1 appears to function as a regulator of bud dormancy and bud break, which has important implications for extending the growing season of deciduous trees in frost-free temperate and subtropical regions to increase crop yield.

Shade avoidance in the context of climate change

When exposed to changes in the light environment caused by neighboring vegetation, shade-avoiding plants modify their growth and/or developmental patterns to access more sunlight. In Arabidopsis (Arabidopsis thaliana), neighbor cues reduce the activity of the photosensory receptors phytochrome B (phyB) and cryptochrome 1, releasing photoreceptor repression imposed on PHYTOCHROME INTERACTING FACTORs (PIFs) and leading to transcriptional reprogramming. The phyB-PIF hub is at the core of all shade-avoidance responses, whilst other photosensory receptors and transcription factors contribute in a context-specific manner. CONSTITUTIVELY PHOTOMORPHOGENIC1 is a master regulator of this hub, indirectly stabilizing PIFs and targeting negative regulators of shade avoidance for degradation. Warm temperatures reduce the activity of phyB, which operates as a temperature sensor and further increases the activities of PIF4 and PIF7 by independent temperature sensing mechanisms. The signaling network controlling shade avoidance is not buffered against climate change; rather, it integrates information about shade, temperature, salinity, drought, and likely flooding. We, therefore, predict that climate change will exacerbate shade-induced growth responses in some regions of the planet while limiting the growth potential in others.

Upregulation of tandem duplicated BoFLC1 genes is associated with the non-flowering trait in Brassica oleracea var. capitata

Tandem duplicated BoFLC1 genes (BoFLC1a and BoFLC1b), which were identified as the candidate causal genes for the non-flowering trait in the cabbage mutant 'nfc', were upregulated during winter in 'nfc'. The non-flowering natural cabbage mutant 'nfc' was discovered from the breeding line 'T15' with normal flowering characteristics. In this study, we investigated the molecular basis underlying the non-flowering trait of 'nfc'. First, 'nfc' was induced to flower using the grafting floral induction method, and three F₂ populations were generated. The flowering phenotype of each F₂ population was widely distributed with non-flowering individuals appearing in two populations. QTL-seq analysis detected a genomic region associated with flowering date at approximately 51 Mb on chromosome 9 in two of the three F₂ populations. Subsequent validation and fine mapping of the candidate genomic region using QTL analysis identified the quantitative trait loci (QTL) at 50,177,696-51,474,818 bp on chromosome 9 covering 241 genes. Additionally, RNA-seq analysis in leaves and shoot apices of 'nfc' and 'T15' plants identified 19 and 15 differentially expressed genes related to flowering time, respectively. Based on these results, we identified tandem duplicated BoFLC1 genes, which are homologs of the floral repressor FLOWERING LOCUS C, as the candidate genes responsible for the non-flowering trait of 'nfc'. We designated the tandem duplicated BoFLC1 genes as BoFLC1a and BoFLC1b. Expression analysis revealed that the expression levels of BoFLC1a and BoFLC1b were downregulated during winter in 'T15' but were upregulated and maintained during winter in 'nfc'. Additionally, the expression level of the floral integrator BoFT was upregulated in the spring in 'T15' but hardly upregulated in 'nfc'. These results suggest that the upregulated levels of BoFLC1a and BoFLC1b contributed to the non-flowering trait of 'nfc'.

The Strigolactone Pathway Is a Target for Modifying Crop Shoot Architecture and Yield

Due to their sessile nature, plants have developed the ability to adapt their architecture in response to their environment. Branching is an integral component of plant architecture, where hormonal signals tightly regulate bud outgrowth. Strigolactones (SLs), being a novel class of phytohormone, are known to play a key role in branching decisions, where they act as a negative regulator of bud outgrowth. They can achieve this by modulating polar auxin transport to interrupt auxin canalisation, and independently of auxin by acting directly within buds by promoting the key branching inhibitor TEOSINTE BRANCHED1. Buds will grow out in optimal conditions; however, when conditions are sub-optimal, SL levels increase to restrict branching. This can be a problem in agricultural applications, as reductions in branching can have deleterious effects on crop yield. Variations in promoter elements of key SL-related genes, such as IDEAL PLANT ARCHITECTURE1, have been identified to promote a phenotype with enhanced yield performance. In this review we highlight how this knowledge can be applied using new technologies to develop new genetic variants for improving crop shoot architecture and yield.

Abscisic acid modulates neighbor proximity-induced leaf hyponasty in Arabidopsis

Leaves of shade-avoiding plants such as Arabidopsis (Arabidopsis thaliana) change their growth pattern and position in response to low red to far-red ratios (LRFRs) encountered in dense plant communities. Under LRFR, transcription factors of the phytochrome-interacting factor (PIF) family are derepressed. PIFs induce auxin production, which is required for promoting leaf hyponasty, thereby favoring access to unfiltered sunlight. Abscisic acid (ABA) has also been implicated in the control of leaf hyponasty, with gene expression patterns suggesting that LRFR regulates the ABA response. Here, we show that LRFR leads to a rapid increase in ABA levels in leaves. Changes in ABA levels depend on PIFs, which regulate the expression of genes encoding isoforms of the enzyme catalyzing a rate-limiting step in ABA biosynthesis. Interestingly, ABA biosynthesis and signaling mutants have more erect leaves than wild-type Arabidopsis under white light but respond less to LRFR. Consistent with this, ABA application decreases leaf angle under white light; however, this response is inhibited under LRFR. Tissue-specific interference with ABA signaling indicates that an ABA response is required in different cell types for LRFR-induced hyponasty. Collectively, our data indicate that LRFR triggers rapid PIF-mediated ABA production. ABA plays a different role in controlling hyponasty under white light than under LRFR. Moreover, ABA exerts its activity in multiple cell types to control leaf position.

Natural variation of Dt2 determines branching in soybean

Shoot branching is fundamentally important in determining soybean yield. Here, through genome-wide association study, we identify one predominant association locus on chromosome 18 that confers soybean branch number in the natural population. Further analyses determine that Dt2 is the corresponding gene and the natural variations in Dt2 result in significant differential transcriptional levels between the two major haplotypes. Functional characterization reveals that Dt2 interacts with GmAgl22 and GmSoc1a to physically bind to the promoters of GmAp1a and GmAp1d and to activate their transcription. Population genetic investigation show that the genetic differentiation of Dt2 display significant geographic structure. Our study provides a predominant gene for soybean branch number and may facilitate the breeding of high-yield soybean varieties.

Genome-wide analysis of citrus TCP transcription factors and their responses to abiotic stresses

BACKGROUND

Citrus is one of the most important fruit crops in the world, and it is worthy to conduct more research on artificially controlling citrus plant growth and development to adapt to different cultivation patterns and environmental conditions. The plant-specific TEOSINTE BRANCHED1, CYCOLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are crucial regulators controlling plant growth and development, as well as responding to abiotic stresses. However, the information about citrus TCP transcription factors remains unclear.

RESULTS

In this study, twenty putative TCP genes (CsTCPs) with the TCP domain were explored from Citrus sinensis genome, of which eleven (CsTCP3, - 4, - 5, - 6, - 10, - 11, - 15, - 16, - 18, - 19, - 20), five (CsTCP1, - 2, - 7, - 9, - 13), and four genes (CsTCP8, - 12, - 14, - 17) were unevenly distributed on chromosomes and divided into three subclades. Cis-acting element analysis indicated that most CsTCPs contained many phytohormone- and environment-responsive elements in promoter regions. All of CsTCPs were predominantly expressed in vegetative tissues or organs (stem, leaf, thorn, and bud) instead of reproductive tissues or organs (flower, fruit, and seed). Combined with collinearity analysis, CsTCP3, CsTCP9, and CsTCP13 may take part in leaf development; CsTCP12 and CsTCP14 may function in shoot branching, leaf development, or thorn development; CsTCP15 may participate in the development of stem, leaf, or thorn. In mature leaf, transcript levels of two CsTCPs (CsTCP19, - 20) were significantly increased while transcript levels of eight CsTCPs (CsTCP2, - 5, - 6, - 7, - 8, - 9, - 10, - 13) were significantly decreased by shading; except for two CsTCPs (CsTCP11, - 19), CsTCPs' transcript levels were significantly influenced by low temperature; moreover, transcript levels of two CsTCPs (CsTCP11, - 12) were significantly increased while five CsTCPs' (CsTCP14, - 16, - 18, - 19, - 20) transcript levels were significantly reduced by drought.

CONCLUSIONS

This study provides significant clues for research on roles of CsTCPs in regulating citrus plant growth and development, as well as responding to abiotic stresses.

The Current Progresses in the Genes and Networks Regulating Cotton Plant Architecture

Cotton is the most important source of natural fiber in the world as well as a key source of edible oil. The plant architecture and flowering time in cotton are crucial factors affecting cotton yield and the efficiency of mechanized harvest. In the model plant arabidopsis, the functions of genes related to plant height, inflorescence structure, and flowering time have been well studied. In the model crops, such as tomato and rice, the similar genetic explorations have greatly strengthened the economic benefits of these crops. Plants of the Gossypium genus have the characteristics of perennials with indeterminate growth and the cultivated allotetraploid cottons, G. hirsutum (Upland cotton), and G. barbadense (Sea-island cotton), have complex branching patterns. In this paper, we review the current progresses in the identification of genes affecting cotton architecture and flowering time in the cotton genome and the elucidation of their functional mechanisms associated with branching patterns, branching angle, fruit branch length, and plant height. This review focuses on the following aspects: (i) plant hormone signal transduction pathway; (ii) identification of cotton plant architecture QTLs and PEBP gene family members; (iii) functions of FT/SFT and SP genes; (iv) florigen and anti-florigen systems. We highlight areas that require further research, and should lay the groundwork for the targeted bioengineering of improved cotton cultivars with flowering times, plant architecture, growth habits and yields better suited for modern, mechanized cultivation.

Overexpression of a novel heat-inducible ethylene-responsive factor gene LlERF110 from Lilium longiflorum decreases thermotolerance

AP2/ERF (APETALA2/ethylene-responsive factor) family transcription factors are involved in various plant-specific processes, especially in plant development and response to abiotic stress. However, their roles in thermotolerance are still largely unknown. In the current study, we identified a heat-inducible ERF member LlERF110 from Lilium longiflorum that was rapidly induced by high temperature. Its protein was localized in the nucleus, and transcriptional activation activity was observed in yeast and plant cells. In addition, LlERF110 was able to bind to GCC- and CGG-elements, but not to DRE-elements. Overexpression of LlERF110 conferred delayed bolting and bushy phenotype, with decreased thermotolerance accompanied by a disrupted ROS (reactive oxygen species) homeostasis in transgenic plants. The accumulation of LlERF110 may activate certain repressors related to heat stress response (HSR) and indirectly damage the normal expression of heat stress (HS)-protective genes such as AtHSFA2, which consequently leads to reduced thermotolerance. Our results implied that LlERF110 might function as a heat-inducible gene but may hinder the establishment of thermotolerance.

The GATA factor HANABA TARANU promotes runner formation by regulating axillary bud initiation and outgrowth in cultivated strawberry

A runner, as an elongated branch, develops from the axillary bud (AXB) in the leaf axil and is crucial for the clonal propagation of cultivated strawberry (Fragaria  ×  ananassa Duch.). Runner formation occurs in at least two steps: AXB initiation and AXB outgrowth. HANABA TARANU (HAN ) encodes a GATA transcription factor that affects AXB initiation in Arabidopsis and promotes branching in grass species, but the underlying mechanism is largely unknown. Here, the function of a strawberry HAN homolog FaHAN in runner formation was characterized. FaHAN transcripts can be detected in the leaf axils. Overexpression (OE) of FaHAN increased the number of runners, mainly by enhancing AXB outgrowth, in strawberry. The expression of the strawberry homolog of BRANCHED1 , a key inhibitor of AXB outgrowth in many plant species, was significantly downregulated in the AXBs of FaHAN -OE lines, whereas the expression of the strawberry homolog of SHOOT MERISTEMLESS, a marker gene for AXB initiation in Arabidopsis, was upregulated. Moreover, several genes of gibberellin biosynthesis and cytokinin signaling pathways were activated, whereas the auxin response pathway genes were repressed. Further assays indicated that FaHAN could be directly activated by FaNAC2, the overexpression of which in strawberry also increased the number of runners. The silencing of FaNAC2 or FaHAN inhibited AXB initiation and led to a higher proportion of dormant AXBs, confirming their roles in the control of runner formation. Taken together, our results revealed a FaNAC2-FaHAN pathway in the control of runner formation and have provided a means to enhance the vegetative propagation of cultivated strawberry.

Shoot Branching Phenotyping in Arabidopsis and Tomato

Shoot branching is an important trait that depends on the activity of axillary meristems and buds and their outgrowth into branches. It is remarkably plastic, being influenced by a number of external cues, such as light, temperature, soil nutrients, and mechanical manipulation. These are transduced into an internal hormone signaling network where auxin, cytokinins, and strigolactones play leading regulatory roles. Recently, sugars have also emerged as important signals promoting bud activation. These signals are in part integrated by the bud-specific growth repressor BRANCHED1 (BRC1).To understand how shoot branching is affected by particular growth conditions or in specific plant lines, it is necessary to count the number of branches and/or quantify other branch-related parameters. Here we describe how to perform such quantifications in Arabidopsis and in tomato.

INTERMEDIUM-C mediates the shade-induced bud growth arrest in barley

Tiller formation is a key agronomic determinant for grain yield in cereal crops. The modulation of this trait is controlled by transcriptional regulators and plant hormones, tightly regulated by external environmental conditions. While endogenous (genetic) and exogenous (environmental factors) triggers for tiller formation have mostly been investigated separately, it has remained elusive how they are integrated into the developmental program of this trait. The transcription factor gene INTERMEDIUM-C (INT-C), which is the barley ortholog of the maize domestication gene TEOSINTE BRANCHED1 (TB1), has a prominent role in regulating tiller bud outgrowth. Here we show that INT-C is expressed in tiller buds, required for bud growth arrest in response to shade. In contrast to wild-type plants, int-c mutant plants are impaired in their shade response and do not stop tiller production after shading. Gene expression levels of INT-C are up-regulated under light-limiting growth conditions, and down-regulated after decapitation. Transcriptome analysis of wild-type and int-c buds under control and shading conditions identified target genes of INT-C that belong to auxin and gibberellin biosynthesis and signaling pathways. Our study identifies INT-C as an integrator of the shade response into tiller formation, which is prerequisite for implementing shading responses in the breeding of cereal crops.

Plasticity of bud outgrowth varies at cauline and rosette nodes in Arabidopsis thaliana

Shoot branching is a complex mechanism in which secondary shoots grow from buds that are initiated from meristems established in leaf axils. The model plant Arabidopsis (Arabidopsis thaliana) has a rosette leaf growth pattern in the vegetative stage. After flowering initiation, the main stem elongates with the top leaf primordia developing into cauline leaves. Meristems in Arabidopsis initiate in the axils of rosette or cauline leaves, giving rise to rosette or cauline buds, respectively. Plasticity in the process of shoot branching is regulated by resource and nutrient availability as well as by plant hormones. However, few studies have attempted to test whether cauline and rosette branching are subject to the same plasticity. Here, we addressed this question by phenotyping cauline and rosette branching in three Arabidopsis ecotypes and several Arabidopsis mutants with varied shoot architectures. Our results showed no negative correlation between cauline and rosette branch numbers in Arabidopsis, demonstrating that there is no tradeoff between cauline and rosette bud outgrowth. Through investigation of the altered branching pattern of flowering pathway mutants and Arabidopsis ecotypes grown in various photoperiods and light regimes, we further elucidated that the number of cauline branches is closely related to flowering time. The number of rosette branches has an enormous plasticity compared with cauline branches and is influenced by genetic background, flowering time, light intensity, and temperature. Our data reveal different levels of plasticity in the regulation of branching at rosette and cauline nodes, and promote a framework for future branching analyses.

Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b

The control of carbon allocation, storage and usage is critical for plant growth and development and is exploited for both crop food production and CO2 capture. Potato tubers are natural carbon reserves in the form of starch that have evolved to allow propagation and survival over winter. They form from stolons, below ground, where they are protected from adverse environmental conditions and animal foraging. We show that BRANCHED1b (BRC1b) acts as a tuberization repressor in aerial axillary buds, which prevents buds from competing in sink strength with stolons. BRC1b loss of function leads to ectopic production of aerial tubers and reduced underground tuberization. In aerial axillary buds, BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground.

Signaling Mechanisms by Arabidopsis Cryptochromes

Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.

How Strigolactone Shapes Shoot Architecture

Despite its central role in the control of plant architecture, strigolactone has been recognized as a phytohormone only 15 years ago. Together with auxin, it regulates shoot branching in response to genetically encoded programs, as well as environmental cues. A central determinant of shoot architecture is apical dominance, i.e., the tendency of the main shoot apex to inhibit the outgrowth of axillary buds. Hence, the execution of apical dominance requires long-distance communication between the shoot apex and all axillary meristems. While the role of strigolactone and auxin in apical dominance appears to be conserved among flowering plants, the mechanisms involved in bud activation may be more divergent, and include not only hormonal pathways but also sugar signaling. Here, we discuss how spatial aspects of SL biosynthesis, transport, and sensing may relate to apical dominance, and we consider the mechanisms acting locally in axillary buds during dormancy and bud activation.

The molecular and genetic regulation of shoot branching

The architecture of flowering plants exhibits both phenotypic diversity and plasticity, determined, in part, by the number and activity of axillary meristems and, in part, by the growth characteristics of the branches that develop from the axillary buds. The plasticity of shoot branching results from a combination of various intrinsic and genetic elements, such as number and position of nodes and type of growth phase, as well as environmental signals such as nutrient availability, light characteristics, and temperature (Napoli et al., 1998; Bennett and Leyser, 2006; Janssen et al., 2014; Teichmann and Muhr, 2015; Ueda and Yanagisawa, 2019). Axillary meristem initiation and axillary bud outgrowth are controlled by a complex and interconnected regulatory network. Although many of the genes and hormones that modulate branching patterns have been discovered and characterized through genetic and biochemical studies, there are still many gaps in our understanding of the control mechanisms at play. In this review, we will summarize our current knowledge of the control of axillary meristem initiation and outgrowth into a branch.

The role of auxin and sugar signaling in dominance inhibition of inflorescence growth by fruit load

Dominance inhibition of shoot growth by fruit load is a major factor that regulates shoot architecture and limits yield in agriculture and horticulture crops. In annual plants, the inhibition of inflorescence growth by fruit load occurs at a late stage of inflorescence development termed the end of flowering transition. Physiological studies show this transition is mediated by production and export of auxin from developing fruits in close proximity to the inflorescence apex. In the meristem, cessation of inflorescence growth is controlled in part by the age-dependent pathway, which regulates the timing of arrest. Here, we show the end of flowering transition is a two-step process in Arabidopsis (Arabidopsis thaliana). The first stage is characterized by a cessation of inflorescence growth, while immature fruit continues to develop. At this stage, dominance inhibition of inflorescence growth by fruit load is associated with a selective dampening of auxin transport in the apical region of the stem. Subsequently, an increase in auxin response in the vascular tissues of the apical stem where developing fruits are attached marks the second stage for the end of flowering transition. Similar to the vegetative and floral transition, the end of flowering transition is associated with a change in sugar signaling and metabolism in the inflorescence apex. Taken together, our results suggest that during the end of flowering transition, dominance inhibition of inflorescence shoot growth by fruit load is mediated by auxin and sugar signaling.

ABA and Bud Dormancy in Perennials: Current Knowledge and Future Perspective

Bud dormancy is an evolved trait that confers adaptation to harsh environments, and affects flower differentiation, crop yield and vegetative growth in perennials. ABA is a stress hormone and a major regulator of dormancy. Although the physiology of bud dormancy is complex, several advancements have been achieved in this field recently by using genetics, omics and bioinformatics methods. Here, we review the current knowledge on the role of ABA and environmental signals, as well as the interplay of other hormones and sucrose, in the regulation of this process. We also discuss emerging potential mechanisms in this physiological process, including epigenetic regulation.

Decapitation Experiments Combined with the Transcriptome Analysis Reveal the Mechanism of High Temperature on Chrysanthemum Axillary Bud Formation

Temperature is an important factor that largely affects the patterns of shoot branching in plants. However, the effect and mechanism of temperature on axillary bud development in chrysanthemum remains poorly defined. The purpose of the present study is to investigate the effect of high temperature on the axillary bud growth and the mechanism of axillary bud formation in chrysanthemum. Decapitation experiments combined with the transcriptome analysis were designed. Results showed that the axillary bud length was significantly inhibited by high temperature. Decapitation of primary shoot (primary decapitation) resulted in slower growth of axillary buds (secondary buds) under 35 °C. However, secondary decapitation resulted in complete arrest of tertiary buds at high temperature. These results demonstrated that high temperature not only inhibited axillary bud formation but also retarded bud outgrowth in chrysanthemum. Comparative transcriptome suggested differentially expressed gene sets and identified important modules associated with bud formation. This research helped to elucidate the regulatory mechanism of high temperature on axillary bud growth, especially bud formation in chrysanthemum. Meanwhile, in-depth studies of this imperative temperature signaling can offer the likelihood of vital future applications in chrysanthemum breeding and branching control.

Witches' Broom Disease of Lime Contributes to Phytoplasma Epidemics and Attracts Insect Vectors

An insect-transmitted phytoplasma causing Witches' Broom Disease of Lime (WBDL) is responsible for the drastic decline in lime production in several countries. However, it is unclear how WBDL phytoplasma (WBDLp) induces witches' broom symptoms and if these symptoms contribute to the spread of phytoplasma. Here we show that the gene encoding SAP11 of WBDLp (SAP11_WBDL) is present in all WBDLp isolates collected from diseased trees. SAP11_WBDL interacts with acid lime (Citrus aurantifolia) TCP transcription factors, specifically members of the TB1/CYC class that have a role in suppressing axillary branching in plants. Sampling of WBDLp-infected lime trees revealed that WBDLp titers and SAP11_WBDL expression levels were higher in symptomatic leaves compared with asymptomatic sections of the same trees. Moreover, the witches' brooms were found to attract the vector leafhopper. Defense genes that have a role in plant defense responses to bacteria and insects are more downregulated in witches' brooms compared with asymptomatic sections of trees. These findings suggest that witches' broom-affected parts of the trees contribute to WBDL epidemics by supporting higher phytoplasma titers and attracting insect vectors.

The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton

Branching determines cotton architecture and production, but the underlying regulatory mechanisms remain unclear. Here, we report that the miR164-GhCUC2 (CUP-SHAPED COTYLEDON2) module regulates lateral shoot development in cotton and Arabidopsis. We generated OE-GhCUC2m (overexpression GhCUC2m) and STTM164 (short tandem target mimic RNA of miR164) lines in cotton and heterologous expression lines for gh-miR164, GhCUC2 and GhCUC2m in Arabidopsis to study the mechanisms controlling lateral branching. GhCUC2m overexpression resulted in a short-branch phenotype similar to STTM164. In addition, heterologous expression of GhCUC2m led to decreased number and length of branches compared with wild type, opposite to the effects of the OE-gh-pre164 line in Arabidopsis. GhCUC2 interacted with GhBRC1 and exhibited similar negative regulation of branching. Overexpression of GhBRC1 in the brc1-2 mutant partially rescued the mutant phenotype and decreased branch number. GhBRC1 directly bound to the NCED1 promoter and activated its transcription, leading to local abscisic acid (ABA) accumulation and response. Mutation of the NCED1 promoter disrupted activation by GhBRC1. This finding demonstrates a direct relationship between BRC1 and ABA signalling and places ABA downstream of BRC1 in the control of branching development. The miR164-GhCUC2-GhBRC1-GhNCED1 module provides a clear regulatory axis for ABA signalling to control plant architecture.

Fatty acid export protein BnFAX6 functions in lipid synthesis and axillary bud growth in Brassica napus

Sugar is considered as the primary regulator of plant apical dominance, whereby the outgrowth of axillary buds is inhibited by the shoot tip. However, there are some deficiencies in this theory. Here, we reveal that Fatty Acid Export 6 (BnFAX6) functions in FA transport, and linoleic acid or its derivatives acts as a signaling molecule in regulating apical dominance of Brassica napus. BnFAX6 is responsible for mediating FA export from plastids. Overexpression of BnFAX6 in B. napus heightened the expression of genes involved in glycolysis and lipid biosynthesis, promoting the flow of photosynthetic products to the biosynthesis of FAs (including linoleic acid and its derivatives). Enhancing expression of BnFAX6 increased oil content in seeds and leaves and resulted in semi-dwarf and increased branching phenotypes with more siliques, contributing to increased yield per plant relative to wild-type. Furthermore, decapitation led to the rapid flow of the carbon from photosynthetic products to FA biosynthesis in axillary buds, consistent with the overexpression of BnFAX6 in B. napus. In addition, free FAs, especially linoleic acid, were rapidly transported from leaves to axillary buds. Increasing linoleic acid in axillary buds repressed expression of a key transcriptional regulator responsible for maintaining bud dormancy, resulting in bud outgrowth. Taken together, we uncovered that BnFAX6 mediating FA export from plastids functions in lipid biosynthesis and in axillary bud dormancy release, possibly through enhancing linoleic acid level in axillary buds of B. napus.

Correlation analysis of the transcriptome and metabolome reveals the role of the flavonoid biosynthesis pathway in regulating axillary buds in upland cotton (Gossypium hirsutum L.)

Flavonoids are involved in axillary bud development in upland cotton. The phenylpropanoid and flavonoid biosynthesis pathways regulate axillary bud growth by promoting the transport of auxin in upland cotton. In cotton production, simplified cultivation and mechanical harvesting are emerging trends that depend on whether the cotton plant type meets production requirements. The axillary bud is an important index of cotton plant-type traits, and the molecular mechanism of axillary bud development in upland cotton has not yet been completely studied. Here, a combined investigation of transcriptome and metabolome analyses in G. hirsutum CCRI 117 at the fourth week (stage 1), fifth week (stage 2) and sixth week (stage 3) after seedling emergence was performed. The metabolome results showed that the total lipid, amino acid and organic acid contents in the first stalk node decreased during axillary bud development. The abundance of 71 metabolites was altered between stage 2 and stage 1, and 32 metabolites exhibited significantly altered abundance between stage 3 and stage 2. According to the correlation analysis of metabolome and transcriptome profiles, we found that phenylpropanoid and flavonoid biosynthesis pathways exhibit high enrichment degrees of both differential metabolites and differential genes in three stages. Based on the verification of hormone, soluble sugar and flavonoid detection, we propose a model for flavonoid-mediated regulation of axillary bud development in upland cotton, revealing that the decrease in secondary metabolites of phenylpropanoid and flavonoid biosynthesis is an essential factor to promote the transport of auxin and subsequently promote the growth of axillary buds. Our findings provide novel insights into the regulation of phenylpropanoid and flavonoid biosynthesis in axillary bud development and could prove useful for cultivating machine-harvested cotton varieties with low axillary buds.

Signaling network regulating plant branching: Recent advances and new challenges

Auxin alone or supplemented with cytokinins and strigolactones were long considered as the main player(s) in the control of apical dominance (AD) and correlative inhibition of the lateral bud outgrowth, the processes that shape the plant phenotype. However, past decade data indicate a more sophisticated pathways of AD regulation, with the involvement of mobile carbohydrates which perform both signal and trophic functions. Here we provide a critical comprehensive overview of the current status of the AD problem. This includes insight into intimate mechanisms regulating directed auxin transport in axillary buds with participation of phytohormones and sugars. Also roles of auxin, cytokinin and sugars in the dormancy or sustained growth of the lateral meristems were assigned. This review not only provides the latest data on implicated phytohormone crosstalk and its relationship with the signaling of sugars and abscisic acid, new AD players, but also focuses on the emerging biochemical mechanisms, at first positive feedback loops involving both sugars and hormones, that ensure the sustained bud growth. Data show that sugars act in concert with cytokinins but antagonistically to strigolactone signaling. A complex bud growth regulating network is demonstrated and unresolved issues regarding the hormone-carbohydrate regulation of AD are highlighted.