Learnings from a century of apical dominance research

The process of apical dominance by which the apical bud/shoot tip of the plant inhibits the outgrowth of axillary buds located below has been studied for more than a century. Different approaches were used over time with first the physiology era, the genetic era, and then the multidisciplinary era. During the physiology era, auxin was thought of as the master regulator of apical dominance acting indirectly to inhibit bud outgrowth via unknown secondary messenger(s). Potential candidates were cytokinin (CK) and abscisic acid (ABA). The genetic era with the screening of shoot branching mutants in different species revealed the existence of a novel carotenoid-derived branching inhibitor and led to the significant discovery of strigolactones (SLs) as a novel class of plant hormones. The re-discovery of the major role of sugars in apical dominance emerged from modern physiology experiments and involves ongoing work with genetic material affected in sugar-signalling. As crops and natural selection rely on the emergent properties of networks such as this branching network, future work should explore the whole network, the details of which are critical but not individually sufficient to solve the wicked problems of sustainable food supply and climate change.

The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa

The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.

Meristem dormancy in Marchantia polymorpha is regulated by a liverwort-specific miRNA and a clade III SPL gene

The shape of modular organisms depends on the branching architecture, which in plants is determined by the fates of generative centers called meristems. The branches of the liverwort Marchantia polymorpha are derived from two adjacent meristems that develop at thallus apices. These meristems may be active and develop branches or may be dormant and do not form branches. The relative number and position of active and dormant meristems define the overall shape and form of the thallus. We show that the clade III SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor MpSPL1 is required for meristem dormancy. The activity of MpSPL1 is regulated by the liverwort-specific Mpo-MR13 miRNA, which, in turn, is regulated by PIF-mediated signaling. An unrelated PIF-regulated miRNA, MIR156, represses a different SPL gene (belonging to clade IV) that inhibits branching during the shade avoidance response in Arabidopsis thaliana. This suggests that a conserved light signaling mechanism modulates branching architecture in liverworts and angiosperms and therefore is likely operated in the last common ancestor. However, PIF-mediated signaling represses the expression of different miRNA genes with different SPL targets during dichotomous, apical branching in liverworts and during lateral, subapical branching in angiosperms. We speculate that the mechanism that acts downstream of light and regulates meristem dormancy evolved independently in liverworts and angiosperms.

Glucose-6-Phosphate Dehydrogenases: The Hidden Players of Plant Physiology

Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes a metabolic hub between glycolysis and the pentose phosphate pathway (PPP), which is the oxidation of glucose-6-phosphate (G6P) to 6-phosphogluconolactone concomitantly with the production of nicotinamide adenine dinucleotide phosphate (NADPH), a reducing power. It is considered to be the rate-limiting step that governs carbon flow through the oxidative pentose phosphate pathway (OPPP). The OPPP is the main supplier of reductant (NADPH) for several "reducing" biosynthetic reactions. Although it is involved in multiple physiological processes, current knowledge on its exact role and regulation is still piecemeal. The present review provides a concise and comprehensive picture of the diversity of plant G6PDHs and their role in seed germination, nitrogen assimilation, plant branching, and plant response to abiotic stress. This work will help define future research directions to improve our knowledge of G6PDHs in plant physiology and to integrate this hidden player in plant performance.

Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest

Perennial rice is a new type of rice that allows the harvest of rice for multiple years without growing new seedlings annually. This technology represents a green and sustainable agricultural production mode with many advantages for balancing agricultural ecology and food security. However, the differences in regeneration patterns between perennial and annual rice and the gene regulatory pathways of the apical dominance in axillary bud growth after harvest in perennial rice are still unclear. In this study, perennial rice (PR23) and annual rice (Chugeng28) were used to investigate axillary bud growth patterns before and after apical spike removal. After elimination of apical dominance at different development stages, perennial rice rhizome axillary buds at the compression nodes germinated more rapidly than others and developed into new seedlings. The axillary buds at the high-position nodes in annual rice grew faster than those at other nodes. Furthermore, the global gene expression patterns of PR23 rhizome buds at compression nodes grown for 1, 3, 4, and 5 days after apical spike removal were analyzed by transcriptome sequencing. Compared with the control buds without apical removal, 264, 3,484, 2,095, and 3,398 genes were up-regulated, and 674, 3,484, 1,594, and 1,824 genes were down-regulated in the buds grown for 1, 3, 4, and 5 days after apical spike removal, respectively. Trend analysis of the expressed genes at different time points was performed and co-expression network was constructed to identify key genes in rhizome axillary bud regrowth. The results showed that 85 hub genes involved in 12 co-regulatory networks were mainly enriched in the light system, photosynthesis-antenna protein, plant hormone signal transduction, ABC transporter and metabolic pathways, which suggested that hormone and photosynthetic signals might play important roles in the regulation of rhizome axillary bud regeneration in perennial rice. Overall, this study clarified the differences in the regeneration patterns of axillary buds between perennial and annual rice and provided insight into the complex regulatory networks during the regeneration of rhizome axillary buds in perennial rice.

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.

Inconsistent annual compensation for floral herbivory by an iterocarpic thistle

PREMISE

Plants experiencing steep reproductive losses from herbivores should favor strategies promoting tolerance or resistance to that herbivory. However, the degree to which such strategies succeed in improving plant fitness under natural conditions needs further evaluation, especially for iterocarpic species. We tested whether reproductive effort by the iterocarpic Cirsium undulatum Spreng. (Wavyleaf thistle) provided within-season tolerance for floral herbivory through response to apical damage.

METHODS

We imposed apical damage and manipulated floral herbivory on later-flowering, non-apical flowerheads for two seasons. We asked: (1) is there evidence of compensatory potential to tolerate apical flowerhead damage? If so, (2) does the amount of herbivore pressure on non-apical flowerheads influence the magnitude of any compensatory response; and (3) is the response to apical damage sufficient to increase plant seed production under ambient floral herbivory over the flowering season?

RESULTS

Plants showed compensatory potential for apical head loss; apical damage increased seed contributions from later, lower positioned flowerheads. Further, the intensity of subsequent herbivore pressure influenced compensation outcomes. Equitable seed production under both levels of ambient herbivory occurred only in the year in which plants were larger and insect pressure was lower. Finally, the response to apical damage was sufficient to compensate for apical seed loss, but it did not consistently increase overall annual seed production under ambient floral herbivory.

CONCLUSIONS

Although this iterocarpic species can compensate for apical damage, tolerance for floral herbivory varied between years.

HEXOKINASE1 signalling promotes shoot branching and interacts with cytokinin and strigolactone pathways

Plant architecture is controlled by several endogenous signals including hormones and sugars. However, only little information is known about the nature and roles of the sugar signalling pathways in this process. Here we test whether the sugar signalling pathway mediated by HEXOKINASE1 (HXK1) is involved in the control of shoot branching. To test the involvement of HXK1 in shoot branching and in the hormonal network controlling this process, we modulated the HXK1 pathway using physiological and genetic approaches in rose, pea and arabidopsis. Mannose-induced HXK signalling triggered bud outgrowth in rose and pea. In arabidopsis, both HXK1 deficiency and defoliation led to decreased shoot branching and conferred hypersensitivity to auxin. Complementation of the HXK1 knockout mutant gin2 with a catalytically inactive HXK1, restored shoot branching to the wild-type level. HXK1-deficient plants displayed decreased cytokinin levels and increased expression of MAX2, which is required for strigolactone signalling. The branching phenotype of HXK1-deficient plants could be partly restored by cytokinin treatment and strigolactone deficiency could override the negative impact of HXK1 deficiency on shoot branching. Our observations demonstrate that HXK1 signalling contributes to the regulation of shoot branching and interacts with hormones to modulate plant architecture.

OsWUS promotes tiller bud growth by establishing weak apical dominance in rice

Two branching strategies are exhibited in crops: enhanced apical dominance, as in maize; or weak apical dominance, as in rice. However, the underlying mechanism of weak apical dominance remains elusive. OsWUS, an ortholog of Arabidopsis WUSCHEL (WUS) in rice, is required for tiller development. In this study, we identified and functionally characterized a low-tillering mutant decreased culm number 1 (dc1) that resulted from loss-of-function of OsWUS. The dc1 tiller buds are viable but repressed by the main culm apex, leading to stronger apical dominance than that of the wild-type (WT). Auxin response is enhanced in the dc1 mutant, and knocking out the auxin action-associated gene ABERRANT SPIKELET AND PANICLE 1 (ASP1) de-repressed growth of the tiller buds in the dc1 mutant, suggesting that OsWUS and ASP1 are both involved in outgrowth of the rice tiller bud. Decapitation triggers higher contents of cytokinins in the shoot base of the dc1 mutant compared with those in the WT, and exogenous application of cytokinin is not sufficient for sustained growth of the dc1 tiller bud. Transcriptome analysis indicated that expression levels of transcription factors putatively bound by ORYZA SATIVA HOMEOBOX 1 (OSH1) are changed in response to decapitation and display a greater fold change in the dc1 mutant than that in the WT. Collectively, these findings reveal an important role of OsWUS in tiller bud growth by influencing apical dominance, and provide the basis for an improved understanding of tiller bud development in rice.

Effect of Pruning Young Branches on Fruit and Seed Set in Cassava

Flowering in cassava is closely linked with branching. Early-flowering genotypes branch low and abundantly. Although farmers prefer late flowering genotypes because of their erect plant architecture, their usefulness as progenitors in breeding is limited by their low seed production. In general, the first inflorescence aborts in cassava. Preventing this abortion would result in early production of seeds and make cassava breeding more efficient. The objective of this study was to assess if pruning young branches prevents the abortion of first inflorescences and promotes early fruit and seed set. Four genotypes with early, late, very late, and no flowering habits were grown under an extended photoperiod (EP) or normal dark night conditions (DN). Additional treatments included pruning young branches at the first or second flowering event and spraying (or not) benzyladenine (BA) after pruning. One genotype failed to flower and was not considered further. For the remaining genotypes, EP proved crucial to induce an earlier flowering, which is a pre-requisite for pruning. Total production of seeds in EP plots was 2,971 versus 150 in DN plots. For plants grown under EP, the average number of seeds per plant without pruning was 3.88, whereas those pruned produced 17.60 seeds per plant. Pruning at the first branching event led to higher number of seeds per plant (26.25) than pruning at the second flowering event (8.95). In general, applying BA was beneficial (38.52 and 13.98 seeds/plant with or without spraying it, respectively). The best combination of treatments was different for each genotype. Pruning young branches and applying BA in the first flowering event not only prevented the abortion of inflorescences but also induced the feminization of male flowers into hermaphrodite or female-only flowers. The procedures suggested from this study (combining EP, pruning young branches, and spraying BA), allowed the production of a high number of seeds from erect cassava genotypes in a short period. The implementation of these procedures will improve the breeding efficiency in cassava.

Virulent Rhodococcus fascians Produce Unique Methylated Cytokinins

Some strains of Rhodococcus fascians exist only as epiphytes on the plant surface whereas others can become endophytic and cause various abnormalities including the release of multiple buds and reduced root growth. The abnormalities reflect the action of cytokinin. The strains that can become endophytic harbour a linear plasmid that carries cytokinin biosynthesis, activation and destruction genes. However, both epiphytic and endophytic forms can release cytokinin into culture, affect cytokinin metabolism within inoculated plants and enhance the expression of sugar and amino acid transporters and cell wall invertases, but only the endophytic form markedly affects the morphology of the plant. A unique methylated cytokinin, dimethylated N⁶-(∆²-isopentenyl)adenine (2-MeiP), operating in a high sugar environment, is the likely causative factor of the severe morphological abnormalities observed when plants are inoculated with R. fascians strains carrying the linear plasmid.

Light Regulation of Axillary Bud Outgrowth Along Plant Axes: An Overview of the Roles of Sugars and Hormones

Apical dominance, the process by which the growing apical zone of the shoot inhibits bud outgrowth, involves an intricate network of several signals in the shoot. Auxin originating from plant apical region inhibits bud outgrowth indirectly. This inhibition is in particular mediated by cytokinins and strigolactones, which move from the stem to the bud and that respectively stimulate and repress bud outgrowth. The action of this hormonal network is itself modulated by sugar levels as competition for sugars, caused by the growing apical sugar sink, may deprive buds from sugars and prevents bud outgrowth partly by their signaling role. In this review, we analyze recent findings on the interaction between light, in terms of quantity and quality, and apical dominance regulation. Depending on growth conditions, light may trigger different pathways of the apical dominance regulatory network. Studies pinpoint to the key role of shoot-located cytokinin synthesis for light intensity and abscisic acid synthesis in the bud for R:FR in the regulation of bud outgrowth by light. Our analysis provides three major research lines to get a more comprehensive understanding of light effects on bud outgrowth. This would undoubtedly benefit from the use of computer modeling associated with experimental observations to deal with a regulatory system that involves several interacting signals, feedbacks, and quantitative effects.

An Update on the Signals Controlling Shoot Branching

Many new questions on the regulation of shoot branching have been raised in recent years, prompting a review and reassessment of the role of each signal involved. Sugars and their signaling networks have been attributed a major role in the early events of axillary bud outgrowth, whereas cytokinin appears to play a critical role in the modulation of this process in response to the environment. Perception of the recently discovered hormone strigolactone is now quite well understood, while the downstream targets remain largely unknown. Recent literature has highlighted that auxin export from a bud is important for its subsequent growth.

Rice Calcineurin B-Like Protein-Interacting Protein Kinase 31 (OsCIPK31) Is Involved in the Development of Panicle Apical Spikelets

Panicle apical abortion (PAA) causes severe yield losses in rice production, but details about its development and molecular basis remain elusive. Herein, a PAA mutant, paa1019, was identified among the progeny of an elite indica maintainer rice line Yixiang 1B (YXB) mutagenized population obtained using ethyl methyl sulfonate. The abortion rate of spikelets in paa1019 was observed up to 60%. Genetic mapping combined with Mutmap analysis revealed that LOC_Os03g20380 harbored a single-bp substitution (C to T) that altered its transcript length. This gene encodes calcineurin B-like protein-interacting protein kinase 31 (OsCIPK31) localized into the cytoplasm, and is preferentially expressed in transport tissues of rice. Complementation of paa1019 by transferring the open reading frame of LOC_Os03g20380 from YXB reversed the mutant phenotype, and conversely, gene editing by knocking out of OsCIPK31 in YXB results in PAA phenotype. Our results support that OsCIPK31 plays an important role in panicle development. We found that dysregulation is caused by the disruption of OsCIPK31 function due to excessive accumulation of ROS, which ultimately leads to cell death in rice panicle. OsCIPK31 and MAPK pathway might have a synergistic effect to lead ROS accumulation in response to stresses. Meanwhile the PAA distribution is related to IAA hormone accumulation in the panicle. Our study provides an understanding of the role of OsCIPK31 in panicle development by responding to various stresses and phytohormones.

Cytosolic glyceraldehyde-3-phosphate dehydrogenases play crucial roles in controlling cold-induced sweetening and apical dominance of potato (Solanum tuberosum L.) tubers

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme that functions in producing energy and supplying intermediates for cellular metabolism. Recent researches indicate that GAPDHs have multiple functions beside glycolysis. However, little information is available for functions of GAPDHs in potato. Here, we identified 4 putative cytosolic GAPDH genes in potato genome and demonstrated that the StGAPC1, StGAPC2, and StGAPC3, which are constitutively expressed in potato tissues and cold inducible in tubers, encode active cytosolic GAPDHs. Cosuppression of these 3 GAPC genes resulted in low tuber GAPDH activity, consequently the accumulation of reducing sugars in cold stored tubers by altering the tuber metabolite pool sizes favoring the sucrose pathway. Furthermore, GAPCs-silenced tubers exhibited a loss of apical dominance dependent on cell death of tuber apical bud meristem (TAB-meristem). It was also confirmed that StGAPC1, StGAPC2, and StGAPC3 interacted with the autophagy-related protein 3 (ATG3), implying that the occurrence of cell death in TAB-meristem could be induced by ATG3 associated events. Collectively, the present research evidences first that the GAPC genes play crucial roles in diverse physiological and developmental processes in potato tubers.

Trehalose 6-phosphate is involved in triggering axillary bud outgrowth in garden pea (Pisum sativum L.)

Trehalose 6-phosphate (Tre6P) is a signal of sucrose availability in plants, and has been implicated in the regulation of shoot branching by the abnormal branching phenotypes of Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) mutants with altered Tre6P metabolism. Decapitation of garden pea (Pisum sativum) plants has been proposed to release the dormancy of axillary buds lower down the stem due to changes in sucrose supply, and we hypothesized that this response is mediated by Tre6P. Decapitation led to a rapid and sustained rise in Tre6P levels in axillary buds, coinciding with the onset of bud outgrowth. This response was suppressed by simultaneous defoliation that restricts the supply of sucrose to axillary buds in decapitated plants. Decapitation also led to a rise in amino acid levels in buds, but a fall in phosphoenolpyruvate and 2-oxoglutarate. Supplying sucrose to stem node explants in vitro triggered a concentration-dependent increase in the Tre6P content of the buds that was highly correlated with their rate of outgrowth. These data show that changes in bud Tre6P levels are correlated with initiation of bud outgrowth following decapitation, suggesting that Tre6P is involved in the release of bud dormancy by sucrose. Tre6P might also be linked to a reconfiguration of carbon and nitrogen metabolism to support the subsequent growth of the bud into a new shoot.

A Growing Stem Inhibits Bud Outgrowth - The Overlooked Theory of Apical Dominance

Three theories of apical dominance, direct, diversion, and indirect, were proposed in the 1930s to explain how auxin synthesized in the shoot apex might inhibit axillary bud outgrowth, and thus shoot branching. The direct and diversion theories of apical dominance have been investigated in detail, and they are replaced with the current auxin transport canalization and second messenger theories, respectively. These two current theories still cannot entirely explain the phenomenon of apical dominance. Although there is ample evidence that the inhibition of bud outgrowth by auxin from the shoot apex is linked to stem elongation and highly branched auxin biosynthesis or signaling mutants are dwarf, the third theory proposed in the 1930s, the indirect theory, that explains apical dominance as auxin-induced stem growth indirectly inhibits bud outgrowth has been overlooked. The indirect theory did not propose how a growing stem might inhibit bud outgrowth. Recent discoveries indicate bud dormancy (syn. quiescence, paradormancy) in response to intrinsic and environmental factors in diverse species is linked to enhanced growth of the main shoot and reduced sugar level in the buds. Since a growing stem is a strong sink for sugars, and sugar is indispensable for shoot branching, the indirect theory of apical dominance might now be explained as auxin-induced stem growth inhibits bud outgrowth by diverting sugars away from buds. Detailed study of the indirect theory and the effect of source-sink status on dormancy and outgrowth of axillary buds will advance our knowledge of apical dominance and shoot branching in plants.

Apoplastic H2 O2 plays a critical role in axillary bud outgrowth by altering auxin and cytokinin homeostasis in tomato plants

Although phytohormones such as indole-3-acetic acid (IAA), cytokinin (CK) and strigolactone are important modulators of plant architecture, it remains unclear whether reactive oxygen species are involved in the regulation of phytohormone-dependent axillary bud outgrowth in plants. We used diverse techniques, including transcriptional suppression, HPLC-MS, biochemical methodologies and gene transcript analysis to investigate the signaling pathway for apoplastic hydrogen peroxide (H2 O2 )-induced axillary bud outgrowth. Silencing of tomato RESPIRATORY BURST OXIDASE HOMOLOG 1 (RBOH1) and WHITEFLY INDUCED 1 (WFI1), two important genes involved in H2 O2 production in the apoplast, enhanced bud outgrowth, decreased transcript of FZY - a rate-limiting gene in IAA biosynthesis and IAA accumulation in the apex - and increased the transcript of IPT2 involved in CK biosynthesis and CK accumulation in the stem node. These effects were fully abolished by the application of exogenous H2 O2 . Both decapitation and the silencing of FZY promoted bud outgrowth, and downregulated and upregulated the transcripts for IAA3 and IAA15, and IPT2, respectively. However, these effects were not blocked by treatment with exogenous H2 O2 but by napthaleneacetic acid (NAA) treatment. These results suggest that RBOHs-dependent apoplastic H2 O2 promotes IAA biosynthesis in the apex, which, in turn, inhibits CK biosynthesis and subsequent bud outgrowth in tomato plants.

Photosynthetic leaf area modulates tiller bud outgrowth in sorghum

Shoot branches or tillers develop from axillary buds. The dormancy versus outgrowth fates of buds depends on genetic, environmental and hormonal signals. Defoliation inhibits bud outgrowth indicating the role of leaf-derived metabolic factors such as sucrose in bud outgrowth. In this study, the sensitivity of bud outgrowth to selective defoliation was investigated. At 6 d after planting (6 DAP), the first two leaves of sorghum were fully expanded and the third was partially emerged. Therefore, the leaves were selectively defoliated at 6 DAP and the length of the bud in the first leaf axil was measured at 8 DAP. Bud outgrowth was inhibited by defoliation of only 2 cm from the tip of the second leaf blade. The expression of dormancy and sucrose-starvation marker genes was up-regulated and cell cycle and sucrose-inducible genes was down-regulated during the first 24 h post-defoliation of the second leaf. At 48 h, the expression of these genes was similar to controls as the defoliated plant recovers. Our results demonstrate that small changes in photosynthetic leaf area affect the propensity of tiller buds for outgrowth. Therefore, variation in leaf area and photosynthetic activity should be included when integrating sucrose into models of shoot branching.

Cytokinin is required for escape but not release from auxin mediated apical dominance

Auxin produced by an active primary shoot apex is transported down the main stem and inhibits the growth of the axillary buds below it, contributing to apical dominance. Here we use Arabidopsis thaliana cytokinin (CK) biosynthetic and signalling mutants to probe the role of CK in this process. It is well established that bud outgrowth is promoted by CK, and that CK synthesis is inhibited by auxin, leading to the hypothesis that release from apical dominance relies on an increased supply of CK to buds. Our data confirm that decapitation induces the expression of at least one ISOPENTENYLTRANSFERASE (IPT) CK biosynthetic gene in the stem. We further show that transcript abundance of a clade of the CK-responsive type-A Arabidopsis response regulator (ARR) genes increases in buds following CK supply, and that, contrary to their typical action as inhibitors of CK signalling, these genes are required for CK-mediated bud activation. However, analysis of the relevant arr and ipt multiple mutants demonstrates that defects in bud CK response do not affect auxin-mediated bud inhibition, and increased IPT transcript levels are not needed for bud release following decapitation. Instead, our data suggest that CK acts to overcome auxin-mediated bud inhibition, allowing buds to escape apical dominance under favourable conditions, such as high nitrate availability.

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

DOI:http://dx.doi.org/10.7554/eLife.06808.001

Most land plants have shoots that form branches and plants can regulate when and where they grow these branches to best exploit their environment. Plants with flowers and the more ancient mosses both have branching shoots, but these two groups of plants evolved to grow in this way independently of each other. Most studies on shoot branching have focused on flowering plants and so it is less clear how branching works in mosses.

Three plant hormones—called auxin, cytokinin and strigolactone—control shoot branching in flowering plants. Auxin moves down the main shoot of the plant to prevent new branches from forming. This movement is controlled by the PIN proteins and several other families of proteins. On the other hand, cytokinin promotes the growth of new branches; and strigolactone can either promote or inhibit shoot branching depending on how the auxin is travelling around the plant.

Coudert, Palubicki et al. studied shoot branching in a species of moss called Physcomitrella patens. The experiments show that cells on the outer surface of the main shoot are essentially reprogrammed to become so-called ‘branch initials’, which will then develop into new branches. Next, Coudert, Palubicki et al. made a computational model that was able to simulate the pattern of shoot branching in the moss.

Further experiments supported the predictions made by the model. Coudert, Palubicki et al. found that, as in flowering plants, auxin from the tip of the main shoot suppresses branching in the moss, and cytokinin promotes branching. The experiments also showed that strigolactone inhibits shoot branching, but its role is restricted to the base of the shoots. The model predicts that, unlike in flowering plants, auxin must flow in both directions in moss shoots to produce the observed patterns of shoot branching. Also, the experiments suggest that the PIN proteins and another group of proteins that control the movement of auxin do not regulate shoot branching in moss. Instead, it appears that auxin may move through microscopic channels that link one moss cell to the next.

Coudert, Palubicki et al.'s findings suggest that both flowering plants and mosses have evolved to use the same three hormones to control shoot branching, but that these hormones interact in different ways. One key next step will be to find out how auxin is transported during shoot branching in moss by manipulating the opening of the channels between the cells. A further challenge will be to find out the precise details of how the hormones control the activity of the branch initial cells.

DOI:http://dx.doi.org/10.7554/eLife.06808.002

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching

BACKGROUND

Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines.

RESULTS

Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations.

CONCLUSIONS

In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most promising target for future functional analyses.

Multiple pathways regulate shoot branching

Shoot branching patterns result from the spatio-temporal regulation of axillary bud outgrowth. Numerous endogenous, developmental and environmental factors are integrated at the bud and plant levels to determine numbers of growing shoots. Multiple pathways that converge to common integrators are most probably involved. We propose several pathways involving not only the classical hormones auxin, cytokinins and strigolactones, but also other signals with a strong influence on shoot branching such as gibberellins, sugars or molecular actors of plant phase transition. We also deal with recent findings about the molecular mechanisms and the pathway involved in the response to shade as an example of an environmental signal controlling branching. We propose the TEOSINTE BRANCHED1, CYCLOIDEA, PCF transcription factor TB1/BRC1 and the polar auxin transport stream in the stem as possible integrators of these pathways. We finally discuss how modeling can help to represent this highly dynamic system by articulating knowledges and hypothesis and calculating the phenotype properties they imply.

Shaping plant architecture

Plants exhibit phenotypical plasticity. Their general body plan is genetically determined, but plant architecture and branching patterns are variable and can be adjusted to the prevailing environmental conditions. The modular design of the plant facilitates such morphological adaptations. The prerequisite for the formation of a branch is the initiation of an axillary meristem. Here, we review the current knowledge about this process. After its establishment, the meristem can develop into a bud which can either become dormant or grow out and form a branch. Many endogenous factors, such as photoassimilate availability, and exogenous factors like nutrient availability or shading, have to be integrated in the decision whether a branch is formed. The underlying regulatory network is complex and involves phytohormones and transcription factors. The hormone auxin is derived from the shoot apex and inhibits bud outgrowth indirectly in a process termed apical dominance. Strigolactones appear to modulate apical dominance by modification of auxin fluxes. Furthermore, the transcription factor BRANCHED1 plays a central role. The exact interplay of all these factors still remains obscure and there are alternative models. We discuss recent findings in the field along with the major models. Plant architecture is economically significant because it affects important traits of crop and ornamental plants, as well as trees cultivated in forestry or on short rotation coppices. As a consequence, plant architecture has been modified during plant domestication. Research revealed that only few key genes have been the target of selection during plant domestication and in breeding programs. Here, we discuss such findings on the basis of various examples. Architectural ideotypes that provide advantages for crop plant management and yield are described. We also outline the potential of breeding and biotechnological approaches to further modify and improve plant architecture for economic needs.

Light Signaling in Bud Outgrowth and Branching in Plants

Branching determines the final shape of plants, which influences adaptation, survival and the visual quality of many species. It is an intricate process that includes bud outgrowth and shoot extension, and these in turn respond to environmental cues and light conditions. Light is a powerful environmental factor that impacts multiple processes throughout plant life. The molecular basis of the perception and transduction of the light signal within buds is poorly understood and undoubtedly requires to be further unravelled. This review is based on current knowledge on bud outgrowth-related mechanisms and light-mediated regulation of many physiological processes. It provides an extensive, though not exhaustive, overview of the findings related to this field. In parallel, it points to issues to be addressed in the near future.

The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development

The CULLIN family of E3 ubiquitin ligases are important regulators of plant development and function. A newly identified class of CULLIN4-RING-E3 ligases (CRL4s) interacts with substrate receptors referred to as DDB1-CUL4 ASSOCIATED FACTORS (DCAFs) via a DDB1 linker protein. We have previously reported that the WD40 protein WDR55 interacts with DDB1A and is thus a putative DCAF. Mutants of WDR55 are embryo lethal, suggesting that a DDB1(WDR55) complex could regulate embryo and endosperm development. Here we report that a weak allele homozygous for wdr55 display pleiotropic phenotypes in the seedling and adult stages, suggesting a novel regulatory role for WDR55 in vegetative development.

Can loss of apical dominance in potato tuber serve as a marker of physiological age?

The potato tuber constitutes a model system for the study of dormancy release and sprouting, suggested to be regulated by endogenous plant hormones and their balance inside the tuber. During dormancy, potato tubers cannot be induced to sprout without some form of stress or exogenous hormone treatment. When dormancy is released, sprouting of the apical bud may be inhibited by sprout control agents or cold temperature. Dominance of the growing apical bud over other lateral buds decreases during storage and is one of the earliest morphophysiological indicators of the tuber's physiological age. Three main types of loss of apical dominance (AD) affect sprouting shape. Hallmarks of programmed cell death (PCD) have been identified in the tuber apical bud meristem (TAB-meristem) during normal growth, and are more extensive when AD is lost following extended cold storage or chemical stress. Nevertheless, the role of hormonal regulation in TAB-meristem PCD remains unclear.

Ontogenetic contingency of tolerance mechanisms in response to apical damage

BACKGROUND AND AIMS

Plants are able to tolerate tissue loss through vigorous branching which is often triggered by release from apical dominance and activation of lateral meristems. However, damage-induced branching might not be a mere physiological outcome of released apical dominance, but an adaptive response to environmental signals, such as damage timing and intensity. Here, branching responses to both factors were examined in the annual plant Medicago truncatula.

METHODS

Branching patterns and allocation to reproductive traits were examined in response to variable clipping intensities and timings in M. truncatula plants from two populations that vary in the onset of reproduction. Phenotypic selection analysis was used to evaluate the strength and direction of selection on branching under the damage treatments.

KEY RESULTS

Plants of both populations exhibited an ontogenetic shift in tolerance mechanisms: while early damage induced greater meristem activation, late damage elicited investment in late-determined traits, including mean pod and seed biomass, and supported greater germination rates. Severe damage mostly elicited simultaneous development of multiple-order lateral branches, but this response was limited to early damage. Selection analyses revealed positive directional selection on branching in plants under early- compared with late- or no-damage treatments.

CONCLUSIONS

The results demonstrate that damage-induced meristem activation is an adaptive response that could be modified according to the plant's developmental stage, severity of tissue loss and their interaction, stressing the importance of considering these effects when studying plastic responses to apical damage.

Redox regulation of auxin signaling and plant development in Arabidopsis

Thioredoxin (NTR/TRX) and glutathione (GSH/GRX) are the two major systems which play a key role in the maintenance of cellular redox homeostasis. They are essential for plant development, cell division or the response to environmental stresses. In a recent article, we studied the interplay between the NADP-linked thioredoxin and glutathione systems in auxin signaling genetically, by associating TRX reductase (ntra ntrb) and glutathione biosynthesis (cad2) mutations. We show that these two thiol reduction pathways interfere with developmental processes. This occurs through modulation of auxin activity as shown by genetic analyses of loss of function mutations in a triple ntra ntrb cad2 mutant. The triple mutant develops almost normally at the rosette stage but fails to generate lateral organs from the inflorescence meristem, producing almost naked stems that are reminiscent of mutants affected in PAT (polar auxin transport) or biosynthesis. The triple mutant exhibits other defects in processes regulated by auxin, including a loss of apical dominance, vasculature defects and reduced secondary root production. Furthermore, it has lower auxin (IAA) levels and decreased capacity for PAT, suggesting that the NTR and glutathione pathways influence inflorescence meristem development through regulation of auxin transport and metabolism.

Warm spring temperatures induce persistent season-long changes in shoot development in grapevines

BACKGROUND AND AIMS

The influence of temperature on the timing of budbreak in woody perennials is well known, but its effect on subsequent shoot growth and architecture has received little attention because it is understood that growth is determined by current temperature. Seasonal shoot development of grapevines (Vitis vinifera) was evaluated following differences in temperature near budbreak while minimizing the effects of other microclimatic variables.

METHODS

Dormant buds and emerging shoots of field-grown grapevines were heated above or cooled below the temperature of ambient buds from before budbreak until individual flowers were visible on inflorescences, at which stage the shoots had four to eight unfolded leaves. Multiple treatments were imposed randomly on individual plants and replicated across plants. Shoot growth and development were monitored during two growing seasons.

KEY RESULTS

Higher bud temperatures advanced the date of budbreak and accelerated shoot growth and leaf area development. Differences were due to higher rates of shoot elongation, leaf appearance, leaf-area expansion and axillary-bud outgrowth. Although shoots arising from heated buds grew most vigorously, apical dominance in these shoots was reduced, as their axillary buds broke earlier and gave rise to more vigorous lateral shoots. In contrast, axillary-bud outgrowth was minimal on the slow-growing shoots emerging from buds cooled below ambient. Variation in shoot development persisted or increased during the growing season, well after temperature treatments were terminated and despite an imposed soil water deficit.

CONCLUSIONS

The data indicate that bud-level differences in budbreak temperature may lead to marked differences in shoot growth, shoot architecture and leaf-area development that are maintained or amplified during the growing season. Although growth rates commonly are understood to reflect current temperatures, these results demonstrate a persistent effect of early-season temperatures, which should be considered in future growth models.

Mechanisms of bamboo witches' broom symptom development caused by endophytic/epiphytic fungi

Aciculosporium take causes continuous shoot growth but maintains normal leaf-arrangement and branching patterns in the host plant, which eventually resulting in witches' broom disease of bamboo. An in situ hybridization technique with a species-specific oligonucleotide probe was recently used to demonstrate that endophytic mycelia of A. take is predominantly distributed in the intercellular spaces of the shoot apical meristem of the host. Endophytic hyphae in meristematic tissues, which may produce auxin, are responsible for continuous primordium initiation within the shoot apex. Here I examine another bamboo witches' broom causal fungus, Heteroepichloë sasae. Both species are biotrophic and belong to family Clavicipitaceae: however, H. sasae does not cause continuous shoot growth. Histological study showed that H. sasae mycelia were distributed superficially, even on shoot apical meristems. These observations suggest that when their stromata develop, endophytic A. take destroys shoot apical meristem and epiphytic H. sasae chokes the shoot apex of the host. Stromata formation consequently causes lateral bud outgrowth because of release from apical dominance. This process repeats and eventually results in the witches' broom symptoms.

A reappraisal of the role of abscisic acid and its interaction with auxin in apical dominance

BACKGROUND AND AIMS

Evidence from pea rms1, Arabidopsis max4 and petunia dad1 mutant studies suggest an unidentified carotenoid-derived/plastid-produced branching inhibitor which moves acropetally from the roots to the shoots and interacts with auxin in the control of apical dominance. Since the plant hormone, abscisic acid (ABA), known to inhibit some growth processes, is also carotenoid derived/plastid produced, and because there has been indirect evidence for its involvement with branching, a re-examination of the role of ABA in apical dominance is timely. Even though it has been determined that ABA probably is not the second messenger for auxin in apical dominance and is not the above-mentioned unidentified branching inhibitor, the similarity of their derivation suggests possible relationships and/or interactions.

METHODS

The classic Thimann-Skoog auxin replacement test for apical dominance with auxin [0.5 % naphthalene acetic acid (NAA)] applied both apically and basally was combined in similar treatments with 1 % ABA in Ipomoea nil (Japanese Morning Glory), Solanum lycopersicum (Better Boy tomato) and Helianthus annuus (Mammoth Grey-striped Sunflower).

KEY RESULTS

Auxin, apically applied to the cut stem surface of decapitated shoots, strongly restored apical dominance in all three species, whereas the similar treatment with ABA did not. However, when ABA was applied basally, i.e. below the lateral bud of interest, there was a significant moderate repression of its outgrowth in Ipomoea and Solanum. There was also some additive repression when apical auxin and basal ABA treatments were combined in Ipomoea.

CONCLUSION

The finding that basally applied ABA is able partially to restore apical dominance via acropetal transport up the shoot suggests possible interactions between ABA, auxin and the unidentified carotenoid-derived branching inhibitor that justify further investigation.

Role of cytokinin and auxin in shaping root architecture: regulating vascular differentiation, lateral root initiation, root apical dominance and root gravitropism

BACKGROUND AND AIMS

Development and architecture of plant roots are regulated by phytohormones. Cytokinin (CK), synthesized in the root cap, promotes cytokinesis, vascular cambium sensitivity, vascular differentiation and root apical dominance. Auxin (indole-3-acetic acid, IAA), produced in young shoot organs, promotes root development and induces vascular differentiation. Both IAA and CK regulate root gravitropism. The aims of this study were to analyse the hormonal mechanisms that induce the root's primary vascular system, explain how differentiating-protoxylem vessels promote lateral root initiation, propose the concept of CK-dependent root apical dominance, and visualize the CK and IAA regulation of root gravitropiosm.

KEY ISSUES

The hormonal analysis and proposed mechanisms yield new insights and extend previous concepts: how the radial pattern of the root protoxylem vs. protophloem strands is induced by alternating polar streams of high IAA vs. low IAA concentrations, respectively; how differentiating-protoxylem vessel elements stimulate lateral root initiation by auxin-ethylene-auxin signalling; and how root apical dominance is regulated by the root-cap-synthesized CK, which gives priority to the primary root in competition with its own lateral roots.

CONCLUSIONS

CK and IAA are key hormones that regulate root development, its vascular differentiation and root gravitropism; these two hormones, together with ethylene, regulate lateral root initiation.

A preliminary investigation of the role of auxin and cytokinin in sylleptic branching of three hybrid poplar clones exhibiting contrasting degrees of sylleptic branching

Sylleptic branches grow out from lateral buds during the same growing season in which the buds are formed. This type of branching is present in poplar and in many tropical species. It results in the production of more branches, more leaves and expanded photosynthetic capacity and is thought to assist in increasing the overall growth and biomass of the tree at a young age. However, very little is known about the physiology of sylleptic branching in poplar, which is an extremely important source of fibre and fuel. In the present study of three hybrid poplar clones (11-11, 47-174 and 49-177) of Populus trichocarpa x P. deltoides exhibiting contrasting degrees of sylleptic branching, an analysis was carried out on parent shoot elongation and sylleptic branching, together with a preliminary comparison of the parent shoots' sensitivity to auxin (naphthaleneacetic acid) as a repressor of lateral bud outgrowth, and cytokinin (benzyladenine) as a promoter. Suggestive evidence was found for an inverse correlation between parent shoot sensitivity to auxin and the degree of sylleptic branching, as well as a partially positive correlation with respect to sensitivity to cytokinin. The present data are consistent with the hypothesis that auxin and cytokinin may play repressive and promotive roles, respectively, in the sylleptic branching of hybrid poplar.

Maintaining apical dominance in the fern gametophyte

A kinetic model is developed for cell differentiation in the fern gametophyte to test hypotheses on the role of spatially patterned plasmodesmata networks in development. Of particular interest is the establishment and maintenance of apical cell type in a single cell, with concurrent suppression of this character in all other cells (apical dominance). Steps towards understanding apical cell localization in geometrically simple gametophytes may shed light on the establishment and maintenance of apical meristems in higher plants. The model, based on the plasmodesmata maps of Tilney and colleagues and involving kinetics for a requisite minimum of two morphogens. successfully produces the apical/non-apical cell differentiation patterns of normal development, and redifferentiation due to cell isolation, in six stages from 0-30 d of development. Our results indicate that increasing apical cell plasmodesmata number, as development progresses, is not required for effective transport across apical cell walls in maintaining apical dominance.

Control of axillary bud initiation and shoot architecture in Arabidopsis through the SUPERSHOOT gene

The aerial architecture of flowering plants is determined to a large extent by shoot growth and shoot branching arising from the initiation and growth of axillary meristems. We have identified an Arabidopsis mutant, supershoot (sps), which is characterized by a massive overproliferation of shoots, such that a single plant can generate 500 or more inflorescences. Analysis of the mutant plants shows that the primary defect is because of an increase in the number of meristems formed in leaf axils, together with release of bud arrest, resulting in reiterative branch formation from rosette and cauline leaves. The SPS gene is shown here to encode a cytochrome P450, and together with a 3- to 9-fold increase in levels of Z-type cytokinins in sps mutant plants, indicate a role for SPS in modulating hormone levels. The expression pattern of SPS, with strong expression at the leaf axils, correlates well with the phenotypic defects. Our results indicate that control of shoot branching in Arabidopsis may be accomplished in part by suppression of axillary meristem initiation and growth through the localized attenuation of cytokinin levels at sites of bud initiation.