Computational modeling and molecular physiology experiments reveal new insights into shoot branching in pea

The Psathyrostachys juncea DWARF27 gene encodes an all-trans-/9-cis-beta-carotene isomerase in the control of plant branches in Arabidopsis thaliana by strigolactones

Strigolactones (SLs), carotenoid-derived plant hormones, govern the growth and development of both monocotyledonous and dicotyledonous plants. DWARF27 (D27), a plastid-targeted protein located at the initiation site of the core pathway in SL synthesis, plays a crucial role in regulating plant tillering (branching). In rice (Oryza sativa) and wheat (Triticum aestivum), OsD27 and TaD27-B proteins modulate the number of plant tillers by participating in SL biosynthesis. Similarly, AtD27 in Arabidopsis thaliana is required for SL production and has a significant impact on phenotypic changes related to branching. At the same time, TaD27 in wheat has been confirmed as a functional orthologue of AtD27 in Arabidopsis, and both Psathyrostachys juncea and wheat belong to the Triticeae, so we speculate that PjD27 gene may also have the same function as AtD27 in Arabidopsis. In this study, we initially screened the PjD27 gene significantly associated with tillering regulation through transcriptome data analysis and subsequently validated its expression levels using qRT-PCR analysis. Furthermore, we conducted phylogenetic analysis using amino acid sequences from 41 species, including P. juncea, to identify closely related species of P. juncea. Here, we analyze the conservation of D27 protein among P. juncea, rice, wheat, and Arabidopsis and provide preliminary evidence suggesting that PjD27 protein is an orthologue of D27 protein in Arabidopsis. Through reverse genetics, we demonstrate the crucial role of PjD27 in regulating plant branching, establishing it as a functional orthologue of D27 in Arabidopsis. Furthermore, following transient expression in tobacco (Nicotiana tabacum), we demonstrate that the subcellular location of the PjD27 protein is consistent with the cellular location of TaD27-B in wheat. Quantitative analysis of SLs shows that PjD27 is a key gene regulating tillering (branching) by participating in SL biosynthesis. By elucidating the function of the PjD27 gene, our findings provide valuable genetic resources for new germplasm creation and improving grain yield in P. juncea.

The Role of FveAFB5 in Auxin-Mediated Responses and Growth in Strawberries

Auxin is a crucial hormone that regulates various aspects of plant growth and development. It exerts its effects through multiple signaling pathways, including the TIR1/AFB-based transcriptional regulation in the nucleus. However, the specific role of auxin receptors in determining developmental features in the strawberry (Fragaria vesca) remains unclear. Our research has identified FveAFB5, a potential auxin receptor, as a key player in the development and auxin responses of woodland strawberry diploid variety Hawaii 4. FveAFB5 positively influences lateral root development, plant height, and fruit development, while negatively regulating shoot branching. Moreover, the mutation of FveAFB5 confers strong resistance to the auxinic herbicide picloram, compared to dicamba and quinclorac. Transcriptome analysis suggests that FveAFB5 may initiate auxin and abscisic acid signaling to inhibit growth in response to picloram. Therefore, FveAFB5 likely acts as an auxin receptor involved in regulating multiple processes related to strawberry growth and development.

Strigolactones and Shoot Branching: What Is the Real Hormone and How Does It Work?

There have been substantial advances in our understanding of many aspects of strigolactone regulation of branching since the discovery of strigolactones as phytohormones. These include further insights into the network of phytohormones and other signals that regulate branching, as well as deep insights into strigolactone biosynthesis, metabolism, transport, perception and downstream signaling. In this review, we provide an update on recent advances in our understanding of how the strigolactone pathway co-ordinately and dynamically regulates bud outgrowth and pose some important outstanding questions that are yet to be resolved.

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.

Integration of the SMXL/D53 strigolactone signalling repressors in the model of shoot branching regulation in Pisum sativum

DWARF53 (D53) in rice (Oryza sativa) and its homologs in Arabidopsis (Arabidopsis thaliana), SUPPRESSOR OF MAX2-LIKE 6 (SMXL6), SMXL7 and SMXL8, are well established negative regulators of strigolactone (SL) signalling in shoot branching regulation. Little is known of pea (Pisum sativum) homologs and whether D53 and related SMXLs are specific to SL signalling pathways. Here, we identify two allelic pea mutants, dormant3 (dor3), and demonstrate through gene mapping and sequencing that DOR3 corresponds to a homolog of D53 and SMXL6/SMXL7, designated PsSMXL7. Phenotype analysis, gene expression, protein and hormone quantification assays were performed to determine the role of PsSMXL7 in regulation of bud outgrowth and the role of PsSMXL7 and D53 in integrating SL and cytokinin (CK) responses. Like D53 and related SMXLs, we show that PsSMXL7 can be degraded by SL and induces feedback upregulation of PsSMXL7 transcript. Here we reveal a system conserved in pea and rice, whereby CK also upregulates PsSMXL7/D53 transcripts, providing a clear mechanism for SL and CK cross-talk in the regulation of branching. To further deepen our understanding of the branching network in pea, we provide evidence that SL acts via PsSMXL7 to modulate auxin content via PsAFB5, which itself regulates expression of SL biosynthesis genes. We therefore show that PsSMXL7 is key to a triple hormone network involving an auxin-SL feedback mechanism and SL-CK cross-talk.

CELL CYCLE SEITCH 52 regulates tillering by interacting with LATERAL SUPPRESSOR in non-heading Chinese cabbage

With the discovery of essential genes regulating tillering, such as MONOCULM 1 (MOC1) in rice and LATERAL SUPPRESSOR (LAS in Arabidopsis, LS in tomato), research on tillering mechanisms has made great progress; however, the study of tillering in non-heading Chinese cabbage (NHCC) is rare. Here, we report that BcLAS, as a member of the GRAS family, plays an important role in the tillering of NHCC during its vegetative growth. BcLAS was almost not expressed in other examed parts except leaf axils throughout life. When the expression of BcLAS was silenced utilizing virus-induced gene silencing (VIGS) technology, we found that the tiller number of 'Maertou' decreased sharply. In 'Suzhouqing', overexpression of BcLAS significantly promoted tillering. BcCCS52, the orthologue to CELL CYCLE SEITCH 52 (CCS52), interacts with BcLAS. Downregulation of the expression of BcCCS52 promoted tillering of 'Suzhouqing'; therefore, we conclude that BcCCS52 plays a negative role in tillering regulation. Our findings reveal the tillering regulation mechanism of NHCCs at the vegetative stage and report an orthologue of CCS52 regulating tillering in NHCC.

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.

Transcriptome analyses provide insights into the homeostatic regulation of axillary buds in upland cotton (G. hirsutum L.)

BACKGROUND

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 reported. We obtained a mutant (designated mZ571) with a high-budding phenotype in axillary bud development from the low-budding phenotype variety G. hirsutum Z571 (CCRI 9A02), which provided ideal materials for the study of complex regulatory networks of axillary bud development. In this study, RNA sequencing was carried out to detect gene expression levels during three stages of axillary buds in Z571 (LB, low budding) and mZ571 mutant (HB, high budding).

RESULTS

A total of 7162 DEGs were identified in the three groups (HB-E vs. LB-E, HB-G1 vs. LB-G1, HB-G2 vs. LB-G2), including 4014 downregulated and 3184 upregulated DEGs. Additionally, 221 DEGs were commonly identified in all three groups, accounting for approximately 3.09% of the total DEGs. These DEGs were identified, annotated and classified. A significant number of DEGs were related to hormone metabolism, hormone signal transduction, and starch and sucrose metabolism. In addition, 45, 22 and 9 DEGs involved in hormone metabolic pathways and 67, 22 and 19 DEGs involved in hormone signal transduction pathwayspathway were identified in HB-E vs. LB-E, HB-G1 vs. LB-G1, and HB-G2 vs. LB-G2, respectively, suggesting that endogenous hormones are the primary factors influencing cotton axillary bud growth. Hormone and soluble sugar content measurements revealed that mZ571 exhibited higher concentrations of zeatin, gibberellins and soluble sugar in all three stages, which confirmed that these hormone metabolism-, hormone signal transduction- and starch metabolism-related genes showed interaction effects contributing to the divergence of axillary bud growth between mZ571 and Z571.

CONCLUSIONS

Our results confirmed the importance of endogenous hormones and sugars in the development of axillary buds, and we found that mZ571 plants, with a high-budding phenotype of axillary buds, exhibited higher endogenous hormone and sugar concentrations. Overall, we present a model for the emergence and development of cotton axillary buds that provides insights into the complexity and dynamic nature of the regulatory network during axillary bud emergence and development.

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.

Red to Far-Red Light Ratio Modulates Hormonal and Genetic Control of Axillary bud Outgrowth in Chrysanthemum (Dendranthema grandiflorum 'Jinba')

Single-flower cut Chrysanthemum (Dendranthema grandiflorum 'Jinba') holds a unique status in global floriculture industry. However, the extensive axillary bud outgrowth presents a major drawback. Shade is an environment cue that inhibits shoot branching. Present study was aimed at investigating the effect of ratio of red to far-red light (R:FR) in regulating the lateral bud outgrowth of Chrysanthemum and the detailed mechanism. Results showed that the fate of axillary buds at specific positions in stem exhibited difference in response to R:FR. Decreasing R:FR resulted in elevation of abscisic acid (ABA) accumulation in axillary buds. Expression of ABA, indole-3-acetic acid (IAA) and strigolactones (SL) -related metabolism and signal transduction genes was significantly changed in response to low R:FR. In addition, low R:FR caused the re-distribution of sucrose across the whole plant, driving more sucrose towards bottom buds. Our results indicate that low R:FR not always inhibits bud outgrowth, rather its influence depends on the bud position in the stem. ABA, SL and auxin pathways were involved in the process. Interestingly, sucrose also appears to be involved in the process which is necessary to pay attention in the further studies. The present study also lays the foundation for developing methods to regulate axillary bud outgrowth in Chrysanthemum.

The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop

Strigolactones (SLs) are well known for their role in repressing shoot branching. In pea, increased transcript levels of SL biosynthesis genes are observed in stems of highly branched SL deficient (ramosus1 (rms1) and rms5) and SL response (rms3 and rms4) mutants indicative of negative feedback control. In contrast, the highly branched rms2 mutant has reduced transcript levels of SL biosynthesis genes. Grafting studies and hormone quantification led to a model where RMS2 mediates a shoot-to-root feedback signal that regulates both SL biosynthesis gene transcript levels and xylem sap levels of cytokinin exported from roots. Here we cloned RMS2 using synteny with Medicago truncatula and demonstrated that it encodes a putative auxin receptor of the AFB4/5 clade. Phenotypes similar to rms2 were found in Arabidopsis afb4/5 mutants, including increased shoot branching, low expression of SL biosynthesis genes and high auxin levels in stems. Moreover, afb4/5 and rms2 display a specific resistance to the herbicide picloram. Yeast-two-hybrid experiments supported the hypothesis that the RMS2 protein functions as an auxin receptor. SL root feeding using hydroponics repressed auxin levels in stems and down-regulated transcript levels of auxin biosynthesis genes within one hour. This auxin down-regulation was also observed in plants treated with the polar auxin transport inhibitor NPA. Together these data suggest a homeostatic feedback loop in which auxin up-regulates SL synthesis in an RMS2-dependent manner and SL down-regulates auxin synthesis in an RMS3 and RMS4-dependent manner.

Understanding and engineering plant form

A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

The ratio of red light to far red light alters Arabidopsis axillary bud growth and abscisic acid signalling before stem auxin changes

Arabidopsis thaliana shoot branching is inhibited by a low red light to far red light ratio (R:FR, an indicator of competition), and by loss of phytochrome B function. Prior studies have shown that phytochrome B deficiency suppresses bud growth by elevating systemic auxin signalling, and that increasing the R:FR promotes the growth of buds suppressed by low R:FR by inhibiting bud abscisic acid (ABA) accumulation and signalling. Here, systemic auxin signalling and bud ABA signalling were examined in the context of rapid bud responses to an increased R:FR. Increasing the R:FR promoted the growth of buds inhibited by a low R:FR within 6 h. Relative to a low R:FR, bud ABA accumulation and signalling in plants given a high R:FR showed a sustained decline within 3 h, prior to increased growth. Main stem auxin levels and signalling showed a weak, transient response. Systemic effects and those localised to the bud were further examined by decapitating plants maintained either under a low R:FR or provided with a high R:FR. Increasing the R:FR promoted bud growth before decapitation, but decapitated plants eventually formed longer branches. The data suggest that rapid responses to an increased R:FR may be mediated by changes in bud ABA physiology, although systemic auxin signalling is necessary for sustained bud repression under a low R:FR.

Strigolactone Inhibition of Branching Independent of Polar Auxin Transport

The outgrowth of axillary buds into branches is regulated systemically via plant hormones and the demand of growing shoot tips for sugars. The plant hormone auxin is thought to act via two mechanisms. One mechanism involves auxin regulation of systemic signals, cytokinins and strigolactones, which can move into axillary buds. The other involves suppression of auxin transport/canalization from axillary buds into the main stem and is enhanced by a low sink for auxin in the stem. In this theory, the relative ability of the buds and stem to transport auxin controls bud outgrowth. Here, we evaluate whether auxin transport is required or regulated during bud outgrowth in pea (Pisum sativum). The profound, systemic, and long-term effects of the auxin transport inhibitor N-1-naphthylphthalamic acid had very little inhibitory effect on bud outgrowth in strigolactone-deficient mutants. Strigolactones can also inhibit bud outgrowth in N-1-naphthylphthalamic acid-treated shoots that have greatly diminished auxin transport. Moreover, strigolactones can inhibit bud outgrowth despite a much diminished auxin supply in in vitro or decapitated plants. These findings demonstrate that auxin sink strength in the stem is not important for bud outgrowth in pea. Consistent with alternative mechanisms of auxin regulation of systemic signals, enhanced auxin biosynthesis in Arabidopsis (Arabidopsis thaliana) can suppress branching in yucca1D plants compared with wild-type plants, but has no effect on bud outgrowth in a strigolactone-deficient mutant background.

Regulation of correlative inhibition of axillary bud outgrowth by basal branches varies with growth stage in Trifolium repens

In Trifolium repens the decline in bud outgrowth that occurs with distance from basal root systems is due to correlative inhibition by the first-formed basal branches. The apical and axillary buds on these basal branches are the source of the inhibitory effect, but their mode of action is unclear. Inhibition might occur via basal branches being a sink for xylem-transported branching stimulants or alternatively by providing a source of inhibitory signals, or by both mechanisms. To distinguish between these mechanisms, four experiments were conducted on plants varying in initial growth stage from 10 to 19 nodes along their main stems to determine any variation in the relative importance of the operative mechanisms of correlative inhibition. Inhibitory signal exported into the main stem, detected as a branching response to girdling of basal branches, was relatively more significant in smaller (initially with 10-15 nodes on the main stem) than in larger (>19 nodes on main stem) plants. This signal was shown not to involve auxin fluxes, and is unidentified. However, across all stages of growth, the predominant mechanism driving correlative inhibition was the action of axillary and apical buds of basal branches as sinks for the stimulatory signal. This study indicates that the relative importance of the mechanisms regulating bud outgrowth in T. repens varies with growth stage and that, during intermediate stages, regulation has some similarity to that in Pisum.

Shoot branching in response to nodal roots is mimicked by application of exogenous cytokinin in Trifolium repens

In nodally-rooting prostrate herbs the outgrowth of shoot axillary buds is highly influenced by the supply of a branch-promoting signal exported from nodal roots to the shoot. The aim of this study was to establish whether cytokinin could be a candidate for the positive component within this net root stimulus (NRS). The approach taken was based on the notion that should cytokinin be the activating signal, then the effects on bud outgrowth induced by exogenous supply of cytokinin (6-benzylaminopurine (BAP)) to plants should largely mimic the responses observed when experimental manipulations alter intra-plant supply of NRS. In Trifolium repens experimental results consistently indicated that supply of BAP into the stem vasculature induced responses mimicking those induced by manipulation of NRS supply: it induced the outgrowth of a similar number of distal axillary buds, activated buds to a similar extent, had similar properties of transport along stems, induced a similar dose dependent response in distal buds and also had the ability to induce bud outgrowth in P-deficient plants. These findings indicate a requirement for further detailed hormonal analytical work to confirm this result and identify the nature of the cytokinin(s) involved in the NRS signalling pathway.

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.

Conditional Auxin Response and Differential Cytokinin Profiles in Shoot Branching Mutants

Strigolactone (SL), auxin, and cytokinin (CK) are hormones that interact to regulate shoot branching. For example, several ramosus (rms) branching mutants in pea (Pisum sativum) have SL defects, perturbed xylem CK levels, and diminished responses to auxin in shoot decapitation assays. In contrast with the last of these characteristics, we discovered that buds on isolated nodes (explants) of rms plants instead respond normally to auxin. We hypothesized that the presence or absence of attached roots would result in transcriptional and hormonal differences in buds and subtending stem tissues, and might underlie the differential auxin response. However, decapitated plants and explants both showed similar up-regulation of CK biosynthesis genes, increased CK levels, and down-regulation of auxin transport genes. Moreover, auxin application counteracted these trends, regardless of the effectiveness of auxin at inhibiting bud growth. Multivariate analysis revealed that stem transcript and CK changes were largely associated with decapitation and/or root removal and auxin response, whereas bud transcript profiles related more to SL defects. CK clustering profiles were indicative of additional zeatin-type CKs in decapitated stems being supplied by roots and thus promoting bud growth in SL-deficient genotypes even in the presence of added auxin. This difference in CK content may explain why rms buds on explants respond better to auxin than those on decapitated plants. We further conclude that rapid changes in CK status in stems are auxin dependent but largely SL independent, suggesting a model in which auxin and CK are dominant regulators of decapitation-induced branching, whereas SLs are more important in intact plants.

Shoot branching in nutrient-limited Trifolium repens is primarily restricted by shortage of root-derived promoter signals

Two experiments were used to test the hypothesis that regulation of axillary bud outgrowth in nutrient-limited Trifolium repens L. (white clover) is primarily via variation in the net supply of root-derived promoter signal rather than via direct nutrient effects or inhibitory influences from apical or basal tissues. In the first experiment, foliar nutrient applications to a non-rooted portion of a nutrient-limited stem increased nutrient content, size of organs and rate of growth in the treated region but branch development remained suppressed, indicating that nutrient supply does not directly regulate branching. The second experiment, using decapitation and basal branch excision treatments, showed that excision of basal branches had a major stimulatory effect on bud outgrowth whereas decapitation of the primary stem had only a minor effect. This indicates dominant and minor roles in branching regulation for, respectively, root-derived promoter signal(s) and inhibitory apical influences (apical dominance), and that any possible influence of the inhibitory strigolactone pathway on bud outgrowth is captured within the net root-derived promoter influence. Thus, the proposed hypothesis was supported by our results. These findings may be relevant for all species within the group of prostrate nodally-rooting clonal herbs.

Impacts of light and temperature on shoot branching gradient and expression of strigolactone synthesis and signalling genes in rose

Light and temperature are two environmental factors that deeply affect bud outgrowth. However, little is known about their impact on the bud burst gradient along a stem and their interactions with the molecular mechanisms of bud burst control. We investigated this question in two acrotonic rose cultivars. We demonstrated that the darkening of distal buds or exposure to cold (5 °C) prior to transfer to mild temperatures (20 °C) both repress acrotony, allowing the burst of quiescent medial and proximal buds. We sequenced the strigolactone pathway MAX-homologous genes in rose and studied their expression in buds and internodes along the stem. Only expressions of RwMAX1, RwMAX2 and RwMAX4 were detected. Darkening of the distal part of the shoot triggered a strong increase of RwMAX2 expression in darkened buds and bark-phloem samples, whereas it suppressed the acropetal gradient of the expression of RwMAX1 observed in stems fully exposed to light. Cold treatment induced an acropetal gradient of expression of RwMAX1 in internodes and of RwMAX2 in buds along the stem. Our results suggest that the bud burst gradient along the stem cannot be explained by a gradient of expression of RwMAX genes but rather by their local level of expression at each individual position.

Differential bud activation by a net positive root signal explains branching phenotype in prostrate clonal herbs: a model

Regulation of branching within perennial prostrate clonal herbs differs from the annual orthotropic species, Arabidopsis and pea, as the dominant signal transported from roots is a branching promoter, not an inhibitor. Trifolium repens, an exemplar of such prostrate species, was used to investigate the interaction between roots and branch development. This study tests whether or not current knowledge when synthesized into a predictive model is sufficient to simulate the branching pattern developing on the shoot distal to a basal root. The major concepts underpinning the model are: (i) bud outgrowth (activation) is stimulated in a dose-dependent manner by branching promoter signals from roots, (ii) the distribution of this net root stimulus (NRS) is uniform throughout the shoot system distal to the basal root but declines geometrically in intensity upon continued enlargement of this shoot system, and (iii) each bud has an outgrowth potential, equal to the activation level of the apical bud in which it forms, that moderates its response to NRS. The validity of these concepts was further tested by running simulations of the branching of a phylogenetically-distanced prostrate perennial monocotyledonous species, Tradescantia fluminensis. For both species the model reasonably accounted for the observed pattern of branching. The outgrowth potential of buds plays an important role in limiting the number of hierarchies of branching that can develop on a plant. In conclusion, for both species, the model accounted for the major factors involved in the correlative regulation of branching and is possibly also pertinent for all prostrate clonal species.

Strigolactones stimulate internode elongation independently of gibberellins

Strigolactone (SL) mutants in diverse species show reduced stature in addition to their extensive branching. Here, we show that this dwarfism in pea (Pisum sativum) is not attributable to the strong branching of the mutants. The continuous supply of the synthetic SL GR24 via the root system using hydroponics can restore internode length of the SL-deficient rms1 mutant but not of the SL-response rms4 mutant, indicating that SLs stimulate internode elongation via RMS4. Cytological analysis of internode epidermal cells indicates that SLs control cell number but not cell length, suggesting that SL may affect stem elongation by stimulating cell division. Consequently, SLs can repress (in axillary buds) or promote (in the stem) cell division in a tissue-dependent manner. Because gibberellins (GAs) increase internode length by affecting both cell division and cell length, we tested if SLs stimulate internode elongation by affecting GA metabolism or signaling. Genetic analyses using SL-deficient and GA-deficient or DELLA-deficient double mutants, together with molecular and physiological approaches, suggest that SLs act independently from GAs to stimulate internode elongation.

The role of the potato (Solanum tuberosum) CCD8 gene in stolon and tuber development

· Strigolactones (SLs) are a class of phytohormones controlling shoot branching. In potato (Solanum tuberosum), tubers develop from underground stolons, diageotropic stems which originate from basal stem nodes. As the degree of stolon branching influences the number and size distribution of tubers, it was considered timely to investigate the effects of SL production on potato development and tuber life cycle. · Transgenic potato plants were generated in which the CAROTENOID CLEAVAGE DIOXYGENASE8 (CCD8) gene, key in the SL biosynthetic pathway, was silenced by RNA interference (RNAi). · The resulting CCD8-RNAi potato plants showed significantly more lateral and main branches than control plants, reduced stolon formation, together with a dwarfing phenotype and a lack of flowering in the most severely affected lines. New tubers were formed from sessile buds of the mother tubers. The apical buds of newly formed transgenic tubers grew out as shoots when exposed to light. In addition, we found that CCD8 transcript levels were rapidly downregulated in tuber buds by the application of sprout-inducing treatments. · These results suggest that SLs could have an effect, solely or in combination with other phytohormones, in the morphology of potato plants and also in controlling stolon development and maintaining tuber dormancy.

Crossing paths: cytokinin signalling and crosstalk

Cytokinins are a major class of plant hormones that are involved in various aspects of plant development, ranging from organ formation and apical dominance to leaf senescence. Cytokinin and auxin have long been known to interact antagonistically, and more recent studies have shown that cytokinins also interact with other plant hormones to regulate plant development. A growing body of research has begun to elucidate the molecular and genetic underpinnings of this extensive crosstalk. The rich interconnections between the synthesis, perception and transport networks of these plant hormones provide a wide range of opportunities for them to modulate, amplify or buffer one another. Here, we review this exciting and rapidly growing area of cytokinin research.

Roles of DgBRC1 in regulation of lateral branching in chrysanthemum (Dendranthema ×grandiflora cv. Jinba)

The diverse plasticity of plant architecture is largely determined by shoot branching. Shoot branching is an event regulated by multiple environmental, developmental and hormonal stimuli through triggering lateral bud response. After perceiving these signals, the lateral buds will respond and make a decision on whether to grow out. TCP transcriptional factors, BRC1/TB1/FC1, were previously proven to be involved in local inhibition of shoot branching in Arabidopsis, pea, tomato, maize and rice. To investigate the function of BRC1, we isolated the BRC1 homolog from chrysanthemum. There were two transcripts of DgBRC1 coming from two alleles in one locus, both of which complemented the multiple branches phenotype of Arabidopsis brc1-1, indicating that both are functionally conserved. DgBRC1 was mainly expressed in dormant axillary buds, and down-regulated at the bud activation stage, and up-regulated by higher planting densities. DgBRC1 transcripts could respond to apical auxin supply and polar auxin transport. Moreover, we found that the acropetal cytokinin stream promoted branch outgrowth whether or not apical auxin was present. Basipetal cytokinin promoted outgrowth of branches in the absence of apical auxin, while strengthening the inhibitory effects on lower buds in the presence of apical auxin. The influence of auxin and strigolactons (SLs) on the production of cytokinin was investigated, we found that auxin locally down-regulated biosynthesis of cytokinin in nodes, SLs also down-regulated the biosynthesis of cytokinin, the interactions among these phytohormones need further investigation.

Dynamics of strigolactone function and shoot branching responses in Pisum sativum

Strigolactones (SLs), or their metabolites, were recently identified as endogenous inhibitors of shoot branching. However, certain key features and dynamics of SL action remained to be physiologically characterized. Here we show that successive direct application of SL to axillary buds at every node along the stem can fully inhibit branching. The SL inhibition of early outgrowth did not require inhibitory signals from other growing buds or the shoot tip. In addition to this very early or initial suppression of outgrowth, we also found SL to be effective, up to a point, at moderating the continuing growth of axillary branches. The effectiveness of SL at affecting bud and branch growth correlated with the ability of SL to regulate expression of PsBRC1. PsBRC1 is a transcription factor that is expressed strongly in axillary buds and is required for SL inhibition of shoot branching. Consistent with a dynamic role of the hormone, SL inhibition of bud growth did not prevent buds from later responding to a decapitation treatment, even though SL treatment immediately after decapitation inhibits the outgrowth response. Also, as expected from the hypothesized branching control network in plants, treatment of exogenous SL caused feedback down-regulation of SL biosynthesis genes within 2 h. Altogether, these results reveal new insights into the dynamics of SL function and support the premise that SLs or SL-derived metabolites function dynamically as a shoot branching hormone and that they act directly in axillary buds.

The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1 in the control of plant development by strigolactones

Strigolactones (SLs) are carotenoid-derived plant hormones that regulate shoot branching, secondary growth, root development, and responses to soil phosphate. In Arabidopsis (Arabidopsis thaliana), SL biosynthesis requires the sequential action of two carotenoid cleavage dioxygenases, MORE AXILLARY GROWTH3 (MAX3) and MAX4, followed by a cytochrome P450, MAX1. In rice (Oryza sativa), the plastid-localized protein DWARF27 (OsD27) is also necessary for SL biosynthesis, but the equivalent gene in Arabidopsis has not been identified. Here, we use phylogenetic analysis of D27-like sequences from photosynthetic organisms to identify AtD27, the likely Arabidopsis ortholog of OsD27. Using reverse genetics, we show that AtD27 is required for the inhibition of secondary bud outgrowth and that exogenous application of the synthetic SL GR24 can rescue the increased branching phenotype of an Atd27 mutant. Furthermore, we use grafting to demonstrate that AtD27 operates on a nonmobile precursor upstream of MAX1 in the SL biosynthesis pathway. Consistent with the plastid localization of OsD27, we also show that AtD27 possesses a functional plastid transit peptide. We demonstrate that AtD27 transcripts are subject to both local feedback and auxin-dependent signals, albeit to a lesser extent than MAX3 and MAX4, suggesting that early steps in SL biosynthesis are coregulated at the transcriptional level. By identifying an additional component of the canonical SL biosynthesis pathway in Arabidopsis, we provide a new tool to investigate the regulation of shoot branching and other SL-dependent developmental processes.

The pea TCP transcription factor PsBRC1 acts downstream of Strigolactones to control shoot branching

The function of PsBRC1, the pea (Pisum sativum) homolog of the maize (Zea mays) TEOSINTE BRANCHED1 and the Arabidopsis (Arabidopsis thaliana) BRANCHED1 (AtBRC1) genes, was investigated. The pea Psbrc1 mutant displays an increased shoot-branching phenotype, is able to synthesize strigolactone (SL), and does not respond to SL application. The level of pleiotropy of the SL-deficient ramosus1 (rms1) mutant is higher than in the Psbrc1 mutant, rms1 exhibiting a relatively dwarf phenotype and more extensive branching at upper nodes. The PsBRC1 gene is mostly expressed in the axillary bud and is transcriptionally up-regulated by direct application of the synthetic SL GR24 and down-regulated by the cytokinin (CK) 6-benzylaminopurine. The results suggest that PsBRC1 may have a role in integrating SL and CK signals and that SLs act directly within the bud to regulate its outgrowth. However, the Psbrc1 mutant responds to 6-benzylaminopurine application and decapitation by increasing axillary bud length, implicating a PsBRC1-independent component of the CK response in sustained bud growth. In contrast to other SL-related mutants, the Psbrc1 mutation does not cause a decrease in the CK zeatin riboside in the xylem sap or a strong increase in RMS1 transcript levels, suggesting that the RMS2-dependent feedback is not activated in this mutant. Surprisingly, the double rms1 Psbrc1 mutant displays a strong increase in numbers of branches at cotyledonary nodes, whereas branching at upper nodes is not significantly higher than the branching in rms1. This phenotype indicates a localized regulation of branching at these nodes specific to pea.

Antagonistic action of strigolactone and cytokinin in bud outgrowth control

Cytokinin (CK) has long been implicated as a promoter of bud outgrowth in plants, but exactly how this is achieved in coordination with other plant hormones is unclear. The recent discovery of strigolactones (SLs) as the long-sought branch-inhibiting hormone allowed us to test how CK and SL coordinately regulate bud outgrowth in pea (Pisum sativum). We found that SL-deficient plants are more sensitive to stimulation of bud growth by low concentrations of locally applied CK than wild-type plants. Furthermore, in contrast with SL mutant plants, buds of wild-type plants are almost completely resistant to stimulation by CK supplied to the vasculature. Regardless of whether the exogenous hormones were supplied locally or to the xylem stream, SL and CK acted antagonistically on bud outgrowth. These data suggest that SLs do not affect the delivery of CK to axillary buds and vice versa. Rather, these data combined with dose-response experiments suggest that SLs and CK can act directly in buds to control their outgrowth. These hormones may converge at a common point in the bud outgrowth regulatory pathway. The expression of pea BRANCHED1, a TCP transcription factor expressed strongly in buds and thought to act downstream of SLs in shoot branching, is regulated by CK and SL without a requirement for protein synthesis and in a manner that correlates with observed bud growth responses.

Towards aspect-oriented functional--structural plant modelling

BACKGROUND AND AIMS

Functional-structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty.

METHODS

The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module.

KEY RESULTS

The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes.

CONCLUSIONS

This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further extended into an aspect-oriented programming language for FSPMs.

Smoke signals and seed dormancy: where next for MAX2?

The Arabidopsis thaliana F-box protein MAX2 has been discovered in four separate genetic screens, indicating that it has roles in leaf senescence, seedling photosensitivity, shoot outgrowth, and seed germination. Both strigolactones and karrikins can regulate A. thaliana seed germination and seedling photomorphogenesis in a MAX2-dependent manner, but only strigolactones inhibit shoot branching. How MAX2 mediates specific responses to both classes of structurally-related signals, and the origin of its dual role remains unknown. The moss Physcomitrella patens utilizes strigolactones and MAX2 orthologs are present across the land plants, suggesting that this signaling system could have an ancient origin. The seed of parasitic Orobanchaceae species germinate preferentially in response to strigolactones over karrikins, and putative Orobanchaceae MAX2 orthologs form a sub-clade distinct from those of other dicots. These observations suggest that lineage-specific evolution of MAX2 may have given rise to specialized responses to these signaling molecules. 

Understanding shoot branching by modelling form and function

Shoot branching plays a pivotal role in the development of the aboveground plant structure. Therefore, to understand branching in relation to the environment, it is not only necessary to integrate the knowledge on mechanisms that regulate branching at multiple levels of biological organisation, but also to include plant structure explicitly. To this end, we propose the application of an established methodology called functional-structural plant modelling.

Signal integration in the control of shoot branching

Shoot branching is a highly plastic developmental process in which axillary buds are formed in the axil of each leaf and may subsequently be activated to give branches. Three classes of plant hormones, auxins, cytokinins and strigolactones (or strigolactone derivatives) are central to the control of bud activation. These hormones move throughout the plant forming a network of systemic signals. The past decade brought great progress in understanding the mechanisms of shoot branching control. Biological and computational studies have led to the proposal of two models, the auxin transport canalization-based model and the second messenger model, which provide mechanistic explanations for apical dominance.

F-box protein MAX2 has dual roles in karrikin and strigolactone signaling in Arabidopsis thaliana

Smoke is an important abiotic cue for plant regeneration in postfire landscapes. Karrikins are a class of compounds discovered in smoke that promote seed germination and influence early development of many plants by an unknown mechanism. A genetic screen for karrikin-insensitive mutants in Arabidopsis thaliana revealed that karrikin signaling requires the F-box protein MAX2, which also mediates responses to the structurally-related strigolactone family of phytohormones. Karrikins and the synthetic strigolactone GR24 trigger similar effects on seed germination, seedling photomorphogenesis, and expression of a small set of genes during these developmental stages. Karrikins also repress MAX4 and IAA1 transcripts, which show negative feedback regulation by strigolactone. We demonstrate that all of these common responses are abolished in max2 mutants. Unlike strigolactones, however, karrikins do not inhibit shoot branching in Arabidopsis or pea, indicating that plants can distinguish between these signals. These results suggest that a MAX2-dependent signal transduction mechanism was adapted to mediate responses to two chemical cues with distinct roles in plant ecology and development.

Seven things we think we know about auxin transport

Polar transport of the phytohormone auxin and the establishment of localized auxin maxima regulate embryonic development, stem cell maintenance, root and shoot architecture, and tropic growth responses. The past decade has been marked by dramatic progress in efforts to elucidate the complex mechanisms by which auxin transport regulates plant growth. As the understanding of auxin transport regulation has been increasingly elaborated, it has become clear that this process is involved in almost all plant growth and environmental responses in some way. However, we still lack information about some basic aspects of this fundamental regulatory mechanism. In this review, we present what we know (or what we think we know) and what we do not know about seven auxin-regulated processes. We discuss the role of auxin transport in gravitropism in primary and lateral roots, phototropism, shoot branching, leaf expansion, and venation. We also discuss the auxin reflux/fountain model at the root tip, flavonoid modulation of auxin transport processes, and outstanding aspects of post-translational regulation of auxin transporters. This discussion is not meant to be exhaustive, but highlights areas in which generally held assumptions require more substantive validation.

VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development

Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.

Existing branches correlatively inhibit further branching in Trifolium repens: possible mechanisms

In Trifolium repens removal of any number of existing branches distal to a nodal root stimulates development of axillary buds further along the stem such that the complement of branches distal to a nodal root remains constant. This study aimed to assess possible mechanisms by which existing branches correlatively inhibit the outgrowth of axillary buds distal to them. Treatments were applied to basal branches to evaluate the roles of three postulated inhibitory mechanisms: (I) the transport of a phloem-mobile inhibitory feedback signal from branches into the main stem; (II) the polar flow of auxin from branches into the main stem acting to limit further branch development; or (III) the basal branches functioning as sinks for a net root-derived stimulatory signal (NRS). Results showed that transport of auxin, or of a non-auxin phloem-mobile signal, from basal branches did not influence regulation of correlative inhibition and were consistent with the possibility that the intra-plant distribution of NRS could be involved in the correlative inhibition of distal buds by basal branches. This study supports existing evidence that regulation of branching in T. repens is dominated by a root-derived stimulatory signal, initially distributed via the xylem, the characterization of which will progress the generic understanding of branching regulation.

Strigolactones enhance competition between shoot branches by dampening auxin transport

Strigolactones (SLs), or their derivatives, were recently demonstrated to act as endogenous shoot branching inhibitors, but their biosynthesis and mechanism of action are poorly understood. Here we show that the branching phenotype of mutants in the Arabidopsis P450 family member, MAX1, can be fully rescued by strigolactone addition, suggesting that MAX1 acts in SL synthesis. We demonstrate that SLs modulate polar auxin transport to control branching and that both the synthetic SL GR24 and endogenous SL synthesis significantly reduce the basipetal transport of a second branch-regulating hormone, auxin. Importantly, GR24 inhibits branching only in the presence of auxin in the main stem, and enhances competition between two branches on a common stem. Together, these results support two current hypotheses: that auxin moving down the main stem inhibits branch activity by preventing the establishment of auxin transport out of axillary branches; and that SLs act by dampening auxin transport, thus enhancing competition between branches.

FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice

Recent studies of highly branched mutants of pea, Arabidopsis and rice have demonstrated that strigolactones (SLs) act as hormones that inhibit shoot branching. The identification of genes that work downstream of SLs is required for a better understanding of how SLs control the growth of axillary buds. We found that the increased tillering phenotype of fine culm1 (fc1) mutants of rice is not rescued by the application of 1 microM GR24, a synthetic SL analog. Treatment with a high concentration of GR24 (10 microM) causes suppression of tiller growth in wild-type plants, but is not effective on fc1 mutants, implying that proper FC1 functioning is required for SLs to inhibit bud growth. Overexpression of FC1 partially rescued d3-2 defects in the tiller growth and plant height. An in situ hybridization analysis showed that FC1 mRNA accumulates in axillary buds, the shoot apical meristem, young leaves, vascular tissues and the tips of crown roots. FC1 mRNA expression was not significantly affected by GR24, suggesting that transcriptional induction may not be the mechanism by which SLs affect FC1 functioning. On the other hand, the expression level of FC1 is negatively regulated by cytokinin treatment. We propose that FC1 acts as an integrator of multiple signaling pathways and is essential to the fine-tuning of shoot branching in rice.

Strigolactones negatively regulate mesocotyl elongation in rice during germination and growth in darkness

Strigolactones (SLs) are newly discovered plant hormones that regulate plant growth and development including shoot branching. They also stimulate symbiosis with arbuscular mycorrhizal fungi. Rice has at least three genes that are involved in SL synthesis (D10, D17/HTD1 and D27) and at least two genes that are involved in SL signaling (D3) and SL signaling or downstream metabolism (D14/D88/HTD2). We observed that mesocotyl elongation in darkness was greater in rice mutants defective in these genes than in the wild type. Exogenous application of a synthetic SL analog, GR24, rescued the phenotype of mesocotyl elongation in the SL-deficient mutants, d10-1, d17-1 and d27-1, in a dose-dependent manner, but did not affect mesocotyl lengths of the SL-insensitive mutants, d3-1 and d14-1. No significant differences in cell length were found between the d mutants and the wild type, except for some cells on the lower half of the d3-1 mesocotyl that were shortened. On the other hand, the number of cells in the mesocotyls was 3- to 6-fold greater in the d mutants than in the wild type. Treatment with GR24 reduced the number of cells in the d10-1 mesocotyl to the wild-type level, but did not affect the number of cells in the d3-1 and d14-1 mesocotyls. These findings indicate that SLs negatively regulate cell division, but not cell elongation, in the mesocotyl during germination and growth of rice in darkness.

Adapting APSIM to model the physiology and genetics of complex adaptive traits in field crops

Progress in molecular plant breeding is limited by the ability to predict plant phenotype based on its genotype, especially for complex adaptive traits. Suitably constructed crop growth and development models have the potential to bridge this predictability gap. A generic cereal crop growth and development model is outlined here. It is designed to exhibit reliable predictive skill at the crop level while also introducing sufficient physiological rigour for complex phenotypic responses to become emergent properties of the model dynamics. The approach quantifies capture and use of radiation, water, and nitrogen within a framework that predicts the realized growth of major organs based on their potential and whether the supply of carbohydrate and nitrogen can satisfy that potential. The model builds on existing approaches within the APSIM software platform. Experiments on diverse genotypes of sorghum that underpin the development and testing of the adapted crop model are detailed. Genotypes differing in height were found to differ in biomass partitioning among organs and a tall hybrid had significantly increased radiation use efficiency: a novel finding in sorghum. Introducing these genetic effects associated with plant height into the model generated emergent simulated phenotypic differences in green leaf area retention during grain filling via effects associated with nitrogen dynamics. The relevance to plant breeding of this capability in complex trait dissection and simulation is discussed.

Computational complementation: a modelling approach to study signalling mechanisms during legume autoregulation of nodulation

Autoregulation of nodulation (AON) is a long-distance signalling regulatory system maintaining the balance of symbiotic nodulation in legume plants. However, the intricacy of internal signalling and absence of flux and biochemical data, are a bottleneck for investigation of AON. To address this, a new computational modelling approach called "Computational Complementation" has been developed. The main idea is to use functional-structural modelling to complement the deficiency of an empirical model of a loss-of-function (non-AON) mutant with hypothetical AON mechanisms. If computational complementation demonstrates a phenotype similar to the wild-type plant, the signalling hypothesis would be suggested as "reasonable". Our initial case for application of this approach was to test whether or not wild-type soybean cotyledons provide the shoot-derived inhibitor (SDI) to regulate nodule progression. We predicted by computational complementation that the cotyledon is part of the shoot in terms of AON and that it produces the SDI signal, a result that was confirmed by reciprocal epicotyl-and-hypocotyl grafting in a real-plant experiment. This application demonstrates the feasibility of computational complementation and shows its usefulness for applications where real-plant experimentation is either difficult or impossible.