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1.  The Making of a Compound Inflorescence in Tomato and Related Nightshades 
PLoS Biology  2008;6(11):e288.
Variation in the branching of plant inflorescences determines flower number and, consequently, reproductive success and crop yield. Nightshade (Solanaceae) species are models for a widespread, yet poorly understood, program of eudicot growth, where short side branches are initiated upon floral termination. This “sympodial” program produces the few-flowered tomato inflorescence, but the classical mutants compound inflorescence (s) and anantha (an) are highly branched, and s bears hundreds of flowers. Here we show that S and AN, which encode a homeobox transcription factor and an F-box protein, respectively, control inflorescence architecture by promoting successive stages in the progression of an inflorescence meristem to floral specification. S and AN are sequentially expressed during this gradual phase transition, and the loss of either gene delays flower formation, resulting in additional branching. Independently arisen alleles of s account for inflorescence variation among domesticated tomatoes, and an stimulates branching in pepper plants that normally have solitary flowers. Our results suggest that variation of Solanaceae inflorescences is modulated through temporal changes in the acquisition of floral fate, providing a flexible evolutionary mechanism to elaborate sympodial inflorescence shoots.
Author Summary
Among the most distinguishing features of plants are the flower-bearing shoots, called inflorescences. Despite a solid understanding of flower development, the molecular mechanisms that control inflorescence architecture remain obscure. We have explored this question in tomato, where mutations in two genes, ANANTHA (AN) and COMPOUND INFLORESCENCE (S), transform the well-known tomato “vine” into a highly branched structure with hundreds of flowers. We find that AN encodes an F-box protein ortholog of a gene called UNUSUAL FLORAL ORGANS that controls the identity of floral organs (petals, sepals, and so on), whereas S encodes a transcription factor related to a gene called WUSCHEL HOMEOBOX 9 that is involved in patterning the embryo within the plant seed. (F-box proteins are known for marking other proteins for degradation, but they can also function in hormone regulation and transcriptional activation) Interestingly, these genes have little or no effect on branching in inflorescences that grow continuously (so-called “indeterminate” shoots), as in Arabidopsis. However, we find that transient sequential expression of S followed by AN promotes branch termination and flower formation in plants where meristem growth ends with inflorescence and flower production (“determinate” shoots). We show that mutant alleles of s dramatically increase branch and flower number and have probably been selected for by breeders during modern cultivation. Moreover, the single-flower inflorescence of pepper (a species related to tomato, within the same Solanaceae family) can be converted to a compound inflorescence upon mutating its AN ortholog. Our results suggest a new developmental mechanism whereby inflorescence elaboration can be controlled through temporal regulation of floral fate.
Plant flower production is largely determined by the number of inflorescences, the branches produced on flower stems. Two genes identified in tomato reveal a new phase transition that may explain the mechanism of evolution of compound inflorescences in the Solanaceae family.
doi:10.1371/journal.pbio.0060288
PMCID: PMC2586368  PMID: 19018664
2.  Switching from a mechanistic model to a continuous model to study at different scales the effect of vine growth on the dynamic of a powdery mildew epidemic 
Annals of Botany  2010;107(5):885-895.
Background and Aims
Epidemiological simulation models coupling plant growth with the dispersal and disease dynamics of an airborne plant pathogen were devised for a better understanding of host–pathogen dynamic interactions and of the capacity of grapevine development to modify the progress of powdery mildew epidemics.
Methods
The first model is a complex discrete mechanistic model (M-model) that explicitly incorporates the dynamics of host growth and the development and dispersion of the pathogen at the vine stock scale. The second model is a simpler ordinary differential equations (ODEs) compartmental SEIRT model (C-model) handling host growth (foliar surface) and the ontogenic resistance of the leaves. With the M-model various levels of vine development are simulated under three contrasting climatic scenarios and the relationship between host and disease variables are examined at key periods in the epidemic process. The ability of the C-model to retrieve the main dynamics of the disease for a range of vine growth given by the M-model is investigated.
Key Results
The M-model strengthens experimental results observed regarding the effect of the rate of leaf emergence and of the number of leaves at flowering on the severity of the disease. However, it also underlines strong variations of the dynamics of disease depending on the vigour and indirectly on the climatic scenarios. The C-model could be calibrated by using the M-model provided that different parameters before and after shoot topping and for various vigour levels and inoculation time are used. Biologically relevant estimations of the parameters that could be used for its extension to the vineyard scale are obtained.
Conclusions
The M-model is able to generate a wide range of growth scenarios with a strong impact on disease evolution. The C-model is a promising tool to be used at a larger scale.
doi:10.1093/aob/mcq233
PMCID: PMC3077982  PMID: 21127356
Host–pathogen models; mechanistic model; SEIRT model; host growth; powdery mildew; grapevine
3.  Reductions in biomass accumulation, photosynthesis in situ and net carbon balance are the costs of protecting Vitis vinifera ‘Semillon’ grapevines from heat stress with shade covering 
AoB Plants  2011;2011:plr023.
Shade cloth can be used to protect grapevines from high temperatures. However, the resulting low light intensity is shown to reduce photosynthesis, leading to lower carbon allocation to vegetative growth and sugar accumulation. Protection from heat by shading is, therefore, costly for the carbon economy of the vines.
Background and aims
Covering whole vines with shade cloth is used to protect the vines from heat stress, but may have costs on vine productivity through reduced light availability. Our aim was to assess the carbon balance of vines growing with and without shade to quantify the impact of the covering.
Methodology
Whole vines were covered with 70 % shade cloth, and shoot leaf area and leaf, stem and bunch growth were followed over two growing seasons. Photosynthesis was measured in situ in all leaves along selected shoots over the growing season. A carbon balance was constructed from the difference in acquisition of carbon and the sequestration of carbon as biomass across the growing seasons.
Principal results
Shade covering had no initial impact on shoot growth but later reduced leaf growth and later still bunch growth. Stem growth was unaffected. Photosynthetic properties were characteristic of shade leaves, with lower rates and lower light saturation compared with well-exposed leaves. Overall, net photosynthesis was reduced by 40 % by the shade covering and was attributed to the reduced photon flux densities. From the carbon balance, vines were reliant on carbon reserves over 6 weeks after budbreak until current photosynthate increased sufficiently to supply the growth. Shade covering impacted most on biomass accumulation to leaves and bunches at the stage when the vines became autotrophic, consistent with the reduction in carbon acquisition. The markedly high carbon demand by bunches caused a mid-season negative carbon balance, implying that shoots had to draw further on reserves to supply the carbon.
Conclusions
Shade covering over whole grapevines exacerbated the imbalance between the supply of and demand for carbon and greatly reduced vine biomass, especially reproductive allocation. Covering vines with shade cloth to protect the vines from heat events, therefore, had major costs in the carbon economy.
doi:10.1093/aobpla/plr023
PMCID: PMC3176522  PMID: 22476493
4.  A Three-dimensional Statistical Reconstruction Model of Grapevine (Vitis vinifera) Simulating Canopy Structure Variability within and between Cultivar/Training System Pairs 
Annals of Botany  2008;101(8):1167-1184.
Background and Aims
In grapevine, canopy-structure-related variations in light interception and distribution affect productivity, yield and the quality of the harvested product. A simple statistical model for reconstructing three-dimensional (3D) canopy structures for various cultivar–training system (C × T) pairs has been implemented with special attention paid to balance the time required for model parameterization and accuracy of the representations from organ to stand scales. Such an approach particularly aims at overcoming the weak integration of interplant variability using the usual direct 3D measurement methods.
Model
This model is original in combining a turbid-medium-like envelope enclosing the volume occupied by vine shoots with the use of discrete geometric polygons representing leaves randomly located within this volume to represent plant structure. Reconstruction rules were adapted to capture the main determinants of grapevine shoot architecture and their variability. Using a simplified set of parameters, it was possible to describe (1) the 3D path of the main shoot, (2) the volume occupied by the foliage around this path and (3) the orientation of individual leaf surfaces. Model parameterization (estimation of the probability distribution for each parameter) was carried out for eight contrasting C × T pairs.
Key Results and Conclusions
The parameter values obtained in each situation were consistent with our knowledge of grapevine architecture. Quantitative assessments for the generated virtual scenes were carried out at the canopy and plant scales. Light interception efficiency and local variations of light transmittance within and between experimental plots were correctly simulated for all canopies studied. The approach predicted these key ecophysiological variables significantly more accurately than the classical complete digitization method with a limited number of plants. In addition, this model accurately reproduced the characteristics of a wide range of individual digitized plants. Simulated leaf area density and the distribution of light interception among leaves were consistent with measurements. However, at the level of individual organs, the model tended to underestimate light interception.
doi:10.1093/aob/mcm170
PMCID: PMC2710267  PMID: 18202006
Canopy; architecture; hemispherical; picture; light interception; radiative; balance; stochastic; modelling; virtual; plants
5.  Conservation and divergence of four kiwifruit SVP-like MADS-box genes suggest distinct roles in kiwifruit bud dormancy and flowering 
Journal of Experimental Botany  2011;63(2):797-807.
MADS-box genes similar to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been implicated in the regulation of flowering in annual species and bud dormancy in perennial species. Kiwifruit (Actinidia spp.) are woody perennial vines where bud dormancy and out-growth affect flower development. To determine the role of SVP-like genes in dormancy and flowering of kiwifruit, four MADS-box genes with homology to Arabidopsis SVP, designated SVP1, SVP2, SVP3, and SVP4, have been identified and analysed in kiwifruit and functionally characterized in Arabidopsis. Phylogenetic analysis indicate that these genes fall into different sub-clades within the SVP-like gene group, suggesting distinct functions. Expression was generally confined to vegetative tissues, and increased transcript accumulation in shoot buds over the winter period suggests a role for these genes in bud dormancy. Down-regulation before flower differentiation indicate possible roles as floral repressors. Over-expression and complementation studies in Arabidopsis resulted in a range of floral reversion phenotypes arising from interactions with Arabidopsis MADS-box proteins, but only SVP1 and SVP3 were able to complement the svp mutant. These results suggest that the kiwifruit SVP-like genes may have distinct roles during bud dormancy and flowering.
doi:10.1093/jxb/err304
PMCID: PMC3254681  PMID: 22071267
Actinidia species; AGL24; Arabidopsis; budbreak; bud dormancy; flowering; hydrogen cyanamide; kiwifruit; SVP
6.  Identification and characterization of flowering genes in kiwifruit: sequence conservation and role in kiwifruit flower development 
BMC Plant Biology  2011;11:72.
Background
Flower development in kiwifruit (Actinidia spp.) is initiated in the first growing season, when undifferentiated primordia are established in latent shoot buds. These primordia can differentiate into flowers in the second growing season, after the winter dormancy period and upon accumulation of adequate winter chilling. Kiwifruit is an important horticultural crop, yet little is known about the molecular regulation of flower development.
Results
To study kiwifruit flower development, nine MADS-box genes were identified and functionally characterized. Protein sequence alignment, phenotypes obtained upon overexpression in Arabidopsis and expression patterns suggest that the identified genes are required for floral meristem and floral organ specification. Their role during budbreak and flower development was studied. A spontaneous kiwifruit mutant was utilized to correlate the extended expression domains of these flowering genes with abnormal floral development.
Conclusions
This study provides a description of flower development in kiwifruit at the molecular level. It has identified markers for flower development, and candidates for manipulation of kiwifruit growth, phase change and time of flowering. The expression in normal and aberrant flowers provided a model for kiwifruit flower development.
doi:10.1186/1471-2229-11-72
PMCID: PMC3103426  PMID: 21521532
7.  A biophysical model of kiwifruit (Actinidia deliciosa) berry development 
Journal of Experimental Botany  2013;64(18):5473-5483.
A model of kiwifruit berry development is presented, building on the model of Fishman and Génard used for peach fruit. That model has been extended to incorporate a number of important features of kiwifruit growth. First, the kiwifruit berry is attached to the stem through a pedicel/receptacle complex which contributes significantly to the hydraulic resistance between the stem and the fruit, and this resistance changes considerably during the season. Second, much of the carbohydrate in kiwifruit berries is stored as starch until the fruit matures late in the season, when the starch hydrolyses to soluble sugars. This starch storage has a major effect on the osmotic potential of the fruit, so an existing model of kiwifruit starch dynamics was included in the model. Using previously published approaches, we also included elasticity and extended the modelling period to cover both the cell division and cell expansion phases of growth. The resulting model showed close simulation of field observations of fresh weight, dry matter, starch, and soluble solids in kiwifruit. Comparison with continuous measurements of fruit diameter confirmed that elasticity was needed to adequately simulate observed diurnal variation in fruit size. Sensitivity analyses suggested that the model is particularly sensitive to variation in inputs relating to water (stem water potential and the humidity of the air), and to parameters controlling cell expansion (cell wall extensibility). Some limitations in the model structure were identified, suggesting that a revised model including current apoplastic/symplastic concepts needs to be developed.
doi:10.1093/jxb/ert317
PMCID: PMC3871809  PMID: 24123250
Fruit growth model; mass flow; osmotic pressure; pedicel; starch; transport; water.
8.  Floral sesquiterpenes and their synthesis in dioecious kiwifruit 
Plant Signaling & Behavior  2010;5(1):61-63.
Kiwifruit species are vigorously growing dioecious vines that rely on bees and other insects for pollen transfer between spatially separated male and female individuals. Floral volatile terpene cues for insect pollinator attraction were characterized from flowers of the most widely grown and economically important kiwifruit cultivar Actinidia deliciosa ‘Hayward’ and its male pollinator ‘Chieftain’. The sesquiterpenes α-farnesene and germacrene D dominated in all floral tissues and the emission of these compounds was detected throughout the day, with lower levels at night. Two terpene synthase (TPS) genes were isolated from A. deliciosa petals that produced (+)-germacrene D and (E,E)-α-farnesene respectively. Both TPS genes were expressed in the same tissues and at the same times as their corresponding floral volatiles. Here we discuss these results with respect to plant and insect ecology and the evolution and structure of sesquiterpene synthases.
PMCID: PMC2835961  PMID: 20592812
terpene; dioecy; kiwifruit; volatile; ecology; evolution; flower
9.  Ethylene-induced modulation of genes associated with the ethylene signalling pathway in ripening kiwifruit 
Journal of Experimental Botany  2008;59(8):2097-2108.
Gene families associated with the ethylene signal transduction pathway in ripening kiwifruit (Actinidia deliciosa [A. Chev.] C.F. Liang et A.R. Ferguson var. deliciosa cv. Hayward) were isolated from a kiwifruit expressed sequence tag (EST) database, including five ethylene receptor genes, two CTR1-like genes, and an EIN3-like gene AdEIL1. All were differentially expressed among various kiwifruit vine tissues, and none was fruit specific. During fruit development, levels of transcripts of AdERS1a, AdETR3, and the two CTR1-like genes decreased, whereas those of AdERS1b and AdETR2 peaked at 97 d after full bloom. In ripening kiwifruit, there was a diverse response of the ethylene receptor family to internal and external ethylene. AdERS1a, AdETR2, and AdETR3 expression increased at the climacteric stage and transcripts were induced by external ethylene treatment, while AdERS1b showed no response to ethylene. AdETR1 was negatively regulated by internal and external ethylene in ripening fruit. The two CTR1-like genes also had different expression patterns, with AdCTR1 increasing at the climacteric stage and AdCTR2 undergoing little change. 1-Methylcyclopropene treatment prevented the ethylene response of all components, but transient down-regulation was only found with AdETR2 and AdCTR1. Similar gene and ethylene responses were found in both fruit flesh and core tissues. The ethylene-induced down-regulation of AdETR1 suggests that it may have a role in sensing ethylene and transmitting this response to other members of the receptor family, thus activating the signal transduction pathway.
doi:10.1093/jxb/ern067
PMCID: PMC2413272  PMID: 18535296
Actinidia; ethylene receptor; ethylene response; ethylene signal transduction; fruit ripening; gene expression; kiwifruit; 1-MCP
10.  Endogenous cytokinin in developing kiwifruit is implicated in maintaining fruit flesh chlorophyll levels 
Annals of Botany  2013;112(1):57-68.
Background and Aims
Green kiwifruit (Actinidia deliciosa) retain high concentrations of chlorophyll in the fruit flesh, whereas in gold-fleshed kiwifruit (A. chinensis) chlorophyll is degraded to colourless catabolites during fruit development, leaving yellow carotenoids visible. The plant hormone group the cytokinins has been implicated in the delay of senescence, and so the aim of this work was to investigate the link between cytokinin levels in ripening fruit and chlorophyll de-greening.
Methods
The expression of genes related to cytokinin metabolism and signal transduction and the concentration of cytokinin metabolites were measured. The regulation of gene expression was assayed using transient activation of the promoter of STAY-GREEN2 (SGR2) by cytokinin response regulators.
Key Results
While the total amount of cytokinin increased in fruit of both species during maturation and ripening, a high level of expression of two cytokinin biosynthetic gene family members, adenylate isopentenyltransferases, was only detected in green kiwifruit fruit during ripening. Additionally, high levels of O-glucosylated cytokinins were detected only in green kiwifruit, as was the expression of the gene for zeatin O-glucosyltransferase, the enzyme responsible for glucosylating cytokinin into a storage form. Season to season variation in gene expression was seen, and some de-greening of the green kiwifruit fruit occurred in the second season, suggesting environmental effects on the chlorophyll degradation pathway. Two cytokinin-related response regulators, RRA17 and RRB120, showed activity against the promoter of kiwifruit SGR2.
Conclusions
The results show that in kiwifruit, levels of cytokinin increase markedly during fruit ripening, and that cytokinin metabolism is differentially regulated in the fruit of the green and gold species. However, the causal factor(s) associated with the maintenance or loss of chlorophyll in kiwifruit during ripening remains obscure.
doi:10.1093/aob/mct093
PMCID: PMC3690984  PMID: 23644363
Actinidia deliciosa; A. chinensis; chlorophyll degradation; cytokinin; fruit ripening; kiwifruit; STAY-GREEN; transcription factor
11.  Independent Control of Organogenesis and Shoot Tip Abortion are Key Factors to Developmental Plasticity in Kiwifruit (Actinidia) 
Annals of Botany  2007;100(3):471-481.
Background and Aims
In kiwifruit (Actinidia), the number of nodes per shoot is highly variable and is influenced by genotype and environmental conditions. To understand this developmental plasticity, three key processes were studied: organogenesis by the shoot apical meristem during shoot growth; expansion of phytomers; and shoot tip abortion.
Methods
Studies were made of organogenesis and shoot tip abortion using light and scanning electron microscopy. The effect of temperature on shoot growth cessation was investigated using temperature indices over the budbreak period, and patterns of shoot tip abortion were quantified using stochastic modelling.
Key Results
All growing buds began organogenesis before budbreak. During shoot development, the number of phytomers initiated by the shoot apical meristem is correlated with the number of expanding phytomers and the mean internode length. Shoot tip abortion is preceded by growth cessation and is not brought about by the death of the shoot apical meristem, but occurs by tissue necrosis in the sub-apical zone. For most genotypes studied, the probability of shoot tip abortion is higher during expansion of the preformed part of the shoot. Lower temperatures during early growth result in a higher probability of shoot tip abortion.
Conclusions
Organogenesis and shoot tip abortion are controlled independently. All buds have the potential to become long shoots. Conditions that increase early growth rate postpone shoot tip abortion.
doi:10.1093/aob/mcm140
PMCID: PMC2533607  PMID: 17650513
Actinidia; kiwifruit; shoot fate; neoformation; organogenesis; shoot tip abortion; developmental plasticity; temperature
12.  Physiological and proteomic approaches to address the active role of ozone in kiwifruit post-harvest ripening 
Journal of Experimental Botany  2012;63(7):2449-2464.
Post-harvest ozone application has recently been shown to inhibit the onset of senescence symptoms on fleshy fruit and vegetables; however, the exact mechanism of action is yet unknown. To characterize the impact of ozone on the post-harvest performance of kiwifruit (Actinidia deliciosa cv. ‘Hayward’), fruits were cold stored (0 °C, 95% relative humidity) in a commercial ethylene-free room for 1, 3, or 5 months in the absence (control) or presence of ozone (0.3 μl l−1) and subsequently were allowed to ripen at a higher temperature (20 °C), herein defined as the shelf-life period, for up to 12 days. Ozone blocked ethylene production, delayed ripening, and stimulated antioxidant and anti-radical activities of fruits. Proteomic analysis using 1D-SDS-PAGE and mass spectrometry identified 102 kiwifruit proteins during ripening, which are mainly involved in energy, protein metabolism, defence, and cell structure. Ripening induced protein carbonylation in kiwifruit but this effect was depressed by ozone. A set of candidate kiwifruit proteins that are sensitive to carbonylation was also discovered. Overall, the present data indicate that ozone improved kiwifruit post-harvest behaviour, thus providing a first step towards understanding the active role of this molecule in fruit ripening.
doi:10.1093/jxb/err418
PMCID: PMC3346216  PMID: 22268155
Actinidia deliciosa; antioxidants; anti-radical activity; ethylene; ozone; post-harvest storage; protein carbonylation
13.  Towards aspect-oriented functional–structural plant modelling 
Annals of Botany  2011;108(6):1025-1041.
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.
doi:10.1093/aob/mcr121
PMCID: PMC3189837  PMID: 21724653
L-system; aspect-oriented programming; Actinidia deliciosa (kiwifruit); functional–structural plant model; plant architecture; carbon dynamics; biomechanics; hormone transport
14.  Strigolactone Can Promote or Inhibit Shoot Branching by Triggering Rapid Depletion of the Auxin Efflux Protein PIN1 from the Plasma Membrane 
PLoS Biology  2013;11(1):e1001474.
Shoot branching is regulated by competition between branches to export the phytohormone auxin into the main stem. The phytohormone strigolactone balances shoot system growth by making auxin export harder to establish, thus modulating the auxin transport network.
Plants continuously extend their root and shoot systems through the action of meristems at their growing tips. By regulating which meristems are active, plants adjust their body plans to suit local environmental conditions. The transport network of the phytohormone auxin has been proposed to mediate this systemic growth coordination, due to its self-organising, environmentally sensitive properties. In particular, a positive feedback mechanism termed auxin transport canalization, which establishes auxin flow from active shoot meristems (auxin sources) to the roots (auxin sinks), has been proposed to mediate competition between shoot meristems and to balance shoot and root growth. Here we provide strong support for this hypothesis by demonstrating that a second hormone, strigolactone, regulates growth redistribution in the shoot by rapidly modulating auxin transport. A computational model in which strigolactone action is represented as an increase in the rate of removal of the auxin export protein, PIN1, from the plasma membrane can reproduce both the auxin transport and shoot branching phenotypes observed in various mutant combinations and strigolactone treatments, including the counterintuitive ability of strigolactones either to promote or inhibit shoot branching, depending on the auxin transport status of the plant. Consistent with this predicted mode of action, strigolactone signalling was found to trigger PIN1 depletion from the plasma membrane of xylem parenchyma cells in the stem. This effect could be detected within 10 minutes of strigolactone treatment and was independent of protein synthesis but dependent on clathrin-mediated membrane trafficking. Together these results support the hypothesis that growth across the plant shoot system is balanced by competition between shoot apices for a common auxin transport path to the root and that strigolactones regulate shoot branching by modulating this competition.
Author Summary
Plants can adapt their form to suit the environment in which they are growing. For example, genetically identical plants can develop as a single unbranched stem or as a highly ramified bush. This broad developmental potential is possible because the shoot system is produced continuously by growing tips, known as shoot meristems. Meristems produce the stem and leaves of a shoot, and at the base of each leaf, a new meristem is formed. This meristem can remain dormant as a small bud or activate to produce a branch. Thus, the shoot system is a community of shoot meristems, the combined activity and inactivity of which shape shoot form. Here we provide evidence that growth is balanced across the Arabidopsis shoot system by competition between the shoot meristems. This competition is likely mediated by the requirement of meristems to export the plant hormone auxin in order to activate bud outgrowth. In our model, auxin in the main stem, exported from active branches, can prevent auxin export by dormant buds, thus preventing their activation. Our findings show that a second hormone, strigolactone, increases the level of competition between branches by making auxin export harder to establish. Together, these hormones balance growth across the shoot system, adjusting it according to the environmental conditions in which a plant is growing.
doi:10.1371/journal.pbio.1001474
PMCID: PMC3558495  PMID: 23382651
15.  Parameter Optimization and Field Validation of the Functional–Structural Model GREENLAB for Maize at Different Population Densities 
Annals of Botany  2007;101(8):1185-1194.
Background and Aims
Plant population density (PPD) influences plant growth greatly. Functional–structural plant models such as GREENLAB can be used to simulate plant development and growth and PPD effects on plant functioning and architectural behaviour can be investigated. This study aims to evaluate the ability of GREENLAB to predict maize growth and development at different PPDs.
Methods
Two field experiments were conducted on irrigated fields in the North China Plain with a block design of four replications. Each experiment included three PPDs: 2·8, 5·6 and 11·1 plants m−2. Detailed observations were made on the dimensions and fresh biomass of above-ground plant organs for each phytomer throughout the seasons. Growth stage-specific target files (a description of plant organ weight and dimension according to plant topological structure) were established from the measured data required for GREENLAB parameterization. Parameter optimization was conducted using a generalized least square method for the entire growth cycles for all PPDs and years. Data from in situ plant digitization were used to establish geometrical symbol files for organs that were then applied to translate model output directly into 3-D representation for each time step of the model execution.
Key Results
The analysis indicated that the parameter values of organ sink variation function, and the values of most of the relative sink strength parameters varied little among years and PPDs, but the biomass production parameter, computed plant projection surface and internode relative sink strength varied with PPD. Simulations of maize plant growth based on the fitted parameters were reasonably good as indicated by the linearity and slopes similar to unity for the comparison of simulated and observed values. Based on the parameter values fitted from different PPDs, shoot (including vegetative and reproductive parts of the plant) and cob fresh biomass for other PPDs were simulated. Three-dimensional representation of individual plant and plant stand from the model output with two contrasting PPDs were presented with which the PPD effect on plant growth can be easily recognized.
Conclusions
This study showed that GREENLAB model has the ability to capture plant plasticity induced by PPD. The relatively stable parameter values strengthened the hypothesis that one set of equations can govern dynamic organ growth. With further validation, this model can be used for agronomic applications such as yield optimization.
doi:10.1093/aob/mcm233
PMCID: PMC2710275  PMID: 17921525
Functional–structural plant model; GREENLAB; plant architecture; source–sink relationship; plant population density; maize (Zea mays); model parameterization
16.  A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds 
Journal of Experimental Botany  2009;60(13):3835-3848.
Budbreak in kiwifruit (Actinidia deliciosa) can be poor in locations that have warm winters with insufficient winter chilling. Kiwifruit vines are often treated with the dormancy-breaking chemical hydrogen cyanamide (HC) to increase and synchronize budbreak. This treatment also offers a tool to understand the processes involved in budbreak. A genomics approach is presented here to increase our understanding of budbreak in kiwifruit. Most genes identified following HC application appear to be associated with responses to stress, but a number of genes appear to be associated with the reactivation of growth. Three patterns of gene expression were identified: Profile 1, an HC-induced transient activation; Profile 2, an HC-induced transient activation followed by a growth-related activation; and Profile 3, HC- and growth-repressed. One group of genes that was rapidly up-regulated in response to HC was the glutathione S-transferase (GST) class of genes, which have been associated with stress and signalling. Previous budbreak studies, in three other species, also report up-regulated GST expression. Phylogenetic analysis of these GSTs showed that they clustered into two sub-clades, suggesting a strong correlation between their expression and budbreak across species.
doi:10.1093/jxb/erp231
PMCID: PMC2736901  PMID: 19651683
Actinidia deliciosa; budbreak; bud dormancy; hydrogen cyanamide; glutathione S-transferase; kiwifruit; microarray
17.  Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit 
BMC Plant Biology  2013;13:49.
Background
Cabernet Sauvignon grapevines were exposed to a progressive, increasing water defict over 16 days. Shoot elongation and photosynthesis were measured for physiological responses to water deficit. The effect of water deficit over time on the abundance of individual proteins in growing shoot tips (including four immature leaves) was analyzed using nanoflow liquid chromatography - tandem mass spectrometry (nanoLC-MS/MS).
Results
Water deficit progressively decreased shoot elongation, stomatal conductance and photosynthesis after Day 4; 2277 proteins were identified by shotgun proteomics with an average CV of 9% for the protein abundance of all proteins. There were 472 out of 942 (50%) proteins found in all samples that were significantly affected by water deficit. The 472 proteins were clustered into four groups: increased and decreased abundance of early- and late-responding protein profiles. Vines sensed the water deficit early, appearing to acclimate to stress, because the abundance of many proteins changed before decreases in shoot elongation, stomatal conductance and photosynthesis. Predominant functional categories of the early-responding proteins included photosynthesis, glycolysis, translation, antioxidant defense and growth-related categories (steroid metabolism and water transport), whereas additional proteins for late-responding proteins were largely involved with transport, photorespiration, antioxidants, amino acid and carbohydrate metabolism.
Conclusions
Proteomic responses to water deficit were dynamic with early, significant changes in abundance of proteins involved in translation, energy, antioxidant defense and steroid metabolism. The abundance of these proteins changed prior to any detectable decreases in shoot elongation, stomatal conductance or photosynthesis. Many of these early-responding proteins are known to be regulated by post-transcriptional modifications such as phosphorylation. The proteomics analysis indicates massive and substantial changes in plant metabolism that appear to funnel carbon and energy into antioxidant defenses in the very early stages of plant response to water deficit before any significant injury.
doi:10.1186/1471-2229-13-49
PMCID: PMC3608200  PMID: 23514573
18.  Metabolic analysis of kiwifruit (Actinidia deliciosa) berries from extreme genotypes reveals hallmarks for fruit starch metabolism 
Journal of Experimental Botany  2013;64(16):5049-5063.
Tomato, melon, grape, peach, and strawberry primarily accumulate soluble sugars during fruit development. In contrast, kiwifruit (Actinidia Lindl. spp.) and banana store a large amount of starch that is released as soluble sugars only after the fruit has reached maturity. By integrating metabolites measured by gas chromatography–mass spectrometry, enzyme activities measured by a robot-based platform, and transcript data sets during fruit development of Actinidia deliciosa genotypes contrasting in starch concentration and size, this study identified the metabolic changes occurring during kiwifruit development, including the metabolic hallmarks of starch accumulation and turnover. At cell division, a rise in glucose (Glc) concentration was associated with neutral invertase (NI) activity, and the decline of both Glc and NI activity defined the transition to the cell expansion and starch accumulation phase. The high transcript levels of β-amylase 9 (BAM9) during cell division, prior to net starch accumulation, and the correlation between sucrose phosphate synthase (SPS) activity and sucrose suggest the occurrence of sucrose cycling and starch turnover. ADP-Glc pyrophosphorylase (AGPase) is identified as a key enzyme for starch accumulation in kiwifruit berries, as high-starch genotypes had 2- to 5-fold higher AGPase activity, which was maintained over a longer period of time and was also associated with enhanced and extended transcription of the AGPase large subunit 4 (APL4). The data also revealed that SPS and galactinol might affect kiwifruit starch accumulation, and suggest that phloem unloading into kiwifruit is symplastic. These results are relevant to the genetic improvement of quality traits such as sweetness and sugar/acid balance in a range of fruit species.
doi:10.1093/jxb/ert293
PMCID: PMC3830485  PMID: 24058160
Actinidia deliciosa; AGPase; berry development; enzyme profiling; fruit quality; glucose; metabolite profiling; neutral invertase; planteose; primary metabolism; starch; sucrose phosphate synthase; transcript profiling.
19.  Dry matter partitioning models for the simulation of individual fruit growth in greenhouse cucumber canopies 
Annals of Botany  2011;108(6):1075-1084.
Background and Aims
Growth imbalances between individual fruits are common in indeterminate plants such as cucumber (Cucumis sativus). In this species, these imbalances can be related to differences in two growth characteristics, fruit growth duration until reaching a given size and fruit abortion. Both are related to distribution, and environmental factors as well as canopy architecture play a key role in their differentiation. Furthermore, events leading to a fruit reaching its harvestable size before or simultaneously with a prior fruit can be observed. Functional–structural plant models (FSPMs) allow for interactions between environmental factors, canopy architecture and physiological processes. Here, we tested hypotheses which account for these interactions by introducing dominance and abortion thresholds for the partitioning of assimilates between growing fruits.
Methods
Using the L-System formalism, an FSPM was developed which combined a model for architectural development, a biochemical model of photosynthesis and a model for assimilate partitioning, the last including a fruit growth model based on a size-related potential growth rate (RP). Starting from a distribution proportional to RP, the model was extended by including abortion and dominance. Abortion was related to source strength and dominance to sink strength. Both thresholds were varied to test their influence on fruit growth characteristics. Simulations were conducted for a dense row and a sparse isometric canopy.
Key Results
The simple partitioning models failed to simulate individual fruit growth realistically. The introduction of abortion and dominance thresholds gave the best results. Simulations of fruit growth durations and abortion rates were in line with measurements, and events in which a fruit was harvestable earlier than an older fruit were reproduced.
Conclusions
Dominance and abortion events need to be considered when simulating typical fruit growth traits. By integrating environmental factors, the FSPM can be a valuable tool to analyse and improve existing knowledge about the dynamics of assimilates partitioning.
doi:10.1093/aob/mcr150
PMCID: PMC3189842  PMID: 21715366
Modelling; individual fruit growth; functional–structural plant model; L-System; Cucumis sativus; cucumber; plant architecture; assimilate distribution
20.  Simulation of fruit-set and trophic competition and optimization of yield advantages in six Capsicum cultivars using functional–structural plant modelling 
Annals of Botany  2010;107(5):793-803.
Background and aims
Many indeterminate plants can have wide fluctuations in the pattern of fruit-set and harvest. Fruit-set in these types of plants depends largely on the balance between source (assimilate supply) and sink strength (assimilate demand) within the plant. This study aims to evaluate the ability of functional–structural plant models to simulate different fruit-set patterns among Capsicum cultivars through source–sink relationships.
Methods
A greenhouse experiment of six Capsicum cultivars characterized with different fruit weight and fruit-set was conducted. Fruit-set patterns and potential fruit sink strength were determined through measurement. Source and sink strength of other organs were determined via the GREENLAB model, with a description of plant organ weight and dimensions according to plant topological structure established from the measured data as inputs. Parameter optimization was determined using a generalized least squares method for the entire growth cycle.
Key Results and Conclusions
Fruit sink strength differed among cultivars. Vegetative sink strength was generally lower for large-fruited cultivars than for small-fruited ones. The larger the size of the fruit, the larger variation there was in fruit-set and fruit yield. Large-fruited cultivars need a higher source–sink ratio for fruit-set, which means higher demand for assimilates. Temporal heterogeneity of fruit-set affected both number and yield of fruit. The simulation study showed that reducing heterogeneity of fruit-set was obtained by different approaches: for example, increasing source strength; decreasing vegetative sink strength, source–sink ratio for fruit-set and flower appearance rate; and harvesting individual fruits earlier before full ripeness. Simulation results showed that, when we increased source strength or decreased vegetative sink strength, fruit-set and fruit weight increased. However, no significant differences were found between large-fruited and small-fruited groups of cultivars regarding the effects of source and vegetative sink strength on fruit-set and fruit weight. When the source–sink ratio at fruit-set decreased, the number of fruit retained on the plant increased competition for assimilates with vegetative organs. Therefore, total plant and vegetative dry weights decreased, especially for large-fruited cultivars. Optimization study showed that temporal heterogeneity of fruit-set and ripening was predicted to be reduced when fruits were harvested earlier. Furthermore, there was a 20 % increase in the number of extra fruit set.
doi:10.1093/aob/mcq223
PMCID: PMC3077981  PMID: 21097946
Source–sink relationship; fruit-set pattern; functional–structural models; Capsicum annuum
21.  Induced polyploidy dramatically increases the size and alters the shape of fruit in Actinidia chinensis 
Annals of Botany  2011;109(1):169-179.
Background and Aims
Some otherwise promising selections of Actinidia chinensis (kiwifruit) have fruit that are too small for successful commercialization. We have therefore made the first detailed study in diploid kiwifruit of the effects of chromosome doubling induced by colchicine on fruit size, shape and crop loading.
Methods
Flow cytometric analysis of young leaves and chromosome analysis of flower buds and root tips was used to confirm the stability of induced autotetraploids. Fruit weight, size and crop load were measured in the third year after planting in the field and for three consecutive years. DNA fingerprinting was used to confirm the origin of the material.
Key Results
There was a very significant increase in fruit size in induced autotetraploids of different genotypes of A. chinensis. With the commercially important diploid cultivar ‘Hort16A’, most regenerants, Type A plants, had fruit which were much the same shape as fruit of the diploid but, at the same fruit load, were much larger and heavier. Some regenerants, Type B plants, produced fruit similar to ‘fasciated’ fruit. Fruit of the autotetraploids induced from three female red-fleshed A. chinensis selections were also 50–60 % larger than fruit of their diploid progenitors. The main increase in fruit dimensions was in their diameters. These improved fruit characteristics were stable over several seasons.
Conclusions
Chromosome doubling has been shown to increase significantly fruit size in autotetraploid A. chinensis, highlighting the considerable potential of this technique to produce new cultivars with fruit of adequate size. Other variants with differently shaped fruit were also produced but the genetic basis of this variation remains to be elucidated. Autoploids of other Actinidia species with commercial potential may also show improved fruit characteristics, opening up many new possibilities for commercial development.
doi:10.1093/aob/mcr256
PMCID: PMC3241580  PMID: 21980192
Actinidia chinensis; autotetraploid; chromosome doubling; chromosome number; colchicine; DNA fingerprinting; flow cytometry; fruit shape; fruit size; kiwifruit; red-fleshed kiwifruit; somaclonal variation
22.  Two terpene synthases are responsible for the major sesquiterpenes emitted from the flowers of kiwifruit (Actinidia deliciosa) 
Journal of Experimental Botany  2009;60(11):3203-3219.
Kiwifruit vines rely on bees for pollen transfer between spatially separated male and female individuals and require synchronized flowering to ensure pollination. Volatile terpene compounds, which are important cues for insect pollinator attraction, were studied by dynamic headspace sampling in the major green-fleshed kiwifruit (Actinidia deliciosa) cultivar ‘Hayward’ and its male pollinator ‘Chieftain’. Terpene volatile levels showed a profile dominated by the sesquiterpenes α-farnesene and germacrene D. These two compounds were emitted by all floral tissues and could be observed throughout the day, with lower levels at night. The monoterpene (E)-β-ocimene was also detected in flowers but was emitted predominantly during the day and only from petal tissue. Using a functional genomics approach, two terpene synthase (TPS) genes were isolated from a ‘Hayward’ petal EST library. Bacterial expression and transient in planta data combined with analysis by enantioselective gas chromatography revealed that one TPS produced primarily (E,E)-α-farnesene and small amounts of (E)-β-ocimene, whereas the second TPS produced primarily (+)-germacrene D. Subcellular localization using GFP fusions showed that both enzymes were localized in the cytoplasm, the site for sesquiterpene production. Real-time PCR analysis revealed that both TPS genes were expressed in the same tissues and at the same times as the corresponding floral volatiles. The results indicate that two genes can account for the major floral sesquiterpene volatiles observed in both male and female A. deliciosa flowers.
doi:10.1093/jxb/erp162
PMCID: PMC2718223  PMID: 19516075
Actinidia; α-farnesene; floral volatiles; germacrene D; kiwifruit; ocimene; terpene; terpene synthases
23.  Bacterial adaptation through distributed sensing of metabolic fluxes 
We present a large-scale differential equation model of E. coli's central metabolism and its enzymatic, transcriptional, and posttranslational regulation. This model reproduces E. coli's known physiological behavior.We found that the interplay of known interactions in E. coli's central metabolism can indirectly recognize the presence of extracellular carbon sources through measuring intracellular metabolic flux patterns.We found that E. coli's system-level adaptations between glycolytic and gluconeogenic carbon sources are realized on the molecular level by global feedback architectures that overarch the enzymatic and transcriptional regulatory layers.We found that the capability for closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously to changing carbon sources (not requiring upstream sensing and signaling).
Adaptations to fluctuating carbon source availability are of particular importance for bacteria. To understand these adaptations, it needs to be understood how a system's behavior emerges from the interactions between the characterized molecules (Kitano, 2002b). To attain such a system understanding of bacterial metabolic adaptations to carbon source availability, the coupling between the recognition and adjustment aspects and between the enzymatic and genetic regulatory layers must be understood. For many carbon sources, neither transmembrane sensors nor regulatory proteins with sensing function have been identified. Also, it remains unclear how multiple local regulations work together to accomplish a coherent adjustment on the systems level. In this paper, we show that (1) the interplay of the known interactions in E. coli's central metabolism is capable of recognizing carbon sources indirectly, and that (2) these molecular interactions can adjust E. coli's metabolic operation between growth on glycolytic and gluconeogenic carbon sources, and that (3) this adaptation is governed by general principles.
We hypothesized that the system-level adaptations between growth on glycolytic and gluconeogenic carbon sources are accomplished by a system-wide regulation architecture that emerges when the known enzymatic and transcriptional regulations become coupled through five transcription factor (TF)–metabolite interactions. To (1) assess whether such coupled molecular interactions can indeed work together to adapt metabolic operation, and if yes, (2) to understand this system-level adaptation in molecular-level detail, we constructed a large-scale differential equation model. The model topology comprises the Embden–Meyerhoff pathway, the tricarboxylic acid (TCA) cycle, the glyoxylate (GLX) shunt, the anaplerotic reactions, the diversion of carbon flux to the GLX shunt, the uptake of glucose, the uptake and excretion of acetate, enzymatic regulation, transcriptional regulation by four TFs, and the regulation of these TFs' activities through TF–metabolite interactions. We translated the topology into differential equations by assigning the most appropriate rate law to each interaction. The kinetic model comprises 47 ordinary differential equations and 193 parameters. Parameter values were estimated through application of the ‘divide-and-conquer approach' (Kotte and Heinemann, 2009) on published experimental steady state-omics data sets.
Model simulations reproduce E. coli's known physiological behavior in an environment with fluctuating carbon source availability. But how does the in silico cell recognize acetate without a transmembrane sensor for extracellular acetate or a TF binding to intracellular acetate? Similarly, it is unclear whether the glucose sensing function of the phosphotransferase system is the exclusive mechanism to recognize glucose, or whether this sensing function is integrated into a larger sensing architecture. The model suggests that the recognition is performed indirectly through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two distinct motifs, which we termed pathway usage and flux direction, to establish defined correlations between metabolic fluxes and the levels of certain, here termed flux-signaling metabolites. The binding of these metabolites to TFs propagates the flux information to the transcriptional regulatory layer. A molecular sensor for intracellular metabolic flux is thus defined as a system of regulations and enzyme kinetics, comprising (1) either of the two motifs pathway usage or flux direction and (2) the binding of the thus established flux-signaling metabolites to TF(s).
As the in silico cell establishes and uses sensors for several intracellular metabolic fluxes, the overall sensing architecture infers the present carbon sources from a pattern of metabolic fluxes and is as such of a distributed nature. The core of this sensing architecture is formed not by transmembrane sensors but by four flux sensors, which establish flux-signaling metabolites according to the two proposed general motifs. These flux sensors use intracellular metabolic flux as a means to correlate the presence of extracellular carbon sources with the levels of intracellular metabolites. The recognition of glucose through the PTS transmembrane complex is embedded as one flux sensor in this distributed sensing architecture; the other three flux sensors function without the help of transmembrane complexes.
The in silico cell achieves the coupling between recognition and adjustment through its TFs, whose activities respond to the available carbon sources and at the same time regulate the expression of target genes. This combined recognition and adjustment, centered on the four TFs, closes four global feedback loops that overarch the metabolic and genetic layers as illustrated in Figure 6. The adaptation of the in silico cell arises from the global feedback loop-embedded, flux sensor-adjusted transcriptional regulation of the four TFs, with each TF performing one part of the overall adaptation. This adaptation incorporates both the influence of the metabolic on the genetic layer, achieved through TF–metabolite interactions, and of the genetic on the metabolic layer, achieved through the impact of adjusted enzyme levels on metabolic fluxes.
The existence of the global feedback architectures challenges the conventional view that top-level regulatory proteins recognize environmental conditions and adjust downstream metabolic operation. It suggests that the capability for closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and regulation) to changing carbon sources.
To conclude, the presented differential equation model of E. coli's central metabolism offers a consistent explanation of how a multitude of known molecular interactions fit into a coherent systems picture; the interactions work together like gear wheels that mesh with one another to adapt central metabolism between growth on the glycolytic substrate glucose and the gluconeogenic substrate acetate. The deduced general functional principles provide the missing link to understand system-level adaptations to carbon sources in molecular-level detail. The proposed principles fall under the umbrella of distributed flux sensing. The flux sensing mechanism entails the binding of TFs to flux-signaling metabolites, which are established through the motifs signaling of pathway usage and signaling of flux direction, and are embedded in global feedback loop architectures. These principles allow an autonomous adaptation of metabolic operation to growth in fluctuating environments.
The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli's central metabolism and its regulation, fundamental aspects of the employed sensing and regulatory adjustment mechanisms remain unclear. In this paper, using a differential equation model that couples enzymatic and transcriptional regulation of E. coli's central metabolism, we show that the interplay of known interactions explains in molecular-level detail the system-wide adjustments of metabolic operation between glycolytic and gluconeogenic carbon sources. We show that these adaptations are enabled by an indirect recognition of carbon sources through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two general motifs to establish flux-signaling metabolites, whose bindings to transcription factors form flux sensors. As these sensors are embedded in global feedback loop architectures, closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and signaling) to fluctuating carbon sources.
doi:10.1038/msb.2010.10
PMCID: PMC2858440  PMID: 20212527
computational model; metabolism; regulation; sensing; systems biology
24.  A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes 
BMC Genomics  2009;10:102.
Background
The genus Actinidia (kiwifruit) consists of woody, scrambling vines, native to China, and only recently propagated as a commercial crop. All species described are dioecious, but the genetic mechanism for sex-determination is unknown, as is the genetic basis for many of the cluster of characteristics making up the unique fruit. It is, however, an important crop in the New Zealand economy, and a classical breeding program would benefit greatly by knowledge of the trait alleles carried by both female and male parents. The application of marker assisted selection (MAS) in seedling populations would also aid the accurate and efficient development of novel fruit types for the market.
Results
Gene-rich female, male and consensus linkage maps of the diploid species A. chinensis have been constructed with 644 microsatellite markers. The maps consist of twenty-nine linkage groups corresponding to the haploid number n = 29. We found that sex-linked sequence characterized amplified region (SCAR) markers and the 'Flower-sex' phenotype consistently mapped to a single linkage group, in a subtelomeric region, in a section of inconsistent marker order. The region also contained markers of expressed genes, some of unknown function. Recombination, assessed by allelic distribution and marker order stability, was, in the remainder of the linkage group, in accordance with other linkage groups. Fully informative markers to other genes in this linkage group identified the comparative linkage group in the female map, where recombination ratios determining marker order were similar to the autosomes.
Conclusion
We have created genetic linkage maps that define the 29 linkage groups of the haploid genome, and have revealed the position and extent of the sex-determining locus in A. chinensis. As all Actinidia species are dioecious, we suggest that the sex-determining loci of other Actinidia species will be similar to that region defined in our maps. As the extent of the non-recombining region is limited, our result supports the suggestion that the subtelomeric region of an autosome is in the early stages of developing the characteristics of a sex chromosome. The maps provide a reference of genetic information in Actinidia for use in genetic analysis and breeding programs.
doi:10.1186/1471-2164-10-102
PMCID: PMC2661093  PMID: 19284545
25.  Rhythms and Alternating Patterns in Plants as Emergent Properties of a Model of Interaction between Development and Functioning 
Annals of Botany  2007;101(8):1233-1242.
Background and Aims
To model plasticity of plants in their environment, a new version of the functional–structural model GREENLAB has been developed with full interactions between architecture and functioning. Emergent properties of this model were revealed by simulations, in particular the automatic generation of rhythms in plant development. Such behaviour can be observed in natural phenomena such as the appearance of fruit (cucumber or capsicum plants, for example) or branch formation in trees.
Methods
In the model, a single variable, the source–sink ratio controls different events in plant architecture. In particular, the number of fruits and branch formation are determined as increasing functions of this ratio. For some sets of well-chosen parameters of the model, the dynamical evolution of the ratio during plant growth generates rhythms.
Key Results and Conclusions
Cyclic patterns in branch formation or fruit appearance emerge without being forced by the model. The model is based on the theory of discrete dynamical systems. The mathematical formalism helps us to explain rhythm generation and to control the behaviour of the system. Rhythms can appear during both the exponential and stabilized phases of growth, but the causes are different as shown by an analytical study of the system. Simulated plant behaviours are very close to those observed on real plants. With a small number of parameters, the model gives very interesting results from a qualitative point of view. It will soon be subjected to experimental data to estimate the model parameters.
doi:10.1093/aob/mcm171
PMCID: PMC2710268  PMID: 17715304
Rhythms; plasticity; plant growth model; GREENLAB; interactions; branching system; fructification; emergent properties

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