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1.  Individual Leaf Development in Arabidopsis thaliana: a Stable Thermal‐time‐based Programme 
Annals of Botany  2002;89(5):595-604.
In crop species, the impact of temperature on plant development is classically modelled using thermal time. We examined whether this method could be used in a non‐crop species, Arabidopsis thaliana, to analyse the response to temperature of leaf initiation rate and of the development of two leaves of the rosette. The results confirmed the large plant‐to‐plant variability in the studied isogenic line of the Columbia ecotype: 100‐fold differences in leaf area among plants sown on the same date were commonly observed at a given date. These differences disappeared in mature leaves, suggesting that they were due to a variability in plant developmental stage. The whole population could therefore be represented by any group of synchronous plants labelled at the two‐leaf stage and followed during their development. Leaf initiation rate, duration of leaf expansion and maximal relative leaf expansion rate varied considerably among experiments performed at different temperatures (from 6 to 26 °C) but they were linearly related to temperature in the range 6–26 °C, with a common x‐intercept of 3 °C. Expressing time in thermal time with a threshold temperature of 3 °C unified the time courses of leaf initiation and of individual leaf development for plants grown at different temperatures and experimental conditions. The two leaves studied (leaf 2 and leaf 6) had a two‐phase development, with an exponential phase followed by a phase with decreasing relative elongation rate. Both phases had constant durations for a given leaf position if expressed in thermal time. Changes in temperature caused changes in both the rate of development and in the expansion rate which mutually compensated such that they had no consequence on leaf area at a given thermal time. The resulting model of leaf development was applied to ten experiments carried out in a glasshouse or in a growth chamber, with plants grown in soil or hydroponically. Because it predicts accurately the stage of development and the relative expansion rate of any leaf of the rosette, this model facilitates precise planning of sampling procedures and the comparison of treatments in growth analyses.
doi:10.1093/aob/mcf085
PMCID: PMC4233892  PMID: 12099534
Arabidopsis thaliana; thermal time; leaf initiation; leaf expansion; model; temperature
2.  From Individual Leaf Elongation to Whole Shoot Leaf Area Expansion: a Comparison of Three Aegilops and Two Triticum Species 
Annals of Botany  2004;94(1):99-108.
• Background and Aims Rapid leaf area expansion is a desirable trait in the early growth stages of cereal crops grown in low‐rainfall areas. In this study, the traits associated with inherent variation in early leaf area expansion rates have been investigated in two wheat species (Triticum aestivum and T. durum) and three of its wild relatives (Aegilops umbellulata, A. caudata and A. tauschii) to find out whether the Aegilops species have a faster leaf area expansion in their early developmental stage than some of the current wheat species.
• Methods Growth of individual leaves, biomass allocation, and gas exchange were measured on hydroponically grown plants for 4 weeks.
• Key Results Leaf elongation rate (LER) was strongly and positively correlated with leaf width but not with leaf elongation duration (LED). The species with more rapidly elongating leaves showed a faster increase with leaf position in LER, leaf width and leaf area, higher relative leaf area expansion rates, and more biomass allocation to leaf sheaths and less to roots. No differences in leaf appearance rate were found amongst the species.
• Conclusions Aegilops tauschii was the only wild species with rapid leaf expansion rates similar to those of wheat, and it achieved the highest photosynthetic rates, making it an interesting species for further study.
doi:10.1093/aob/mch110
PMCID: PMC4242366  PMID: 15155374
Aegilops; biomass allocation; leaf elongation duration; leaf elongation rate; leaf expansion; leaf width; photosynthesis; relative growth rate; Triticum; wheat; wild relatives
3.  The Leaf Size–Twig Size Spectrum of Temperate Woody Species Along an Altitudinal Gradient: An Invariant Allometric Scaling Relationship 
Annals of Botany  2006;97(1):97-107.
• Background and Aims The leaf size–twig size spectrum is one of the leading dimensions of plant ecological variation, and now it is under development. The purpose of this study was to test whether the relationship between leaf size and twig size is isometric or allometric, and to examine the relationship between plant allometric growth and life history strategies in the spectrum.
• Methods Leaf and stem characters—including leaf and stem mass, total leaf area, individual leaf area, stem cross-sectional area, leaf number and stem length—at the twig level for 59 woody species were investigated along an altitudinal gradient on Changbaishan Mountain in the temperate zone of China. The environmental gradient ranges from temperate broad-leaved mixed forest at low altitude, to conifer forest at middle altitude, and to sub-alpine birch forest at high altitude. The scaling relationships between stem cross-sectional area and stem mass, stem mass and leaf mass, and leaf mass and leaf area at the twig level were simultaneously determined.
• Key Results Twig cross-sectional area was found to have invariant allometric scaling relationships with the stem mass, leaf mass, total leaf area and individual leaf area, all with common slopes being significantly larger than 1, for three altitudinal-zoned vegetation types under investigation. However, leaf mass was found to be isometrically related to stem mass and leaf area along the environmental gradient. Based on the predictions of previous models, the exponent value of the relationship between twig cross-sectional area and total leaf area can be inferred to be 1·5, which falls between the confidence intervals of the relationship at each altitude, and between the confidence intervals of the common slope value (1·17–1·56) of this study. This invariant scaling relationship is assumed to result from the fractural network and/or developmental constraints of plants. The allometric constants (y-intercepts) of the relationships between the stem cross-sectional area and leaf area (both total leaf area and individual leaf area) were found to decrease significantly along the altitudinal gradient. This suggests that the species would support less leaf area at a given twig cross-sectional area with increasing environmental stress.
• Conclusions This study demonstrated that plants respond to the environmental gradient by changing the y-intercepts of the relationship between leaf size–twig size, while keeping the exponent value of the allometric relationship as an invariant constant. The allometric growth in the twig size–leaf size spectrum is related to many other components of plant life history strategy, including the well established life history trade-off between efficiency and safety in the hydraulic transport of water.
doi:10.1093/aob/mcj004
PMCID: PMC2803375  PMID: 16254019
Allometric growth; altitudinal gradient; leaf area; stem mass; leaf mass; life history trade-off; scaling; twig cross-sectional area
4.  LEAF-E: a tool to analyze grass leaf growth using function fitting 
Plant Methods  2014;10(1):37.
In grasses, leaf growth is often monitored to gain insights in growth processes, biomass accumulation, regrowth after cutting, etc. To study the growth dynamics of the grass leaf, its length is measured at regular time intervals to derive the leaf elongation rate (LER) profile over time. From the LER profile, parameters such as maximal LER and leaf elongation duration (LED), which are essential for detecting inter-genotype growth differences and/or quantifying plant growth responses to changing environmental conditions, can be determined. As growth is influenced by the circadian clock and, especially in grasses, changes in environmental conditions such as temperature and evaporative demand, the LER profiles show considerable experimental variation and thus often do not follow a smooth curve. Hence it is difficult to quantify the duration and timing of growth. For these reasons, the measured data points should be fitted using a suitable mathematical function, such as the beta sigmoid function for leaf elongation.
In the context of high-throughput phenotyping, we implemented the fitting of leaf growth measurements into a user-friendly Microsoft Excel-based macro, a tool called LEAF-E. LEAF-E allows to perform non-linear regression modeling of leaf length measurements suitable for robust and automated extraction of leaf growth parameters such as LER and LED from large datasets. LEAF-E is particularly useful to quantify the timing of leaf growth, which forms an important added value for detecting differences in leaf growth development. We illustrate the broad application range of LEAF-E using published and unpublished data sets of maize, Miscanthus spp. and Brachypodium distachyon, generated in independent experiments and for different purposes. In addition, we show that LEAF-E could also be used to fit datasets of other growth-related processes that follow the sigmoidal profile, such as cell length measurements along the leaf axis.
Given its user-friendliness, ability to quantify duration and timing of leaf growth and broad application range, LEAF-E is a tool that could be routinely used to study growth processes following the sigmoidal profile.
Electronic supplementary material
The online version of this article (doi:10.1186/1746-4811-10-37) contains supplementary material, which is available to authorized users.
doi:10.1186/1746-4811-10-37
PMCID: PMC4246515  PMID: 25435898
Leaf elongation rate; Non-linear regression; Leaf length; Cell length; Growth zone
5.  Identification of Nitrogen, Phosphorus, and Potassium Deficiencies in Rice Based on Static Scanning Technology and Hierarchical Identification Method 
PLoS ONE  2014;9(11):e113200.
Establishing an accurate, fast, and operable method for diagnosing crop nutrition is very important for crop nutrient management. In this study, static scanning technology was used to collect images of a rice sample's fully expanded top three leaves and corresponding sheathes. From these images, 32 spectral and shape characteristic parameters were extracted using an RGB mean value function and using the Regionprops function in MATLAB. Hierarchical identification was used to identify NPK deficiencies. First, the normal samples and non-normal (NPK deficiencies) samples were identified. Then, N deficiency and PK deficiencies were identified. Finally, P deficiency and K deficiency were identified. In the identification of every hierarchy, SVFS was used to select the optimal characteristic set for different deficiencies in a targeted manner, and Fisher discriminant analysis was used to build the diagnosis model. In the first hierarchy, the selected characteristics were the leaf sheath R, leaf sheath G, leaf sheath B, leaf sheath length, leaf tip R, leaf tip G, leaf area and leaf G. In the second hierarchy, the selected characteristics were the leaf sheath G, leaf sheath B, white region of the leaf sheath, leaf B, and leaf G. In the third hierarchy the selected characteristics were the leaf G, leaf sheath length, leaf area/leaf length, leaf tip G, difference between the 2nd and 3rd leaf lengths, leaf sheath G, and leaf lightness. The results showed that the overall identification accuracies of NPK deficiencies were 86.15, 87.69, 90.00 and 89.23% for the four growth stages. Data from multiple years were used for validation, and the identification accuracies were 83.08, 83.08, 89.23 and 90.77%.
doi:10.1371/journal.pone.0113200
PMCID: PMC4245116  PMID: 25426712
6.  Multi-trait interactions, not phylogeny, fine-tune leaf size reduction with increasing altitude 
Annals of Botany  2011;107(3):455-465.
Background and Aims
Despite long-held interest, knowledge on why leaf size varies widely among species is still incomplete. This study was conducted to assess whether abiotic factors, phylogenetic histories and multi-trait interactions act together to shape leaf size.
Methods
Fifty-seven pairs of altitudinal vicariant species were selected in northern Spain, and leaf area and a number of functionally related leaf, shoot and whole plant traits were measured for each pair. Structural equation modelling helped unravel trait interactions affecting leaf size, and Mantel tests weighed the relative relevance of phylogeny, environment and trait interactions to explain leaf size reduction with altitude.
Key Results
Leaves of highland vicariants were generally smaller than those of lowlands. However, the extent of leaf size reduction with increasing altitude was widely variable among genera: from approx. 700 cm2 reduction (96 % in Polystichum) to approx. 30 cm2 increase (37 % in Sorbus). This was partially explained by shifts in leaf, shoot and whole plant traits (35–64 % of explained variance, depending on models), with size/number trade-offs more influential than shifts in leaf form and leaf economics. Shifts in traits were more important than phylogenetic distances or site-specific environmental variation in explaining the degree of leaf size reduction with altitude.
Conclusions
Ecological filters, constraints due to phylogenetic history (albeit modest in the study system), and phenotypic integration contribute jointly to shape single-trait evolution. Here, it was found that phenotypic change was far more important than shared ancestry to explaine leaf size differences of closely related species segregated along altitudes.
doi:10.1093/aob/mcq261
PMCID: PMC3043936  PMID: 21199835
Leaf size evolution; leaf economics; phylogeny; traits; altitude; indirect selection; morphological correlates; structural equation models
7.  Polyploidy and Cellular Mechanisms Changing Leaf Size: Comparison of Diploid and Autotetraploid Populations in Two Species of Lolium 
Annals of Botany  2005;96(5):931-938.
• Background and Aims Growth and development of plant organs, including leaves, depend on cell division and expansion. Leaf size is increased by greater cell ploidy, but the mechanism of this effect is poorly understood. Therefore, in this study, the role of cell division and expansion in the increase of leaf size caused by polyploidy was examined by comparing various cell parameters of the mesophyll layer of developing leaves of diploid and autotetraploid cultivars of two grass species, Lolium perenne and L. multiflorum.
• Methods Three cultivars of each ploidy level of both species were grown under pot conditions in a controlled growth chamber, and leaf elongation rate and the cell length profile at the leaf base were measured on six plants in each cultivar. Cell parameters related to division and elongation activities were calculated by a kinematic method.
• Key Results Tetraploid cultivars had faster leaf elongation rates than did diploid cultivars in both species, resulting in longer leaves, mainly due to their longer mature cells. Epidermal and mesophyll cells differed 20-fold in length, but were both greater in the tetraploid cultivars of both species. The increase in cell length of the tetraploid cultivars was caused by a faster cell elongation rate, not by a longer period of cell elongation. There were no significant differences between cell division parameters, such as cell production rate and cell cycle time, in the diploid and tetraploid cultivars.
• Conclusion The results demonstrated clearly that polyploidy increases leaf size mainly by increasing the cell elongation rate, but not the duration of the period of elongation, and thus increases final cell size.
doi:10.1093/aob/mci245
PMCID: PMC4247059  PMID: 16100224
Cell division; cell elongation; kinematic method; leaf elongation rate; leaf size; Lolium; mesophyll cells; tetraploid
8.  Measurement of Leaf Hydraulic Conductance and Stomatal Conductance and Their Responses to Irradiance and Dehydration Using the Evaporative Flux Method (EFM) 
Water is a key resource, and the plant water transport system sets limits on maximum growth and drought tolerance. When plants open their stomata to achieve a high stomatal conductance (gs) to capture CO2 for photosynthesis, water is lost by transpiration1,2. Water evaporating from the airspaces is replaced from cell walls, in turn drawing water from the xylem of leaf veins, in turn drawing from xylem in the stems and roots. As water is pulled through the system, it experiences hydraulic resistance, creating tension throughout the system and a low leaf water potential (Ψleaf). The leaf itself is a critical bottleneck in the whole plant system, accounting for on average 30% of the plant hydraulic resistance3. Leaf hydraulic conductance (Kleaf = 1/ leaf hydraulic resistance) is the ratio of the water flow rate to the water potential gradient across the leaf, and summarizes the behavior of a complex system: water moves through the petiole and through several orders of veins, exits into the bundle sheath and passes through or around mesophyll cells before evaporating into the airspace and being transpired from the stomata. Kleaf is of strong interest as an important physiological trait to compare species, quantifying the effectiveness of the leaf structure and physiology for water transport, and a key variable to investigate for its relationship to variation in structure (e.g., in leaf venation architecture) and its impacts on photosynthetic gas exchange. Further, Kleaf responds strongly to the internal and external leaf environment3. Kleaf can increase dramatically with irradiance apparently due to changes in the expression and activation of aquaporins, the proteins involved in water transport through membranes4, and Kleaf declines strongly during drought, due to cavitation and/or collapse of xylem conduits, and/or loss of permeability in the extra-xylem tissues due to mesophyll and bundle sheath cell shrinkage or aquaporin deactivation5-10. Because Kleaf can constrain gs and photosynthetic rate across species in well watered conditions and during drought, and thus limit whole-plant performance they may possibly determine species distributions especially as droughts increase in frequency and severity11-14.
We present a simple method for simultaneous determination of Kleaf and gs on excised leaves. A transpiring leaf is connected by its petiole to tubing running to a water source on a balance. The loss of water from the balance is recorded to calculate the flow rate through the leaf. When steady state transpiration (E, mmol • m-2 • s-1) is reached, gs is determined by dividing by vapor pressure deficit, and Kleaf by dividing by the water potential driving force determined using a pressure chamber (Kleaf= E /- Δψleaf, MPa)15.
This method can be used to assess Kleaf responses to different irradiances and the vulnerability of Kleaf to dehydration14,16,17.
doi:10.3791/4179
PMCID: PMC3577864  PMID: 23299126
Plant Biology; Issue 70; Molecular Biology; Physiology; Ecology; Biology; Botany; Leaf traits; hydraulics; stomata; transpiration; xylem; conductance; leaf hydraulic conductance; resistance; evaporative flux method; whole plant
9.  Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance 
Journal of Experimental Botany  2009;60(14):4089-4103.
Plants show varied cellular responses to salinity that are partly associated with maintaining low cytosolic Na+ levels and a high K+/Na+ ratio. Plant metabolites change with elevated Na+, some changes are likely to help restore osmotic balance while others protect Na+-sensitive proteins. Metabolic responses to salt stress are described for two barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differed in salinity tolerance under the experimental conditions used. After 3 weeks of salt treatment, Clipper ceased growing whereas Sahara resumed growth similar to the control plants. Compared with Clipper, Sahara had significantly higher leaf Na+ levels and less leaf necrosis, suggesting they are more tolerant to accumulated Na+. Metabolite changes in response to the salt treatment also differed between the two cultivars. Clipper plants had elevated levels of amino acids, including proline and GABA, and the polyamine putrescine, consistent with earlier suggestions that such accumulation may be correlated with slower growth and/or leaf necrosis rather than being an adaptive response to salinity. It is suggested that these metabolites may be an indicator of general cellular damage in plants. By contrast, in the more tolerant Sahara plants, the levels of the hexose phosphates, TCA cycle intermediates, and metabolites involved in cellular protection increased in response to salt. These solutes remain unchanged in the more sensitive Clipper plants. It is proposed that these responses in the more tolerant Sahara are involved in cellular protection in the leaves and are involved in the tolerance of Sahara leaves to high Na+.
doi:10.1093/jxb/erp243
PMCID: PMC2755029  PMID: 19666960
Barley; GC-MS; metabolomics; salt stress; tissue tolerance
10.  Delivering high-resolution landmarks using inkjet micropatterning for spatial monitoring of leaf expansion 
Plant Methods  2011;7:1.
Background
Inkjet micropatterning is a versatile deposition technique with broad applications in numerous fields. However, its application in plant science is largely unexplored. Leaf expansion is one of the most important parameters in the field of plant science and many methods have been developed to examine differential expansion rates of different parts of the leaf lamina. Among them, methods based on the tracking of natural landmarks through digital imaging require a complicated setup in which the leaf must remain fixed and under tension. Furthermore, the resolution is limited to that of the natural landmarks, which are often difficult to find, particularly in young leaves. To study the fine scale expansion dynamics of the leaf lamina using artificial landmarks it is necessary to place small, noninvasive marks on a leaf surface and then recover the location of those marks after a period of time.
Results
To monitor leaf expansion in two dimensions, at very fine scales, we used a custom designed inkjet micropatterning system to print a grid composed of c. 0.19 mm2 cells on small developing leaves of ivy (Hedera helix) using 40 μm dots at a spacing of c. 91 μm. The leaves in different growing stages were imaged under magnification to extract the coordinates of the marks which were then used in subsequent computer-assisted leaf expansion analyses. As an example we obtained quantified global and local expansion information and created expansion maps over the entire leaf surface. The results reveal a striking pattern of fine-scale expansion differences over short periods of time. In these experiments, the base of the leaf is a "cold spot" for expansion, while the leaf sinuses are "hot spots" for expansion. We have also measured a strong shading effect on leaf expansion. We discuss the features required to build an inkjet printing apparatus optimized for use in plant science, which will further maximize the range of tissues that can be printed at these scales.
Conclusions
To apply inkjet micropatterning to plant studies, we have successfully delivered landmarks on ivy leaf surfaces and achieved high-resolution, two-dimensional monitoring of leaf expansion at different growing stages. The measurement is capable of reliably identifying the fine scale changes during plant growth. As well as delivering landmarks, this technology may be used to deliver microscale targeted biological components such as growth hormones, and possibly be used to pattern sensors directly on the leaves.
doi:10.1186/1746-4811-7-1
PMCID: PMC3035580  PMID: 21266074
11.  Sugar promotes vegetative phase change in Arabidopsis thaliana by repressing the expression of MIR156A and MIR156C 
eLife  2013;2:e00260.
Nutrients shape the growth, maturation, and aging of plants and animals. In plants, the juvenile to adult transition (vegetative phase change) is initiated by a decrease in miR156. In Arabidopsis, we found that exogenous sugar decreased the abundance of miR156, whereas reduced photosynthesis increased the level of this miRNA. This effect was correlated with a change in the timing of vegetative phase change, and was primarily attributable to a change in the expression of two genes, MIR156A and MIR156C, which were found to play dominant roles in this transition. The glucose-induced repression of miR156 was dependent on the signaling activity of HEXOKINASE1. We also show that the defoliation-induced increase in miR156 levels can be suppressed by exogenous glucose. These results provide a molecular link between nutrient availability and developmental timing in plants, and suggest that sugar is a component of the leaf signal that mediates vegetative phase change.
DOI: http://dx.doi.org/10.7554/eLife.00260.001
eLife digest
Like animals, plants go through several stages of development before they reach maturity, and it has long been thought that some of the transitions between these stages are triggered by changes in the nutritional status of the plant. Now, based on experiments with the plant Arabidopsis thaliana, Yang et al. and, independently, Yu et al. have provided fresh insights into the role of sugar in ‘vegetative phase change'—the transition from the juvenile form of a plant to the adult plant.
The new work takes advantage of the fact that vegetative phase change is controlled by two genes that encode microRNAs (MIRNAs). Arabidopsis has eight MIR156 genes and both groups confirmed that supplying plants with sugar reduces the expression of two of these—MIR156A and MIR156C—whereas sugar deprivation increases their expression. Removing leaves also leads to upregulation of both genes, and delays the juvenile to adult transition. Given that this effect can be partially reversed by providing the plant with sugar, it is likely that sugar produced in the leaves—or one of its metabolites—is the signal that triggers the juvenile to adult transition through the reduction of miR156 levels.
Consistent with this idea, Yang and co-workers revealed that mutant plants that are deficient in chlorophyll show elevated levels of miR156 and a delayed transition to the adult form. In addition, they showed that a gene called HXK1, which encodes a glucose signaling protein, helps to keep plants in the juvenile form under conditions of low sugar availability. HXK1 also contributes to the glucose-induced decrease in miR156 levels and does so, at least in part, by regulating the transcription of MIR156A and MIR156C genes into messenger mRNA. HXK1 is not solely responsible for the juvenile to adult transition, however, because plants that lack this protein are only slightly precocious in their transition to the adult form.
The works of Yang et al. and Yu et al. have thus provided key insights into the mechanisms by which a leaf-derived signal controls a key developmental change in plants. Just as fruit flies use their nutritional status to regulate the onset of metamorphosis, and mammals use it to control the onset of puberty, so plants use the level of sugar in their leaves to trigger the transition from juvenile to adult forms.
DOI: http://dx.doi.org/10.7554/eLife.00260.002
doi:10.7554/eLife.00260
PMCID: PMC3608266  PMID: 23538384
phase change; heteroblasty; Nicotiana benthamiana; heterochrony; miRNAs; nutrition; Arabidopsis
12.  Quantitative Analysis of the Phenotypic Variability of Shoot Architecture in Two Grapevine (Vitis vinifera) Cultivars 
Annals of Botany  2007;99(3):425-437.
Background and Aims
Plant architecture and its interaction with agronomic practices and environmental constraints are determinants of the structure of the canopy, which is involved in carbon acquisition and fruit quality development. A framework for the quantitative analysis of grapevine (Vitis vinifera) shoot architecture, based on a set of topological and geometrical parameters, was developed for the identification of differences between cultivars and the origins of phenotypic variability.
Methods
Two commercial cultivars (‘Grenache N’, ‘Syrah’) with different shoot architectures were grown in pots, in well-irrigated conditions. Shoot topology was analysed, using a hidden semi-Markov chain and variable-order Markov chains to identify deviations from the normal pattern of succession of phytomer types (P0–P1–P2), together with kinematic analysis of shoot axis development. Shoot geometry was characterized by final internode and individual leaf area measurements.
Key Results
Shoot architecture differed significantly between cultivars. Secondary leaf area and axis length were greater for ‘Syrah’. Secondary leaf area distribution along the main axis also differed between cultivars, with secondary leaves preferentially located towards the basal part of the shoot in ‘Syrah’. The main factors leading to differences in leaf area between the cultivars were: (a) slight differences in main shoot structure, with the supplementary P0 phytomer on the lower part of the shoot in ‘Grenache N’, which bears a short branch; and (b) an higher rate and duration of development of branches bearing by P1–P2 phytomers related to P0 ones at the bottom of the shoot in ‘Syrah’. Differences in axis length were accounted for principally by differences in individual internode morphology, with ‘Syrah’ having significantly longer internodes. This trait, together with a smaller shoot diameter, may account for the characteristic ‘droopy’ habit of ‘Syrah’ shoots.
Conclusions
This study highlights the architectural parameters involved in the phenotypic variability of shoot architecture in two grapevine cultivars. Differences in primary shoot structure and in branch development potential accounted for the main differences in leaf area distribution between the two cultivars. By contrast, shoot shape seemed to be controlled by differences in axis length due principally to differences in internode length.
doi:10.1093/aob/mcl276
PMCID: PMC2802955  PMID: 17204533
Architecture; shoot; organogenesis; morphogenesis; branching; leaf area; genotypic variability; Vitis vinifera
13.  Investigations of the Host Range of the Corn Cyst Nematode, Heterodera zeae, from Maryland 
Journal of Nematology  1987;19(Annals 1):97-106.
The host range of the corn cyst nematode, Heterodera zeae, recently detected in Maryland, was investigated. A total of 269 plant entries, representing 68 families, 172 genera, and 204 species, was inoculated with cysts or a mixture of eggs and second-stage juveniles of H. zeae. The host range of the Maryland population of H. zeae was limited to plants of the Gramineae and included 11 tribes, 33 genera, 42 species, and 77 entries. All 22 corn (Zea mays) cultivars tested were hosts. Other economic hosts included certain cultivars of barley (Hordeum vulgare), oat (Arena sativa), rice (Oryza sativa), sorghum (Sorghum bicolor), sugar cane (Saccharum interspecific hybrid), and wheat (Triticum aestivum). Fall panicum (Panicum dichotomiflorum), a weed species common to cultivated fields in Maryland, was also a host for H. zeae. Other hosts included meadow foxtail (Alopecurus pratensis), Calamagrostis eipgeios, Job's tears (Coix Lachryma-Jobi), green sprangletop (Leptochloa dubia), witchgrass (Panicum capillare), broomcorn (Panicum miliaceum), fountain grass (Pennisetum rueppeli), reed canary grass (Phalaris arundinacea), common reed (Phragmites australis), eastern gamagrass (Tripsacum dactyloides), corn (Zea mays), and teosinte (Zea mexicana).
PMCID: PMC2618679  PMID: 19290286
corn; corn cyst nematode; Heterodera zeae; host range; maize; Zea mays
14.  Native Environment Modulates Leaf Size and Response to Simulated Foliar Shade across Wild Tomato Species 
PLoS ONE  2012;7(1):e29570.
The laminae of leaves optimize photosynthetic rates by serving as a platform for both light capture and gas exchange, while minimizing water losses associated with thermoregulation and transpiration. Many have speculated that plants maximize photosynthetic output and minimize associated costs through leaf size, complexity, and shape, but a unifying theory linking the plethora of observed leaf forms with the environment remains elusive. Additionally, the leaf itself is a plastic structure, responsive to its surroundings, further complicating the relationship. Despite extensive knowledge of the genetic mechanisms underlying angiosperm leaf development, little is known about how phenotypic plasticity and selective pressures converge to create the diversity of leaf shapes and sizes across lineages. Here, we use wild tomato accessions, collected from locales with diverse levels of foliar shade, temperature, and precipitation, as a model to assay the extent of shade avoidance in leaf traits and the degree to which these leaf traits correlate with environmental factors. We find that leaf size is correlated with measures of foliar shade across the wild tomato species sampled and that leaf size and serration correlate in a species-dependent fashion with temperature and precipitation. We use far-red induced changes in leaf length as a proxy measure of the shade avoidance response, and find that shade avoidance in leaves negatively correlates with the level of foliar shade recorded at the point of origin of an accession. The direction and magnitude of these correlations varies across the leaf series, suggesting that heterochronic and/or ontogenic programs are a mechanism by which selective pressures can alter leaf size and form. This study highlights the value of wild tomato accessions for studies of both morphological and light-regulated development of compound leaves, and promises to be useful in the future identification of genes regulating potentially adaptive plastic leaf traits.
doi:10.1371/journal.pone.0029570
PMCID: PMC3257252  PMID: 22253737
15.  High-contrast three-dimensional imaging of the Arabidopsis leaf enables the analysis of cell dimensions in the epidermis and mesophyll 
Plant Methods  2010;6:17.
Background
Despite the wide spread application of confocal and multiphoton laser scanning microscopy in plant biology, leaf phenotype assessment still relies on two-dimensional imaging with a limited appreciation of the cells' structural context and an inherent inaccuracy of cell measurements. Here, a successful procedure for the three-dimensional imaging and analysis of plant leaves is presented.
Results
The procedure was developed based on a range of developmental stages, from leaf initiation to senescence, of soil-grown Arabidopsis thaliana (L.) Heynh. Rigorous clearing of tissues, made possible by enhanced leaf permeability to clearing agents, allowed the optical sectioning of the entire leaf thickness by both confocal and multiphoton microscopy. The superior image quality, in resolution and contrast, obtained by the latter technique enabled the three-dimensional visualisation of leaf morphology at the individual cell level, cell segmentation and the construction of structural models. Image analysis macros were developed to measure leaf thickness and tissue proportions, as well as to determine for the epidermis and all layers of mesophyll tissue, cell density, volume, length and width. For mesophyll tissue, the proportion of intercellular spaces and the surface areas of cells were also estimated. The performance of the procedure was demonstrated for the expanding 6th leaf of the Arabidopsis rosette. Furthermore, it was proven to be effective for leaves of another dicotyledon, apple (Malus domestica Borkh.), which has a very different cellular organisation.
Conclusions
The pipeline for the three-dimensional imaging and analysis of plant leaves provides the means to include variables on internal tissues in leaf growth studies and the assessment of leaf phenotypes. It also allows the visualisation and quantification of alterations in leaf structure alongside changes in leaf functioning observed under environmental constraints. Data obtained using this procedure can further be integrated in leaf development and functioning models.
doi:10.1186/1746-4811-6-17
PMCID: PMC2909956  PMID: 20598116
16.  Leaf Shape Responds to Temperature but Not CO2 in Acer rubrum 
PLoS ONE  2012;7(11):e49559.
The degree of leaf dissection and the presence of leaf teeth, along with tooth size and abundance, inversely correlate with mean annual temperature (MAT) across many plant communities. These relationships form the core of several methods for reconstructing MAT from fossils, yet the direct selection of temperature on tooth morphology has not been demonstrated experimentally. It is also not known if atmospheric CO2 concentration affects leaf shape, limiting confidence in ancient climate reconstructions because CO2 has varied widely on geologic timescales. Here I report the results of growing Acer rubrum (red maple) in growth cabinets at contrasting temperature and CO2 conditions. The CO2 treatment imparted no significant differences in leaf size and shape, while plants grown at cooler temperatures tended to have more teeth and more highly dissected leaves. These results provide direct evidence for the selection of temperature on leaf shape in one species, and support a key link in many leaf-climate methods. More broadly, these results increase confidence for using leaf shape in fossils to reconstruct paleoclimate.
doi:10.1371/journal.pone.0049559
PMCID: PMC3495865  PMID: 23152921
17.  Effects of Nitrogen Application Rate and Leaf Age on the Distribution Pattern of Leaf SPAD Readings in the Rice Canopy 
PLoS ONE  2014;9(2):e88421.
A Soil-Plant Analysis Development (SPAD) chlorophyll meter can be used as a simple tool for evaluating N concentration of the leaf and investigating the combined effects of nitrogen rate and leaf age on N distribution. We conducted experiments in a paddy field over two consecutive years (2008–2009) using rice plants treated with six different N application levels. N distribution pattern was determined by SPAD readings based on the temporal dynamics of N concentrations in individual leaves. At 62 days after transplantation (DAT) in 2008 and DAT 60 in 2009, leaf SPAD readings increased from the upper to lower in the rice canopy that received N levels of 150 to 375 kg ha−1The differences in SPAD readings between the upper and lower leaf were larger under higher N application rates. However, as plants grew, this atypical distribution of SPAD readings in canopy leaf quickly reversed to the general order. In addition, temporal dynamics of the leaf SPAD readings (N concentrations) were fitted to a piecewise function. In our model, changes in leaf SPAD readings were divided into three stages: growth, functioning, and senescence periods. The leaf growth period lasted approximately 6 days, and cumulative growing days were not affected by N application rates. The leaf functioning period was represented with a relatively stable SPAD reading related to N application rate, and cumulative growing days were extended with increasing N application rates. A quadratic equation was utilized to describe the relationship between SPAD readings and leaf age during the leaf senescence period. The rate of decrease in SPAD readings increased with the age of leaves, but the rate was slowed by N application. As leaves in the lower canopy were physiologically older than leaves in the upper canopy, the rate of decrease in SPAD readings was faster in the lower leaves.
doi:10.1371/journal.pone.0088421
PMCID: PMC3919772  PMID: 24520386
18.  Contemporary Seasonal and Altitudinal Variations of Leaf Structural Features in Oregano (Origanum vulgare L.) 
Annals of Botany  2003;92(5):635-645.
The effects of elevation (200, 950 and 1760 m) and season (April–October) on leaf morphological, anatomical, ultrastructural, morphometrical and photosynthetic parameters were studied in Origanum vulgare plants. Observations aimed at the determination of the alterations in leaf structure and function associated with differential growth and adaptation of plants. Raising elevation results in a progressive decrease of plant height. During the growing period, summer plants are taller than spring and autumn plants at all elevations examined. In high‐altitude populations (O. vulgare ssp. vulgare), the blade size becomes reduced in June leaves as compared with October leaves, while it does not change remarkably in low‐altitude populations (O. vulgare ssp. hirtum). Leaf thickness remains more or less stable during the growing period. Expanded leaves in June and October at 200 m elevation contain dark phenolics only in their epidermis, whereas leaves of August are densely filled with phenolics in all of their tissues. In June at 1760 m elevation, leaves are devoid of phenolics, which, however, occur in the epidermis of the leaves in August and October. At higher altitudes, larger mesophyll chloroplasts with more starch grains are present in June leaves, whereas in August and October leaves chloroplasts are smaller with fewer starch grains. Leaf stomata and non‐glandular hairs increase in number from the lowland to the upland habitats, whereas glandular hairs decrease in number. During the growing season, the density of stomata and of glandular and non‐glandular hairs progressively increases. In the low‐ and mid‐altitude oregano populations, leaf chlorophyll a content and PSII activity significantly increase in October, whereas they simultaneously decrease in the high‐altitude population, suggesting a phenomenon of chilling‐induced photoinhibition. The highest photochemical efficiency of PSII appears in the mid‐altitude population (having characteristics intermediate between those of O. vulgare ssp. hirtum and ssp. vulgare) where environmental conditions are more favourable. This conclusion is also confirmed by the observation that the 950 m O. vulgare population has larger and thicker leaves with highly developed palisade and spongy parenchymas.
doi:10.1093/aob/mcg180
PMCID: PMC4244847  PMID: 12967906
Origanum vulgare L.; oregano; altitude; season; leaf; structure and ultrastructure; morphometry; chlorophyll fluorescence
19.  Rice Morphogenesis and Plant Architecture: Measurement, Specification and the Reconstruction of Structural Development by 3D Architectural Modelling 
Annals of Botany  2005;95(7):1131-1143.
• Background and Aims The morphogenesis and architecture of a rice plant, Oryza sativa, are critical factors in the yield equation, but they are not well studied because of the lack of appropriate tools for 3D measurement. The architecture of rice plants is characterized by a large number of tillers and leaves. The aims of this study were to specify rice plant architecture and to find appropriate functions to represent the 3D growth across all growth stages.
• Methods A japonica type rice, ‘Namaga’, was grown in pots under outdoor conditions. A 3D digitizer was used to measure the rice plant structure at intervals from the young seedling stage to maturity. The L-system formalism was applied to create ‘3D virtual rice’ plants, incorporating models of phenological development and leaf emergence period as a function of temperature and photoperiod, which were used to determine the timing of tiller emergence.
• Key Results The relationships between the nodal positions and leaf lengths, leaf angles and tiller angles were analysed and used to determine growth functions for the models. The ‘3D virtual rice’ reproduces the structural development of isolated plants and provides a good estimation of the tillering process, and of the accumulation of leaves.
• Conclusions The results indicated that the ‘3D virtual rice’ has a possibility to demonstrate the differences in the structure and development between cultivars and under different environmental conditions. Future work, necessary to reflect both cultivar and environmental effects on the model performance, and to link with physiological models, is proposed in the discussion.
doi:10.1093/aob/mci136
PMCID: PMC4246908  PMID: 15820987
Rice; Oryza sativa; morphogenesis; plant architecture; L-system; 3D modelling
20.  The Derivation of Sink Functions of Wheat Organs using the GREENLAB Model 
Annals of Botany  2007;101(8):1099-1108.
Background and Aims
In traditional crop growth models assimilate production and partitioning are described with empirical equations. In the GREENLAB functional–structural model, however, allocation of carbon to different kinds of organs depends on the number and relative sink strengths of growing organs present in the crop architecture. The aim of this study is to generate sink functions of wheat (Triticum aestivum) organs by calibrating the GREENLAB model using a dedicated data set, consisting of time series on the mass of individual organs (the ‘target data’).
Methods
An experiment was conducted on spring wheat (Triticum aestivum, ‘Minaret’), in a growth chamber from, 2004 to, 2005. Four harvests were made of six plants each to determine the size and mass of individual organs, including the root system, leaf blades, sheaths, internodes and ears of the main stem and different tillers. Leaf status (appearance, expansion, maturity and death) of these 24 plants was recorded. With the structures and mass of organs of four individual sample plants, the GREENLAB model was calibrated using a non-linear least-square-root fitting method, the aim of which was to minimize the difference in mass of the organs between measured data and model output, and to provide the parameter values of the model (the sink strengths of organs of each type, age and tiller order, and two empirical parameters linked to biomass production).
Key Results and Conclusions
The masses of all measured organs from one plant from each harvest were fitted simultaneously. With estimated parameters for sink and source functions, the model predicted the mass and size of individual organs at each position of the wheat structure in a mechanistic way. In addition, there was close agreement between experimentally observed and simulated values of leaf area index.
doi:10.1093/aob/mcm212
PMCID: PMC2710274  PMID: 18045794
Wheat; Triticum aestivum ‘Minaret’; tiller; GREENLAB; organ mass; functional–structural model; model calibration; multi-fitting; source–sink
21.  Key Plant Structural and Allocation Traits Depend on Relative Age in the Perennial Herb Pimpinella saxifraga 
Annals of Botany  2005;96(2):323-330.
• Background and Aims Perennial plant formations always include a mixture of various-aged individuals of community-creating species, but the physiological and competitive potentials of plants of differing age and the importance on whole community functioning are still not entirely known. The current study tested the hypothesis that ontogenetically old plants have limited biomass investments in leaves and enhanced foliage support costs.
• Methods Leaf structure, size and biomass allocation were studied in the perennial herb Pimpinella saxifraga during plant ontogeny from seedling to senile phases to determine age-dependent controls on key plant structural traits. The average duration of the full ontogenetic cycle is approx. 5–10 years in this species. Plants were sampled from shaded and open habitats.
• Key Results Leaflet dry mass per unit area (MA) increased, and the fraction of plant biomass in leaflets (FL) decreased with increasing age, leading to a 5- to 11-fold decrease in leaf area ratio (LAR = FL/MA) between seedlings and senescent plants. In contrast, the fraction of below-ground biomass increased with increasing age. Leaflet size and number per leaf increased with increasing age. This was not associated with enhanced support cost in older plants as age-dependent changes in leaf shape and increased foliage packing along the rachis compensated for an overall increase in leaf size. Age-dependent trends were the same in habitats with various irradiance, but the LAR of plants of varying age was approx. 1·5-fold larger in the shade due to lower MA and larger FL.
• Conclusions As plant light interception per unit total plant mass scales with LAR, these data demonstrate major age-dependent differences in plant light-harvesting efficiency that are further modified by site light availability. These ontogenetic changes reduce the differences among co-existing species in perennial communities, and therefore need consideration in our understanding of how herbaceous communities function.
doi:10.1093/aob/mci180
PMCID: PMC4246880  PMID: 15965271
Age-dependent changes; biomass allocation; leaf morphology; leaf area ratio; plasticity; support costs
22.  Effect of light on the growth and photosynthesis of an invasive shrub in its native range 
AoB Plants  2014;6:plu033.
We studied the growth and photosynthetic capacity of Berberis darwinii shrub growing under different light conditions in their native area of Argentina to test if plant physiology differs from invaded area (using studies carried out in New Zealand). In its native range B. darwinii grows under different light conditions by adjusting shoot and leaf morphology and physiology. Plants of B. darwinii growing under the same light environments show similar physiology in native and invasive ranges. Therefore, intra-specific variations of the functional traits in native area do not condition successful invasiveness.
Invasive species' success may depend on ecophysiological attributes present in their native area or those derived from changes that took place in the invaded environment. We studied the growth and photosynthetic capacity of Berberis darwinii shrubs growing under different light conditions (gap, forest edge and below the canopy) in their native area of Patagonia, Argentina. Leaf photosynthesis results determined in the native area were discussed in relation to information provided by studies carried out under the same light conditions in an invaded area in New Zealand. Shoot elongation, leaf production, stem and leaf biomass per shoot, and specific leaf area (SLA, cm2 g−1) were determined in five adult plants, randomly selected in each of the three light conditions at two forest sites. Net photosynthesis as a function of PPFD (photosynthetic photon flux density), stomatal conductance (gs), maximum light-saturated photosynthesis rate (Pmax), Pmass (on mass bases) and water-use efficiency (WUEi) were determined in plants of one site. We predicted that functional traits would differ between populations of native and invasive ranges. In their native area, plants growing under the canopy produced the longest shoots and had the lowest values for shoot emergence and foliar biomass per shoot, while their SLA was higher than gap and forest edge plants. Leaf number and stem biomass per shoot were independent of light differences. Leaves of gap plants showed higher Pmax, Pmass and gs but lower WUEi than plants growing at the forest edge. In its native range B. darwinii grows under different light conditions by adjusting shoot and leaf morphology and physiology. Plants of B. darwinii growing under the same light conditions show similar physiology in native and invasive ranges. This means that for B. darwinii, intra-specific variation of the functional traits studied here does not condition successful spread in new areas.
doi:10.1093/aobpla/plu033
PMCID: PMC4240251  PMID: 24969502
Berberis darwinii; ecophysiological attributes; light environments; native and invasion area; plant invasion.
23.  Shoot Development in Grapevine (Vitis vinifera) is Affected by the Modular Branching Pattern of the Stem and Intra‐ and Inter‐shoot Trophic Competition 
Annals of Botany  2004;93(3):263-274.
• Background and Aims Shoot architecture variability in grapevine (Vitis vinifera) was analysed using a generic modelling approach based on thermal time developed for annual herbaceous species. The analysis of shoot architecture was based on various levels of shoot organization, including pre‐existing and newly formed parts of the stem, and on the modular structure of the stem, which consists of a repeated succession of three phytomers (P0–P1–P2).
• Methods Four experiments were carried out using the cultivar ‘Grenache N’: two on potted vines (one of which was carried out in a glasshouse) and two on mature vines in a vineyard. These experiments resulted in a broad diversity of environmental conditions, but none of the plants experienced soil water deficit.
• Key Results Development of the main axis was highly dependent on air temperature, being linearly related to thermal time for all stages of leaf development from budbreak to veraison. The stable progression of developmental stages along the main stem resulted in a thermal‐time based programme of leaf development. Leaf expansion rate varied with trophic competition (shoot and cluster loads) and environmental conditions (solar radiation, VPD), accounting for differences in final leaf area. Branching pattern was highly variable. Classification of the branches according to ternary modular structure increased the accuracy of the quantitative analysis of branch development. The rate and duration of leaf production were higher for branches derived from P0 phytomers than for branches derived from P1 or P2 phytomers. Rates of leaf production, expressed as a -function of thermal time, were not stable and depended on trophic competition and environmental conditions such as solar radiation or VPD.
• Conclusions The application to grapevine of a generic model developed in annual plants made it possible to identify constants in main stem development and to determine the hierarchical structure of branches with respect to the modular structure of the stem in response to intra‐ and inter‐shoot trophic competition.
doi:10.1093/aob/mch038
PMCID: PMC4242199  PMID: 14749253
Shoot architecture; shoot development; leaf expansion; branching; temperature; thermal time; model; trophic competition; Vitis vinifera L
24.  Leaf Area and Water Content Changes after Permanent and Temporary Storage 
PLoS ONE  2012;7(8):e42604.
Accurate measurements of leaf morphology must be taken to develop models of ecosystem productivity and climate change projections. Once leaves are removed from a plant they begin to lose water and degrade. If specimens cannot be measured immediately after harvest, it is important to store the leaves in a manner that reduces morphological changes. If preserved specimens are used, estimates that closely match fresh measurements need to be calculated. This study examined the change in leaf area after storage treatments and developed models that can be used to more accurately estimate initial leaf area. Fresh leaf area was measured from ten plant species then stored in one of two common storage treatments. After storage, leaf area was re-measured and comparisons were made between species and growth forms. Leaf area decreased the most after permanent storage treatments and the least after temporary storage. Pressed leaves shrunk over 18% while cold storage leaves shrunk under 4%. The woody dicot growth form shrunk the least in all treatments. Shrinkage was positively correlated with initial water content and dissection index, a measure of leaf shape and complexity.
doi:10.1371/journal.pone.0042604
PMCID: PMC3411807  PMID: 22880051
25.  52Fe Translocation in Barley as Monitored by a Positron-Emitting Tracer Imaging System (PETIS): Evidence for the Direct Translocation of Fe from Roots to Young Leaves via Phloem 
Plant and Cell Physiology  2008;50(1):48-57.
The real-time translocation of iron (Fe) in barley (Hordeum vulgare L. cv. Ehimehadaka no. 1) was visualized using the positron-emitting tracer 52Fe and a positron-emitting tracer imaging system (PETIS). PETIS allowed us to monitor Fe translocation in barley non-destructively under various conditions. In all cases, 52Fe first accumulated at the basal part of the shoot, suggesting that this region may play an important role in Fe distribution in graminaceous plants. Fe-deficient barley showed greater translocation of 52Fe from roots to shoots than did Fe-sufficient barley, demonstrating that Fe deficiency causes enhanced 52Fe uptake and translocation to shoots. In the dark, translocation of 52Fe to the youngest leaf was equivalent to or higher than that under the light condition, while the translocation of 52Fe to the older leaves was decreased, in both Fe-deficient and Fe-sufficient barley. This suggests the possibility that the mechanism and/or pathway of Fe translocation to the youngest leaf may be different from that to the older leaves. When phloem transport in the leaf was blocked by steam treatment, 52Fe translocation from the roots to older leaves was not affected, while 52Fe translocation to the youngest leaf was reduced, indicating that Fe is translocated to the youngest leaf via phloem in addition to xylem. We propose a novel model in which root-absorbed Fe is translocated from the basal part of the shoots and/or roots to the youngest leaf via phloem in graminaceous plants.
doi:10.1093/pcp/pcn192
PMCID: PMC2638711  PMID: 19073647
Barley; Fe translocation; Phloem; Positron-emitting tracer; Real-time imaging; Xylem

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