Interpreting the principal component analysis of multivariate density functions

Functional principal component analysis (FPCA) as a reduction data technique of a finite number T of functions can be used to identify the dominant modes of variation of numeric three-way data. We carry out the FPCA on multidimensional probability density functions, relate this method to other standard methods and define its centered or standardized versions. Grounded on the relationship between FPCA of densities, FPCA of their corresponding characteristic functions, PCA of the MacLaurin expansions of these characteristic functions and dual STATIS method applied to their variance matrices, we propose a method for interpreting the results of the FPCA of densities. This method is based on the investigations of the relationships between the scores of the FPCA and the moments associated to the densities. The method is illustrated using known Gaussian densities. In practice, FPCA of densities deals with observations of multidimensional variables on T occasions. These observations can be used to estimate the T associated densities (i) by estimating the parameters of these densities, assuming that they are Gaussian, or (ii) by using the Gaussian kernel method and choosing the matrix bandwidth by the normal reference rule. Thereafter, FPCA estimate is derived from these estimates and the interpretation method is carried out to explore the dominant modes of variation of the types of three-way data encountered in sensory analysis and archaeology

Light and nitrogen nutrition regulate apical control in Rosa hybrida L.

Apical control is defined as the inhibition of basal axillary bud outgrowth by an upper actively growing axillary axis, whose regulation is poorly understood yet differs markedly from the better-known apical dominance. We studied the regulation of apical control by environmental factors in decapitated Rosa hybrida in order to remove the apical hormonal influence and nutrient sink. In this plant model, all the buds along the main axis have a similar morphology and are able to burst in vitro. We concentrated on the involvement of light intensity and nitrate nutrition on bud break and axillary bud elongation in the primary axis pruned above the fifth leaf of each rose bush. We observed that apical control took place in low light (92 μmol m−2 s−1), where only the 2-apical buds grew out, both in low (0.25 mM) and high (12.25 mM) nitrate. In contrast, in high light (453 μmol m−2 s−1), the apical control only operates in low nitrate while all the buds along the stem grew out when the plant was supplied with a high level of nitrate. We found a decreasing photosynthetic activity from the top to the base of the plant concomitant with a light gradient along the stem. The quantity of sucrose, fructose, glucose and starch are higher in high light conditions in leaves and stem. The expression of the sucrose transporter RhSUC2 was higher in internodes and buds in this lighting condition, suggesting an increased capacity for sucrose transport. We propose that light intensity and nitrogen availability both contribute to the establishment of apical control

Nitrogen deficiency increases basal branching and modifies visual quality of the rose bushes

Rosebush architecture resulting from the spatial organisation of the plant axes induces plant shape and consequently within ornamental horticulture context, its visual quality and commercial value. This architecture can be modulated by environmental conditions, particularly in the horticulture context in which the possibilities to control growing conditions are numerous. The objectives of the study were to determine, in young rose bushes, (1) whether short periods of nitrogen deficiency affect branching and (2) whether this effect is sufficient to modify the visual quality of the plant in a sustainable manner. Between vegetative bud burst and the petal colour visible stage of the generated primary branch, young rooted cuttings of bush rose (cv Radrazz) were subjected to one of three nitrogen regimes: (1) no nitrogen deficiency, (2) continuous nitrogen deficiency, i.e. 35 days of N deficiency, and (3) nitrogen deficiency restricted to the flowering stages, i.e. 18 days of N deficiency. After the petal colour visible stage, all three groups of plants were supplied continuously with nitrogen. We observed the morphology of the axes and the kinetics of axillary bud burst. Twelve weeks after the petal colour visible stage, the visual quality of the rose bushes was evaluated by an expert jury. We found that nitrogen deficiencies (1) increased bud burst ratios in the medial and basal zones of the primary branch, (2) delayed the bud burst in the apical zone of the primary branch and (3) had long-term effects on plant visual quality. The continuous nitrogen deficiency regime produced flatter, more asymmetric and less vigorous rose bushes than the no nitrogen deficiency regime. By contrast, nitrogen deficiency during the flowering stages only resulted in more symmetric, taller and more vigorous rose bushes than the no nitrogen deficiency regime. Based on these results, the role of nitrogen on bud burst was discussed and candidate processes at the origin of the visual quality modification were suggested. This new approach combining ecophysiology and sensory assessment of ornamental plants enabled the identification of some early architecture components to be correlated with later visual quality characteristics and then to better target the physiological processes of interest

Coordinated developement of the architecture of the primary shoot in bush rose

The development of the architecture of ornamental bushes needs to be explicitly described because it defines both their visual appearance and their interface with the environment. The aim of this work was to describe the dynamics of organ development in the primary shoot of rose bushes and their coordination. Rosa hybrida L. \u27Radrazz\u27 was grown in a glasshouse in two seasons. Internodes and leaflets were measured frequently and elongation curves were fitted to a linear-plateau model. The number of leaflets per leaf displayed clear patterns of organization along the shoot. Allometric relationships linked all leaf dimensions to terminal leaflet length. The differences in internode length between successive phytomers resulted from differences in the extension rate and the duration of extension. Conversely, the differences in the terminal leaflet size resulted almost solely from differences in extension rate. Internodes and terminal leaflets extensions were closely coordinated. This work provides the basic elements for establishing a virtual plant model

Assessment of the visual quality of ornamental plants: Comparison of three methodologies in the case of the rosebush

The quality of ornamental plants can be appraised with several types of criteria: tolerance to biotic and abiotic stresses, development potentialities and aesthetics. This last criterion, aesthetic quality, is specific to ornamental plants and objective measurements are required. Three methodologies for measuring aesthetic quality have been proposed. The first involves classical measurements of morphological features, such as flower number and diameter or leaf size. The second is based on sensory methods recently adapted to ornamental plants. The third, used by the International Union for the Protection of New Varieties of Plants (UPOV) for distinctness, uniformity and stability (DUS) tests, is based on morphological characteristics calibrated on specific reference varieties. The aim of this work was to compare these three methodologies for assessing some flowering and foliage characteristics of rosebushes. Six plants from 10 rose varieties identified by UPOV as reference varieties were cultivated for two years in a greenhouse and outdoors in Angers, France. They were measured and photographed weekly during flowering. Photographs of the plants in full bloom were submitted to a panel of judges for sensory assessment. The results of the three assessment methodologies were compared. Sensory and morphometric measurements were highly correlated and sensory measurements confirmed UPOV scales, whereas some morphometric measures diverged slightly from UPOV scales. We discuss the advantages, disadvantages and complementarity of these three methodologies

Temporary water restriction or light intensity limitation promotes branching in rose bush

Plant branching, which results from axillary bud burst, governs plant architectural development, shape and visual quality. Bud burst is known to be sensitive to environmental conditions, including long-term changes in water status or light intensity. However, little is known about the effects of temporary water or light intensity constraints. We therefore studied the impact of temporary water restriction or light limitation on the branching and development of rose bush axes. Rooted cuttings of Rosa hybrida ‘Radrazz’ were grown until the secondary axes had ceased to elongate, in a greenhouse for water experiment and in growth chambers for light experiment. During the water experiment, the irrigation threshold was maintained at −8 kPa to ensure that water was not limiting until the primary axis reached the floral bud visible stage. Plants were then subjected to water restriction for 0, 7, 14, 21 or 35 days, with an irrigation threshold of −26 kPa. They were then returned to the initial conditions and grown without water constraint until the end of the experiment. During the light experiment, plants subjected to light limitation were illuminated with low-intensity light (91 μmol m−2 s−1) from cutting bud burst until the floral bud visible stage (16 days), or to the petal color visible stage (27 days). Plants were then placed at high light intensity (580 μmol m−2 s−1). Control plants were maintained continuously in high-light intensity conditions. We found that, during constraint, a similar number (water restriction) or fewer (light limitation) buds burst than in control plants. When constraints were released, bud burst rapidly increased to levels +41–54% higher than those of control plants for water-restricted plants and +34–45% higher than those of control plants for light-limited plants. Excess bud burst occurred in the median zone of the primary axis. Flowering shoot number was 35% and 22% higher than control levels in plants subjected to 16 and 27 days of light limitation, respectively. Water limitation did not increase the number of flowering shoots despite the increase in bud burst it induced, due to an increase in the number of blind shoots. Overall, our findings show, for the first time, that temporary water or light restrictions promote the branching and development of rose bush axes. We suggest that sugar metabolism and hormonal regulation may be involved in stimulating branching after the release of these two types of constraint

Rose bush leaf and internode expansion dynamics: analysis and development of a model capturing interplant variability

Rose bush architecture, among other factors, such as plant health, determines plant visual quality. The commercial product is the individual plant and interplant variability may be high within a crop. Thus, both mean plant architecture and interplant variability should be studied. Expansion is an important feature of architecture, but it has been little studied at the level of individual organs in rose bushes. We investigated the expansion kinetics of primary shoot organs, to develop a model reproducing the organ expansion of real crops from non-destructive input variables. We took interplant variability in expansion kinetics and the model\u27s ability to simulate this variability into account. Changes in leaflet and internode dimensions over thermal time were recorded for primary shoot expansion, on 83 plants from three crops grown in different climatic conditions and densities. An empirical model was developed, to reproduce organ expansion kinetics for individual plants of a real crop of rose bush primary shoots. Leaflet or internode length was simulated as a logistic function of thermal time. The model was evaluated by cross-validation. We found that differences in leaflet or internode expansion kinetics between phytomer positions and between plants at a given phytomer position were due mostly to large differences in time of organ expansion and expansion rate, rather than differences in expansion duration. Thus, in the model, the parameters linked to expansion duration were predicted by values common to all plants, whereas variability in final size and organ expansion time was captured by input data. The model accurately simulated leaflet and internode expansion for individual plants (RMSEP = 7.3 and 10.2% of final length, respectively). Thus, this study defines the measurements required to simulate expansion and provides the first model simulating organ expansion in rosebush to capture interplant variability

Impacts of contrasting light on bud burst and on RwMAX1 and RwMAX2 expression in rose

Bud burst is a crucial factor in plant architecture and is strongly induced by light. In Rosa sp., this light effect was correlated with the growth of axillary buds and RwMAX1 and RwMAX2 expression within buds. In this paper, we investigated whether strigolactone pathway is involved in the regulation of axillary bud in response to light intensity. Hence, young roses were subjected to two contrasting light intensity regimes: high/high and high/low. The phenotype was characterized in both conditions and the expression of RwMAX1 and RwMAX2 genes was measured in the basal, middle and apical parts of rose primary branch. Light treatments showed a strong impact on axillary bud. The percentage of bud burst was severely reduced in the treatment high/low compared to the treatment high/high in all branch parts. In addition, the expression of RwMAX1 and RwMAX2 was strongly inhibited by high/high light regime and was conversely correlated with the rate of bud burst. In in vitro-grown axillary buds supplied with sucrose, glucose and fructose, RwMAX1 expression was significantly stimulated whereas that of RwMAX2 was significantly inhibited. Our results suggest that although RwMAX1 and RwMAX2 expression can be regulated by light, this expression does not explain the ability of bud burst

Sensory profiles and preference analysis in ornamental horticulture: The case of the rosebush

The context of ornamental horticulture is considered in order to extend the techniques of sensory and preference evaluation by taking the rosebush as a plant model. In a preliminary study (Boumaza, Demotes-Mainard, Huché-Thélier, & Guérin, 2009), a sensory evaluation was conducted in order to set up a list of attributes. Subsequently, this list was adapted to assess 10 rosebushes. After the control of the panel performance using a multivariate strategy of analysis, the average scores were used in product mapping. The evaluation of the preferences with regard to these rosebushes was undertaken: 253 subjects were asked to rank the products by decreasing order of liking. Thereafter, the preference data were subjected to an internal preference mapping and a cluster analysis. Six homogeneous segments of consumers were eventually retained. By way of performing an external preference mapping, the average ranks were regressed upon the sensory attributes using principal component regression: the preferences of 67% of the consumers were satisfactorily explained by the attributes

Plant responses to red and far-red lights, applications in horticulture

Light drives plant growth and development, so its control is increasingly used as an environment-friendly tool to manage horticultural crops. However, this implies a comprehensive view of the main physiological processes under light control, and bridging knowledge gaps. This review presents the state of the art in i) perception of red (R) and far-red (FR) wavelengths and of the R:FR ratio by plants, ii) phenotypic plant responses, and iii) the molecular mechanisms related to these responses. Changes in red or far red radiation and R:FR ratios are perceived by phytochromes. Phytochrome-mediated regulation is complex and specific to each physiological process. Our review presents the effects of red and far-red lights on germination, aerial architectural development, flowering, photosynthesis and plant nutrition. It also addresses how red and far-red radiations interact with tolerance to drought, pathogens and herbivores. Current knowledge about the mechanisms whereby red, far-red and R:FR regulate these different processes is presented. The specific actors of light signal transduction are better known for germination or flowering than for other processes such as internode elongation or bud outgrowth. The phenotypic response to red, far-red and R:FR can vary among species, but also with growing conditions. The mechanisms underlying these differences in plant responses still need to be unveiled. Current knowledge about plants\u27 response to light is being applied in horticulture to improve crop yield and quality. To that purpose, it is now possible to manipulate light quality thanks to recent technological evolutions such as the development of photo-selective films and light-emitting diodes