Active Vision and Surface Reconstruction for 3D Plant Shoot Modelling.

Plant phenotyping is the quantitative description of a plant's physiological, biochemical, and anatomical status which can be used in trait selection and helps to provide mechanisms to link underlying genetics with yield. Here, an active vision- based pipeline is presented which aims to contribute to reducing the bottleneck associated with phenotyping of architectural traits. The pipeline provides a fully automated response to photometric data acquisition and the recovery of three-dimensional (3D) models of plants without the dependency of botanical expertise, whilst ensuring a non-intrusive and non-destructive approach. Access to complete and accurate 3D models of plants supports computation of a wide variety of structural measurements. An Active Vision Cell (AVC) consisting of a camera-mounted robot arm plus combined software interface and a novel surface reconstruction algorithm is proposed. This pipeline provides a robust, flexible, and accurate method for automating the 3D reconstruction of plants. The reconstruction algorithm can reduce noise and provides a promising and extendable framework for high throughput phenotyping, improving current state-of-the-art methods. Furthermore, the pipeline can be applied to any plant species or form due to the application of an active vision framework combined with the automatic selection of key parameters for surface reconstruction.

Deep machine learning provides state-of-the-art performance in image-based plant phenotyping.

In plant phenotyping, it has become important to be able to measure many features on large image sets in order to aid genetic discovery. The size of the datasets, now often captured robotically, often precludes manual inspection, hence the motivation for finding a fully automated approach. Deep learning is an emerging field that promises unparalleled results on many data analysis problems. Building on artificial neural networks, deep approaches have many more hidden layers in the network, and hence have greater discriminative and predictive power. We demonstrate the use of such approaches as part of a plant phenotyping pipeline. We show the success offered by such techniques when applied to the challenging problem of image-based plant phenotyping and demonstrate state-of-the-art results (>97% accuracy) for root and shoot feature identification and localization. We use fully automated trait identification using deep learning to identify quantitative trait loci in root architecture datasets. The majority (12 out of 14) of manually identified quantitative trait loci were also discovered using our automated approach based on deep learning detection to locate plant features. We have shown deep learning-based phenotyping to have very good detection and localization accuracy in validation and testing image sets. We have shown that such features can be used to derive meaningful biological traits, which in turn can be used in quantitative trait loci discovery pipelines. This process can be completely automated. We predict a paradigm shift in image-based phenotyping bought about by such deep learning approaches, given sufficient training sets.

Exploring the fossil history of pleurocarpous mosses: Tricostaceae fam. nov. from the Cretaceous of Vancouver Island, Canada.

PREMISE OF THE STUDY: Mosses, very diverse in modern ecosystems, are currently underrepresented in the fossil record. For the pre-Cenozoic, fossil mosses are known almost exclusively from compression fossils, while anatomical preservation, which is much more taxonomically informative, is rare. The Lower Cretaceous of Vancouver Island (British Columbia, Canada) hosts a diverse anatomically preserved flora at Apple Bay. While the vascular plant component of the Apple Bay flora has received much attention, the numerous bryophytes identified at the locality have yet to be characterized. METHODS: Fossil moss gametophytes in more than 20 carbonate concretions collected from the Apple Bay locality on Vancouver Island were studied in serial sections prepared using the cellulose acetate peel technique. KEY RESULTS: We describe Tricosta plicata gen. et sp. nov., a pleurocarpous moss with much-branched gametophytes, tricostate plicate leaves, rhizoid-bearing bases, and delicate gametangia (antheridia and archegonia) borne on specialized branches. A new family of hypnanaean mosses, Tricostaceae fam. nov., is recognized based on the novel combination of characters of T. plicata. CONCLUSIONS: Tricosta plicata reveals pleurocarpous moss diversity unaccounted for in extant floras. This new moss adds the first bryophyte component to an already diverse assemblage of vascular plants described from the Early Cretaceous at Apple Bay and, as the oldest representative of the Hypnanae, provides a hard minimum age for the group (136 Ma).

Nut crop yield records show that budbreak-based chilling requirements may not reflect yield decline chill thresholds.

Warming winters due to climate change may critically affect temperate tree species. Insufficiently cold winters are thought to result in fewer viable flower buds and the subsequent development of fewer fruits or nuts, decreasing the yield of an orchard or fecundity of a species. The best existing approximation for a threshold of sufficient cold accumulation, the "chilling requirement" of a species or variety, has been quantified by manipulating or modeling the conditions that result in dormant bud breaking. However, the physiological processes that affect budbreak are not the same as those that determine yield. This study sought to test whether budbreak-based chilling thresholds can reasonably approximate the thresholds that affect yield, particularly regarding the potential impacts of climate change on temperate tree crop yields. County-wide yield records for almond (Prunus dulcis), pistachio (Pistacia vera), and walnut (Juglans regia) in the Central Valley of California were compared with 50 years of weather records. Bayesian nonparametric function estimation was used to model yield potentials at varying amounts of chill accumulation. In almonds, average yields occurred when chill accumulation was close to the budbreak-based chilling requirement. However, in the other two crops, pistachios and walnuts, the best previous estimate of the budbreak-based chilling requirements was 19-32 % higher than the chilling accumulations associated with average or above average yields. This research indicates that physiological processes beyond requirements for budbreak should be considered when estimating chill accumulation thresholds of yield decline and potential impacts of climate change.

Influence of pre- and postharvest summer pruning on the growth, yield, fruit quality, and carbohydrate content of early season peach cultivars.

Winter and summer pruning are widely applied processes in all fruit trees, including in peach orchard management. This study was conducted to determine the effects of summer prunings (SP), as compared to winter pruning (WP), on shoot length, shoot diameter, trunk cross sectional area (TCSA) increment, fruit yield, fruit quality, and carbohydrate content of two early ripening peach cultivars ("Early Red" and "Maycrest") of six years of age, grown in semiarid climate conditions, in 2008 to 2010. The trees were grafted on GF 677 rootstocks, trained with a central leader system, and spaced 5 × 5 m apart. The SP carried out after harvesting in July and August decreased the shoot length significantly; however, it increased its diameter. Compared to 2009, this effect was more marked in year 2010. In general, control and winter pruned trees of both cultivars had the highest TCSA increment and yield efficiency. The SP increased the average fruit weight and soluble solids contents (SSC) more than both control and WP. The titratable acidity showed no consistent response to pruning time. The carbohydrate accumulation in shoot was higher in WP and in control than in SP trees. SP significantly affected carbohydrate accumulation; postharvest pruning showed higher carbohydrate content than preharvest pruning.

New evidence of the reproductive organs of Glossopteris based on permineralized fossils from Queensland, Australia. II: pollen-bearing organ Ediea gen. nov.

Ediea homevalensis H. Nishida, Kudo, Pigg & Rigby gen. et sp. nov. is proposed for permineralized pollen-bearing structures from the Late Permian Homevale Station locality of the Bowen Basin, Queensland, Australia. The taxon represents unisexual fertile shoots bearing helically arranged leaves on a central axis. The more apical leaves are fertile microsporophylls bearing a pair of multi-branched stalks on their adaxial surfaces that each supports a cluster of terminally borne pollen sacs. Proximal to the fertile leaves there are several rows of sterile scale-like leaves. The pollen sacs (microsporangia) have thickened and dark, striate walls that are typical of the Arberiella type found in most pollen organs presumed to be of glossopterid affinity. An examination of pollen organs at several developmental stages, including those containing in situ pollen of the Protohaploxypinus type, provides the basis for a detailed analysis of these types of structures, which bear similarities to both compression/impression Eretmonia-type glossopterid microsporangiate organs and permineralized Eretmonia macloughlinii from Antarctica. These fossils demonstrate that at least some Late Permian pollen organs were simple microsporophyll-bearing shoot systems and not borne directly on Glossopteris leaves.

Fruit structure in Magnoliaceae s.l. and Archaeanthus and their relationships.

PREMISE OF THE STUDY: The family Magnoliaceae s.l. is a basal angiosperm family with two subfamilies-Magnolioideae and Liriodendroideae, which differ by the types and structure of their fruits and seeds. The late Albian genus Archaeanthus shares many features of its reproductive organs with Magnoliaceae s.l., but its pericarp anatomy was never studied in detail. A broad-scale carpological investigation of Archaeanthus and Magnoliaceae s.l. was undertaken to reveal the nature of the similarities in fruit structure and to reconstruct Archaeanthus pericarp anatomy. These data are important to determine the early stages of fruit morphogenesis and thus to clarify relationships of Archaeanthus to the taxa of Magnoliaceae s.l. METHODS: The pericarp anatomy was studied with light microscopy, SEM, and polarizing microscopy. KEY RESULTS: The dehiscent, polyspermous follicles shed from the receptacle of Archaeanthus share similarities with dehiscent follicles of Magnoliaceae s.s. and shedding nutlets of Liriodendron. The seeds of Archaeanthus are dorsiventrally flattened, ovoid, and encircled with a single circular wing. The pericarps of all the taxa studied are differentiated into exocarp (epidermis), multilayered mesocarp, and endocarp (fiber-like sclereids). The mesocarp consists of parenchyma with scattered secretory cells and sclereid clusters (Magnoliaceae s.s., Archaeanthus) or composed by sclerenchyma (Liriodendron). CONCLUSIONS: The specializations of dehiscent multifollicles of unknown Cretaceous ancestors for different modes of seed and fruitlet dispersal formed the basis for the differentiation of two evolutionary lines with their divergence occurring more than 100 million years ago: Magnoliaceae s.s. and the Archaeanthus-Liriodendroidea-Liriodendron line (Liriodendraceae s.l.) within the order Magnoliales.

Screening for heavy metal accumulators amongst autochtonous plants in a polluted site in Italy.

The site around ACNA factory (Northern Italy) is characterized by multi-metal contamination, therefore it can be considered as a source of autochthonous plants able to tolerate or accumulate heavy metals (HMs). The hill A5, a waste dump of the chemical factory, was chosen as the study area, in order to assess the metal accumulation ability of the vegetation growing under HM stress. The plant species, biodiversity and health were related to the concentration of HMs in four areas of the hill A5, and to the metal accumulation in shoots and roots. Uptake of HMs occurred at different extent in the various plant species and differed according to the considered organ and metal. Polygonum aviculare hyperaccumulated Hg in the shoot suggesting its possible exploitation in phytoextraction. A number of species, that can be useful in phytoremediation plans, accumulated simultaneously more than two heavy metals both in the shoot and in the root.

Differentiating Arabidopsis shoots from leaves by combined YABBY activities.

In seed plants, leaves are born on radial shoots, but unlike shoots, they are determinate dorsiventral organs made of flat lamina. YABBY genes are found only in seed plants and in all cases studied are expressed primarily in lateral organs and in a polar manner. Despite their simple expression, Arabidopsis thaliana plants lacking all YABBY gene activities have a wide range of morphological defects in all lateral organs as well as the shoot apical meristem (SAM). Here, we show that leaves lacking all YABBY activities are initiated as dorsiventral appendages but fail to properly activate lamina programs. In particular, the activation of most CINCINNATA-class TCP genes does not commence, SAM-specific programs are reactivated, and a marginal leaf domain is not established. Altered distribution of auxin signaling and the auxin efflux carrier PIN1, highly reduced venation, initiation of multiple cotyledons, and gradual loss of the SAM accompany these defects. We suggest that YABBY functions were recruited to mold modified shoot systems into flat plant appendages by translating organ polarity into lamina-specific programs that include marginal auxin flow and activation of a maturation schedule directing determinate growth.

Evaluación morfológica de brotes regenerados de callos de arroz (variedad IACuba-28) resistentes a higromicina / Morphological evaluation of shoots regenerated from hygromycin-resistant rice callus (cv IACuba-28)

Se estableció un sistema de evaluación de brotes de arroz regenerados de callos resistentes a higromicina, que permitió relacionar las características morfológicas de dichos brotes con su resistencia al antibiótico. Callos embriogénicos de arroz se transformaron con Agrobacterium tumefaciens (EHA105/ pCAMBIA1300),con el gen de la higromicina-fosfotransferasa como marcador de selección. Después de dos semanas en medio de cultivo con higromicina, los callos resistentes fueron transferidos a regeneración. Durante 30 días se realizaron extracciones sucesivas de brotes emitidos de los callos, en seis intervalos de cinco días cada uno. Estos brotes se clasificaron según su morfología en: clase I – brote vigoroso con una estructura bipolar típica, de ápice y raíz con longitudes proporcionales; clase II – brote con raíz pequeña respecto al ápice, o sin raíz; clase III – brote con alteraciones fenotípicas, albinismo, hojas muy anchas o enrolladas. Los brotes clasificados se transfirieron a medio MS con higromicina para evaluar su viabilidad. Los declase I, que predominaron en las primeras extracciones, presentaron la mayor viabilidad durante el enraizamiento y crecimiento del follaje. En las últimas dos extracciones ocurrió una drástica reducción de los brotes clase I, y aumentaron los de clases II y III, simultáneamente disminuyó la viabilidad de estos últimos en MS con higromicina. Este resultado puede aplicarse para mejorar la eficiencia de obtención de plantas transgénicas de arroz en estas condiciones, debido a que precisa el momento óptimo para lograr brotes con características morfológicas normales y que sean resistentes a higromicina.

Effect of root system morphology on root-sprouting and shoot-rooting abilities in 123 plant species from eroded lands in North-east Spain.

BACKGROUND AND AIMS: The objective of this study was to test whether the mean values of several root morphological variables were related to the ability to develop root-borne shoots and/or shoot-borne roots in a wide range of vascular plants. METHODS: A comparative study was carried out on the 123 most common plant species from eroded lands in north-east Spain. After careful excavations in the field, measurements were taken of the maximum root depth, absolute and relative basal root diameter, specific root length (SRL), and the root depth/root lateral spread ratio on at least three individuals per species. Shoot-rooting and root-sprouting were observed in a large number of individuals in many eroded and sedimentary environments. The effect of life history and phylogeny on shoot-rooting and root-sprouting abilities was also analysed. KEY RESULTS: The species with coarse and deep tap-roots tended to be root-sprouting and those with fine, fasciculate and long main roots (which generally spread laterally), tended to be shoot-rooting. Phylogeny had an important influence on root system morphology and shoot-rooting and root-sprouting capacities. However, the above relations stood after applying analyses based on phylogenetically independent contrasts (PICs). CONCLUSIONS: The main morphological features of the root system of the study species are related to their ability to sprout from their roots and form roots from their shoots. According to the results, such abilities might only be functionally viable in restricted root system morphologies and ecological strategies.

Classical and dynamic morphology: toward a synthesis through the space of forms.

In plant morphology, most structures of vascular plants can easily be assigned to pre-established organ categories. However, there are also intermediate structures that do not fit those categories associated with a classical approach to morphology. To integrate the diversity of forms in the same general framework, we constructed a theoretical morphospace based on a variety of modalities where it is possible to calculate the morphological distance between plant organs. This paper gives emphasis on shoot, leaf, leaflet and trichomes while ignoring the root. This will allow us to test the hypothesis that classical morphology (typology) and dynamic morphology occupy the same theoretical morphospace and the relationship between the two approaches remains a question of weighting of criteria. Our approach considers the shoot (i.e. leafy stem) as the basic morphological structural unit. A theoretical data table consisting of as many lines as there are possible combinations between different modalities of characters of a typical shoot was generated. By applying a principal components analysis (PCA) to these data it is possible to define a theoretical morphospace of shoots. Typical morphological elements (shoots, leaves, trichomes) and atypical structures (phylloclades, cladodes) including particular cases representing 'exotic' structures such as the epiphyllous appendages of Begonia and 'water shoot' and 'leaf' of aquatic Utricularia were placed in the morphospace. The more an organ differs from a typical shoot, the further away it will be from the barycentre of shoots. By giving a higher weight to variables used in classical typology, the different organ categories appear to be separate, as expected. If we do not make any particular arbitrary choice in terms of character weighting, as it is the case in the context of dynamic morphology, the clear separation between organs is replaced by a continuum. Contrary to typical structures, "intermediate" structures are only compatible with a dynamic morphology approach whether they are placed in the morphospace based on a ponderation compatible with typology or dynamic morphology. The difference in points of view between typology and continuum leads to a particular mode of weighting. By using an equal weighting of characters, contradictions due to the ponderation of characters are avoided, and the morphological concepts of continuum' and 'typology' appear as sub-classes of 'process' or 'dynamic morphology'.

[Karyotype of blue honeysuckle species (Lonicera subset. Caeruleae, Caprifoliaceae]. / Issledovanie kariotipa u vidov zhimolosti goluboi (Lonicera subset. Caeruleae, Caprifoliaceae).

For the first time the karyotypes of diploid (2n = 2x = 18) and tetraploid (2n = 4x = 36) species of Lonicera from the Caeruleae subsection: L. altaica Pall., L. boczkarnikowii Plekh. (L. regeliana Boczkarn.), L. edulis Turcz. ex Freyn (2x, 4x), L. emphyllocalyx Maxim., L. iliensis Pojark., L. kamtschatica Pojark., L. pallasii Ledeb., L. stenantha Pojark., L. turczaninowii Pojark., L. villosa (2x, 4x) (Michx.) Muhl. are described. The species karyotypes from 23 natural populations have shown the considerable generic resemblance that expressed in the similar chromosome morphology and variation range of their length from 1 to 3 microns. The species with the same level of ploidy had the same karyotype formula: 2m + 6sm + 1st in diploids and 4m + 11sm + 3st in tetraploids, respectively. The amphiploid origin of the tetraploid Lonicera species has been shown. Diploid and tetraploid forms of L. edulis and L. villosa were the particular karyotypes but not the 2x and 4x races of the same species, respectively. Specific differences were revealed in the total chromosome length in the haploid set and in the number of satellites and secondary constrictions. Generic resemblance and specific peculiarities of Lonicera karyotypes indicate a common center of the blue honeysuckle origin and a common initial population of karyotypes which evolved into several phylogenetic branches of the Caeruleae subsection: the Central Asiatic--L. iliensis and L. stenantha; the Siberian--L. altaica, L. edulis, and L. pallasii; the Beringian--L. emphyllocalyx, L. kamtschatica, and L. villosa; the Manchurian--L. boczkarnikowii (L. regeliana), and L. turczaninowii.

Alkaloid production by callous tissue cultures of Cereus peruvianus (Cactaceae).

The morphologically undifferentiated cells of nonregenerant callous tissue of Cereus peruvianus cultured in the original medium and in medium supplemented with tyrosine were used as an alkaloid source. Comparison of alkaloid production by C. peruvianus plants and by callous tissues indicated that alkaloid levels were almost twice as high in callous tissues as in shoots of C. peruvianus plants. The ratio of alkaloid concentration between mature plant and morphologically undifferentiated cells of callous tissue was 1:1.7. A relationship between culture medium containing tyrosine and alkaloid production was also observed in the callous tissues of C. peruvianus. Since increased alkaloid production may be induced by additional factors such as tyrosine, increasing levels of tyrosine or other conditions of the culture medium may be considered factors for inducing higher alkaloid production by C. peruvianus callous tissues.