Background Geophytes possess specialized storage organs - bulbs, tubers, corms or rhizomes, which allow their survival during unfovarable periods and provide energy support for sprouting and sexual and vegetative reproduction. Bulbing and flowering of the geophyte depend on the combined effects of the internal and external factors, especially temperature and photoperiod. Many geophytes are extensively used in agriculture, but mechanisms of regulation of their flowering and bulbing are still unclear. Results Comparative morpho-physiological and transcriptome analyses and quantitative validation of gene expression shed light on the molecular regulation of the responses to vernalization in garlic, a typical bulbous plant. Long dark cold exposure of bulbs is a major cue for flowering and bulbing, and its interactions with the genetic makeup of the individual plant dictate the phenotypic expression during growth stage. Photoperiod signal is not involved in the initial nuclear and metabolic processes, but might play role in the later stages of development, flower stem elongation and bulbing. Vernalization for 12 weeks at 4 degrees C and planting in November resulted in flower initiation under short photoperiod in December-January, and early blooming and bulbing. In contrast, non-vernalized plants did not undergo meristem transition. Comparisons between vernalized and non-vernalized bulbs revealed 14,000 differentially expressed genes. Conclusions Low temperatures stimulate a large cascades of molecular mechanisms in garlic, and a variety of flowering pathways operate together for the benefit of meristem transition, annual life cycle and viable reproduction results.The circadian clock appears to play a central role in the transition of the meristem from vegetative to reproductive stage in bulbous plant, serving as integrator of the low-temperature signals and the expression of the genes associated with vernalization, photoperiod and meristem transition. The reserved photoperiodic pathway is integrated at an upstream point, possibly by the same receptors. Therefore, in bulb, low temperatures stimulate cascades of developmental mechanisms, and several genetic flowering pathways intermix to achieve successful sexual and vegetative reproduction.

Background The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. Results We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. Conclusions In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

Compound leaves are composed of multiple separate blade units termed leaflets. In tomato (Solanum lycopersicum) compound leaves, auxin promotes both leaflet initiation and blade expansion. However, it is unclear how these two developmental processes interact. With highly variable complexity, tomato compound leaves provide an ideal system to address this question. In this study, we obtained and analyzed mutants of theWUSCHEL-RELATED HOMEOBOX(WOX) family geneSlLAM1from tomato, whose orthologs in tobacco (Nicotiana sylvestris) and other species are indispensable for blade expansion. We show thatSlLAM1is expressed in the middle and marginal domains of leaves, and is required for blade expansion in leaflets. We demonstrate thatsllam1mutants cause a delay of leaflet initiation and slightly alter the arrangement of first-order leaflets, whereas the overall leaflet number is comparable to that of wild-type leaves. Analysis of the genetic interactions betweenSlLAM1and key auxin signaling components revealed an epistatic effect ofSlLAM1in determining the final leaf form. Finally, we show thatSlLAM1is also required for floral organ growth and affects the fertility of gametophytes. Our data suggest thatSlLAM1promotes blade expansion in multiple leaf types, and leaflet initiation can be largely uncoupled from blade expansion during compound leaf morphogenesis.

The 1,4-linked glucans such as xyloglucan and amylose are known to form a complex with iodine/iodide ions and to also be precipitated with CaCl(2)in the presence of iodine. Here, we show that iodine gas could be specifically incorporated into xyloglucan. Furthermore, we show that [I-125]I(2)gas is, over time, incorporated at high levels into the entire outer surface of poplar seedlings but that spraying seedlings with abscisic acid to close stomata decreases the incorporation of the gas. There was less incorporation of the gas in a transgenic poplar overexpressing xyloglucanase at the early stages when compared with a wild type. This shows that xyloglucan serves as a key absorber of iodine gas into a plant body. After individual leaves of cultured seedlings were exposed to the gas for 30 min, no radioiodine was emitted from those leaves over the following two weeks, indicating that no turnover occurs in radioiodine once it is bound to the polysaccharides in plant tissues. We conclude that forest trees could serve as one of the largest enormous capture systems for the radioiodine fallout following the nuclear power plant accident in Fukushima.

Forest trees possess high genetic diversity and high heterozygosity which allow adaptation to changing environmental conditions. There is a tendency to propagate successful and unique genotypes, which are identified at their mature stage in the forests, for future improvement programs and conservation purposes. However, vegetative propagation of mature forest trees is still a challenge in many conifers. In this study, we focused on improving the rooting of cuttings of mature and old Pinus halepensis and its hybrids. We observed that storage of cuttings before rooting at 4 degrees C for 4 weeks and prolong immersion of cuttings in a solution containing 400 mg/I of indole-3-butyric acid, 5 mg/I of the auxin conjugate 2-(2,4-dichlorophenoxy)propanoicacid-glycine methyl ester, and 0.01% of Amistar fungicide significantly improved rooting of mature cuttings. The active ingredient in Amistar is azoxystrobin, an uncoupler of respiration, which seems to directly promote rooting. Rooted cuttings of selected clones demonstrated unique and uniform growth performance, most likely delivering the intrinsic growth parameters of the mother trees. It was also observed that trees growing under drought stress possess improved rooting ability. By using rooted cuttings, it will be possible to study the relationship between growth rate and adaptation to semi-arid climate conditions. The ability to clonal propagate mature and old P halepensis trees not only enables vegetative propagation of elite trees for improvement programs, but also provides an opportunity to preserve unique naturally occurring old P. halepensis genotypes.

The abscission process occurs in a specific abscission zone (AZ) as a consequence of the middle lamella dissolution, cell wall degradation, and formation of a defense layer. The proteins and metabolites related to these processes are secreted by vesicle trafficking through the plasma membrane to the cell wall and middle lamella of the separating cells in the AZ. We investigated this process, since the regulation of vesicle trafficking in abscission systems is poorly understood. The data obtained describe, for the first time, the kinetics of the upregulated expression of genes encoding the components involved in vesicle trafficking, occurring specifically in the tomato (Solanum lycopersicum) flower AZ (FAZ) during pedicel abscission induced by flower removal. The genes encoding vesicle trafficking components included soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), SNARE regulators, and small GTPases. Our results clearly show how the processes of protein secretion by vesicle trafficking are regulated, programmed, and orchestrated at the level of gene expression in the FAZ. The data provide evidence for target proteins, which can be further used for affinity purification of plant vesicles in their natural state. Such analyses and dissection of the complex vesicle trafficking networks are essential for further elucidating the mechanism of organ abscission.

Juvenile and vegetative adult shoot apical meristems (SAM) are actively involved in acquisition of flowering competence, while the embryonic SAM is regarded as ``responsible'' only for germination. Comparative analyses of imbibed and stratified seeds of garlic Allium sativum show that only stratified seedlings produced bulbs and flower stems at the end of the season. Since the seed morphology of stratified and non-stratified seeds prior to sowing was similar, the differences are attributed to the molecular alterations in the embryonic SAM. Functional annotation analysis of 3000 differentially expressed genes suggests that seed imbibition reactivates the embryonic cell cycle, initiates the metabolism, and primes garlic seed germination. Stratification enhances DNA modifications, biosynthesis, cellular transport, and tissue development. Similar to vernalization of the vegetative buds, stratification of the embryonic SAM resulted in altered expression of meristem-identity and flowering homologs. Phase transitions from seed germination to flowering and bulbing in A. sativum are tightly connected, and possibly associated with downregulation of specific flowering repressor(s). The embryonic SAM plays an important role not only in seed germination, but in the entire plant life cycle, providing the foundation for the genetic regulation of major functional shifts in metabolism and development.

Tef (Eragrostis tef (Zucc.) Trotter) is a panicle-bearing cereal crop plant, originating from and grown mainly in Ethiopia. Tef yields highly nutritious gluten-free grain as well as high-quality forage, therefore, interest is rising regarding tef cultivation for grain and forage outside Ethiopia. Lodging is a major factor limiting tef quality and yield, with losses estimated at 30%-35% and presumably higher under mechanical harvest. Studies in other cereal crops suggested that lowering plant density would lead to sturdier plants less prone to lodging. In this work, we reported on the effects of sowing rate on lodging, lodging-related traits, and productivity of tef under irrigated conditions. Four tef genotypes were grown under irrigation across two years at three sowing rates: low (3 kg/ha), medium (6 kg/ha), and high (common, 9 kg/ha). Grain yield and biomass did not differ significantly among sowing rates. The visually assessed lodging index (LI) increased as the season progressed, with the lowest values recorded under low sowing density. A significant difference in LI values among the tested genotypes suggested potential for crop improvement. Aerial RGB images of the field taken by an unmanned aerial vehicle twice during the second season produced a high-resolution crop surface model, which was used to assess lodging. Aerial-based LI values were significantly correlated with the ground-based ones and exhibited better capacity to identify minor differences in lodging. Among the morphological traits assessed, crown diameter, crown root number, and crown root diameter were significantly affected by sowing rate and genotype and were correlated with LI values. In summary, this study demonstrated for the first time the feasibility of tef production under irrigated Mediterranean conditions and the potential of a reduced sowing rate as a remedy for lodging.

Leaf nitrogen concentration often is higher in leguminous plants, which associate with dinitrogen-fixing bacteria, compared with nonlegume plants. However, the range of nitrogen concentrations in legumes is wide, likely related to the range of nitrogen fixation strategies. We evaluated how carbon and nitrogen allocation to roots, stems and leaves is influenced by the type of strategy of nitrogen fixation regulation. We grew herbaceous annual legumes (Medicago truncatula, Hymenocarpos circinnatus and Vicia palaestina) under two nitrogen availability treatments (none/sufficient), with and without bacterial inoculation. We found facultative downregulation of the rate of nitrogen fixation when nitrogen was available in H. circinnatus, and an obligate similar fixation rate in both nitrogen treatments in M. truncatula and V. palaestina. Uninoculated plants invested more biomass in roots and contained lower nitrogen concentrations. However, nitrogen concentration in the entire plant and in the leaves was lower and more plastic in the species with a facultative fixation strategy, whereas species with an obligate fixation strategy also maintained high nitrogen concentrations. Our results suggest a suite of functional traits associated with the strategies of allocation and symbiotic nitrogen fixation. This suite of traits probably shapes successional and functional niches of different leguminous species in specious plant communities.

Remote-sensing tools and satellite data are often used to map and monitor changes in vegetation cover in forests and other perennial woody vegetation. Large-scale vegetation mapping from remote sensing is usually based on the classification of its spectral properties by means of spectral Vegetation Indices (VIs) and a set of rules that define the connection between them and vegetation cover. However, observations show that, across a gradient of precipitation, similar values of VI can be found for different levels of vegetation cover as a result of concurrent changes in the leaf density (Leaf Area Index-LAI) of plant canopies. Here we examine the three-way link between precipitation, vegetation cover, and LAI, with a focus on the dry range of precipitation in semi-arid to dry sub-humid zones, and propose a new and simple approach to delineate woody vegetation in these regions. By showing that the range of values of Normalized Difference Vegetation Index (NDVI) that represent woody vegetation changes along a gradient of precipitation, we propose a data-based dynamic lower threshold of NDVI that can be used to delineate woody vegetation from non-vegetated areas. This lower threshold changes with mean annual precipitation, ranging from less than 0.1 in semi-arid areas, to over 0.25 in mesic Mediterranean area. Validation results show that this precipitation-sensitive dynamic threshold provides a more accurate delineation of forests and other woody vegetation across the precipitation gradient, compared to the traditional constant threshold approach.

Global climate change and the increasing human population require crop varieties with higher yield and draught resistance. But meeting both goals is not an easy task for breeders and plant science.

Developing new crops adapted to arid conditions is a promising approach to meet the increasing demand for food production under expanding aridity. Tef [Eragrostis tef (Zucc.) Trotter] is a C4 cereal crop cultivated mainly in Ethiopia and the Horn of Africa, and known for its high resilience to stressful environments. Due to their tiny size, tef seeds are traditionally sown by broadcasting and lightly covering with soil. Under semiarid Mediterranean conditions, a deeper sowing may guarantee seedling establishment while saving on irrigation water. The objective of this study was, therefore, to determine the effects of sowing depth on tef emergence, development, lodging, and productivity. Tef seeds were sown at different depths in test tubes and pots, and in two field experiments. In tubes and pots, time from sowing to emergence increased about twofold and emergence rate decreased in the deepest sowing (3 cm) treatment compared to controls (0 cm). In the pot and field trials, deep sowing (3 cm) significantly reduced plant height, shoot and root biomass, and lodging. Sowing depths of 1-2 cm allowed successful plant establishment while not exacting penalties on plant emergence or development; hence this range appears to be optimal for sowing irrigated tef.

A protease is an enzyme that catalyzes proteolysis of proteins into smaller polypeptides or single amino acids. As crucial elements in many biological processes, proteases have been shown to be informative biomarkers for several pathological conditions in humans, animals, and plants. Therefore, fast, reliable, and cost-effective protease biosensors suitable for point-of-care (POC) sensing may aid in diagnostics, treatment, and drug discovery for various diseases. This work presents an affordable and simple paper-based dipstick biosensor that utilizes peptide-encapsulated single-wall carbon nanotubes (SWCNTs) for protease detection. Upon enzymatic digestion of the peptide, a significant drop in the photoluminescence (PL) of the SWCNTs was detected. As the emitted PL is in the near-infrared region, the developed biosensor has a good signal to noise ratio in biological fluids. One of the diseases associated with abnormal protease activity is pancreatitis. In acute pancreatitis, trypsin concentration could reach up to 84 mu g/mL in the urine. For proof of concept, we demonstrate the feasibility of the proposed biosensor for the detection of the abnormal levels of trypsin activity in urine samples.

Silicon is absorbed by plant roots as silicic acid. The acid moves with the transpiration stream to the shoot, and mineralizes as silica. In grasses, leaf epidermal cells called silica cells deposit silica in most of their volume using an unknown biological factor. Using bioinformatics tools, we identified a previously uncharacterized protein in Sorghum bicolor, which we named Siliplant1 (Slp1). Slp1 is a basic protein with seven repeat units rich in proline, lysine, and glutamic acid. We found Slp1 RNA in sorghum immature leaf and immature inflorescence. In leaves, transcription was highest just before the active silicification zone (ASZ). There, Slp1 was localized specifically to developing silica cells, packed inside vesicles and scattered throughout the cytoplasm or near the cell boundary. These vesicles fused with the membrane, releasing their content in the apoplastic space. A short peptide that is repeated five times in Slp1 precipitated silica in vitro at a biologically relevant silicic acid concentration. Transient overexpression of Slp1 in sorghum resulted in ectopic silica deposition in all leaf epidermal cell types. Our results show that Slp1 precipitates silica in sorghum silica cells.

Silicon dioxide in the form of hydrated silica is a component of plant tissues that can constitute several percent by dry weight in certain taxa. Nonetheless, the mechanism of plant silica formation is mostly unknown. Silicon (Si) is taken up from the soil by roots in the form of monosilicic acid molecules. The silicic acid is carried in the xylem and subsequently polymerizes in target sites to silica. In roots of sorghum (Sorghum bicolor), silica aggregates form in an orderly pattern along the inner tangential cell walls of endodermis cells. Using Raman microspectroscopy, autofluorescence, and scanning electron microscopy, we investigated the structure and composition of developing aggregates in roots of sorghum seedlings. Putative silica aggregation loci were identified in roots grown under Si starvation. These micrometer-scale spots were constructed of tightly packed modified lignin, and nucleated trace concentrations of silicic acid. Substantial variation in cell wall autofluorescence between Si+ and Si-roots demonstrated the impact of Si on cell wall chemistry. We propose that in Si-roots, the modified lignin cross-linked into the cell wall and lost its ability to nucleate silica. In Si+ roots, silica polymerized on the modified lignin and altered its structure. Our work demonstrates a high degree of control over lignin and silica deposition in cell walls.

Due to climate change, winter temperatures are predicted to increase worldwide. For thermophilic trees, highly sensitive to low temperatures, an increase in winter temperatures may be beneficial for survival and regeneration. Ziziphus spina-christi is a thermophilic tree that has recently become more abundant and widespread in the eastern Mediterranean, presumably due to a gradual increase in winter temperatures. We aim to define the temperature limitations for seed germination and the growth and survival of young seedlings to broaden our understanding of the future geographical distribution of this species. We studied effects of temperature on germination, growth, and photosynthesis in a controlled environment with four different day/night temperature regimes (34/28 degrees C, 28/22 degrees C, 22/16 degrees C and 16/10 degrees C). Effects of endocarp on germination and seed germination in the field were also studied. Results showed that germination has a lower thermal optimum (34-22 degrees C, 63.5-67.5% germination) than growth and photosynthesis (34-28 degrees C). Moderate cold stress (22/16 degrees C), did not affect germination capacity, but strongly reduced seedling growth (71%) and photosynthetic capacity (44.6%). Under severe cold stress (16/10 degrees C), germination still occurs (22%), but seedlings cannot perform growth and photosynthesis. We conclude that slow seedling growth, not germination, is the main barrier for successful establishment of Z. spina-christi under low temperature. Warmer winters could lead to earlier establishment of seedlings and increase their chance of survival the following summer. This may explain the recent increase in the tree's relative abundance and further highlight the potential spread of this species at higher altitudes and latitudes across the Mediterranean.

In-vivo foliar spectroscopy, also known as contact hyperspectral reflectance, enables rapid and non-destructive characterization of plant physiological status. This can be used to assess pathogen impact on plant condition both prior to and after visual symptoms appear. Challenging this capacity is the fact that dead tissue yields relatively consistent changes in leaf optical properties, negatively impacting our ability to distinguish causal pathogen identity. Here, we used in-situ spectroscopy to detect and differentiate Phytophthora infestans (late blight) and Alternaria solani (early blight) on potato foliage over the course of disease development and explored non-destructive characterization of contrasting disease physiology. Phytophthora infestans, a hemibiotrophic pathogen, undergoes an obligate latent period of two–seven days before disease symptoms appear. In contrast, A. solani, a necrotrophic pathogen, causes symptoms to appear almost immediately when environmental conditions are conducive. We found that respective patterns of spectral change can be related to these differences in underlying disease physiology and their contrasting pathogen lifestyles. Hyperspectral measurements could distinguish both P. infestans-infected and A. solani-infected plants with greater than 80% accuracy two–four days before visible symptoms appeared. Individual disease development stages for each pathogen could be differentiated from respective controls with 89–95% accuracy. Notably, we could distinguish latent P. infestans infection from both latent and symptomatic A. solani infection with greater than 75% accuracy. Spectral features important for late blight detection shifted over the course of infection, whereas spectral features important for early blight detection remained consistent, reflecting their different respective pathogen biologies. Shortwave infrared wavelengths were important for differentiation between healthy and diseased, and between pathogen infections, both pre- and post-symptomatically. This proof-of-concept work supports the use of spectroscopic systems as precision agriculture tools for rapid and early disease detection and differentiation tools, and highlights the importance of careful consideration of underlying pathogen biology and disease physiology for crop disease remote sensing.

The capability of unmanned aerial vehicle (UAV) spectral imagery to assess maize yield under full and deficit irrigation is demonstrated by a Tetracam MiniMCA12 11 bands camera. The MiniMCA12 was used to image an experimental field of 19 maize hybrids. Yield prediction models were explored for different maize development stages, with the best model found using maize plant development stage reproductive 2 (R2) for both maize grain yield and ear weight (respective R2 values of 0.73 and 0.49, and root mean square error of validation (RMSEV) values of 2.07 and 3.41 metric tons per hectare using partial least squares regression (PLS-R) validation models). Models using vegetation indices for inputs rather than superspectral data showed similar R2 but higher RMSEV values, and produced best results for the R4 development stage. In addition to being able to predict yield, spectral models were able to distinguish between different development stages and irrigation treatments. These abilities potentially allow for yield prediction of maize plants whose development stage and water status are unknown.

Understanding plant disease resistance is important in the integrated management of Phytophthora infestans, causal agent of potato late blight. Advanced field-based methods of disease detection that can identify infection before the onset of visual symptoms would improve management by greatly reducing disease potential and spread as well as improve both the financial and environmental sustainability of potato farms. In-vivo foliar spectroscopy offers the capacity to rapidly and non-destructively characterize plant physiological status, which can be used to detect the effects of necrotizing pathogens on plant condition prior to the appearance of visual symptoms. Here, we tested differences in spectral response of four potato cultivars, including two cultivars with a shared genotypic background except for a single copy of a resistance gene, to inoculation with Phytophthora infestans clonal lineage US-23 using three statistical approaches: random forest discrimination (RF), partial least squares discrimination analysis (PLS-DA), and normalized difference spectral index (NDSI). We find that cultivar, or plant genotype, has a significant impact on spectral reflectance of plants undergoing P. infestans infection. The spectral response of four potato cultivars to infection by Phytophthora infestans clonal lineage US-23 was highly variable, yet with important shared characteristics that facilitated discrimination. Early disease physiology was found to be variable across cultivars as well using non-destructively derived PLS-regression trait models. This work lays the foundation to better understand host-pathogen interactions across a variety of genotypic backgrounds, and establishes that host genotype has a significant impact on spectral reflectance, and hence on biochemical and physiological traits, of plants undergoing pathogen infection.

Plant domestication is often discussed as a form of mutualism between humans and crop plants. Ethnographies provide records of a multitude of adaptive strategies employed by human societies with varying degrees of reliance on manipulation of wild plant resources. These manipulations have included vegetation clearance, controlled burning, pruning, coppicing, tilling, sowing and more. Such activities can be viewed as cultivation of wild plants (known as “pre-domestication cultivation” in the Near Eastern research milieu, or in a somewhat different framework as “low level food production”), often considered a necessary step leading to domestication. Since cultivated fields are constructed niches, Niche Construction Theory (NCT) has recently been recruited to provide a theoretical evolutionary framework for explaining plant domestication. This review on plant domestication in the Near East discusses elements that we consider intimately related to the abovementioned trajectories of thought: the concept of “pre-domestication cultivation”; the view that domesticated plants arose via evolutionary mutualism; and the conceptualization of plant domestication in terms of NCT. We review and discuss the logic of these approaches, their biological, cultural and archaeological foundations; and highlight their association with the old “dump heap” scenario. We argue that based on the biology of the Near Eastern crop plants and the available archaeological evidence, these approached and respective arguments are inadequate. Rather, we contend that the biological idiosyncrasies of the Near Eastern founder crops depict a picture of a knowledge-based and conscious domestication that emanated from the newly emerging Neolithic world view and Humans-World relationships.