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Background Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement. Result An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant ‘Halo’ and salt intolerant ‘Vernal’. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m− 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for ‘Halo’, 34 and 50 for ‘Vernal’, respectively. In root tissue, ‘Halo’ maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for ‘Vernal’. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in ‘Halo’ compared to ‘Vernal’ under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress. Conclusion The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.

Plant cell walls (CW) are composed mainly of cellulose–hemicellulose networks embedded in a pectin matrix. CW apposition, including papilla formation, is often associated with plant defence...

Advances in Infrared (IR) spectroscopies have entered a new era of research with applications in phytobiome, plant microbiome and health. Fusarium graminearum 3-ADON is the most aggressive mycotoxigenic chemotype causing Fusarium head blight (FHB) in cereals, while Sphaerodes mycoparasitica is the specific Fusarium mycoparasite with biotrophic lifestyle discovered in cereal seeds and roots. Fourier transform infrared (FTIR) spectroscopy analyses depicted shifts in the spectral peaks related to mycoparasitism mainly within the region of proteins, lipids, also indicating a link between carbohydrates and protein regions, involving potential phenolic compounds. Especially, S. mycoparasitica contributes to significant changes in lipid region 3050–2800 cm−1, while in the protein region, an increasing trend was observed for the peaks 1655–1638 cm−1 (amide I) and 1549–1548 cm−1 (amide II) with changes in indicative protein secondary structures. Besides, the peak extending on the region 1520–1500 cm−1 insinuates a presence of aromatic compounds in presence of mycoparasite on the F. graminearum root sample. Monitoring shift in improved seed germination, fungus-fungus interface through scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM), and FTIR molecular signatures combined with principal component analysis (PCA) proved useful tools to detect an early mycoparasitism as a vital asset of the preventive biocontrol strategy against plant pathogens.

Fusarium head blight, caused primarily by Fusarium graminearum (Fg), is one of the most devastating diseases of wheat. Host resistance in wheat is classified into five types (Type-I to Type-V), and a majority of moderately resistant genotypes carry Type-II resistance (resistance to pathogen spread in the rachis) alleles, mainly from the Chinese cultivar Sumai 3. Histopathological studies in the past failed to identify the key tissue in the spike conferring resistance to pathogen spread, and most of the studies used destructive techniques, potentially damaging the tissue(s) under study. In the present study, nondestructive synchrotron-based phase contrast X-ray imaging and computed tomography techniques were used to confirm the part of the wheat spike conferring Type-II resistance to Fg spread, thus showcasing the application of synchrotron-based techniques to image host-pathogen interactions. Seven wheat genotypes of moderate resistance to Fusarium head blight were studied for changes in the void space volume fraction and grayscale/voxel intensity following Fg inoculation. Cell-wall biopolymeric compounds were quantified using Fourier-transform midinfrared spectroscopy for all genotype-treatment combinations. The study revealed that the rachilla and rachis nodes together are structurally important in conferring Type-II resistance. The structural reinforcement was not necessarily observed from lignin deposition but rather from an unknown mechanism.

Field pea (Pisum sativum), a major grain legume crop, is autogamous and adapted to temperate climates. The objectives of this study were to investigate effects of high temperature stress on stamen chemical composition, anther dehiscence, pollen viability, pollen interactions with pistil and ovules, and ovule growth and viability. Two cultivars ("CDC Golden" and "CDC Sage") were exposed to 24/18°C (day/night) continually or to 35/18°C for 4 or 7 days. Heat stress altered stamen chemical composition, with lipid composition of "CDC Sage" being more stable compared with "CDC Golden." Heat stress reduced pollen viability and the proportion of ovules that received a pollen tube. After 4 days at 35°C, pollen viability in flower buds decreased in "CDC Golden," but not in "CDC Sage." After 7 days, partial to full failure of anthers to dehisce resulted in subnormal pollen loads on stigmas. Although growth (ovule size) of fertilized ovules was stimulated by 35°C, heat stress tended to decrease ovule viability. Pollen appears susceptible to stress, but not many grains are needed for successful fertilization. Ovule fertilization and embryos are less susceptible to heat, but further research is warranted to link the exact degree of resilience to stress intensity.

Soil salinity is a global concern and often the primary factor contributing to land degradation, limiting crop growth and production. Alfalfa (Medicago sativa L.) is a low input high value forage legume with a wide adaptation. Examining the tissue-specific responses to salt stress will be important to understanding physiological changes of alfalfa. The responses of two alfalfa cultivars (salt tolerant ‘Halo’, salt intolerant ‘Vernal’) were studied for 12 weeks in five gradients of salt stress in a sand based hydroponic system in the greenhouse. The accumulation and localization of elements and organic compounds in different tissues of alfalfa under salt stress were evaluated using synchrotron beamlines. The pattern of chlorine accumulation for ‘Halo’ was: root > stem ~ leaf at 8 dSm−1, and root ~ leaf > stem at 12 dSm−1, potentially preventing toxic ion accumulation in leaf tissues. In contrast, for ‘Vernal’, it was leaf > stem ~ root at 8 dSm−1 and leaf > root ~ stem at 12 dSm−1. The distribution of chlorine in ‘Halo’ was relatively uniform in the leaf surface and vascular bundles of the stem. Amide concentration in the leaf and stem tissues was greater for ‘Halo’ than ‘Vernal’ at all salt gradients. This study determined that low ion accumulation in the shoot was a common strategy in salt tolerant alfalfa up to 8 dSm−1 of salt stress, which was then replaced by shoot tissue tolerance at 12 dSm−1.

Arabidopsis eceriferum (cer) mutants with unique alterations in their rosette leaf cuticular wax accumulation and composition established by gas chromatography have been investigated using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy in combination with univariate and multivariate analysis. Objectives of this study were to evaluate the utility of ATR-FTIR for detection of chemical diversity in leaf cuticles, obtain spectral profiles of cer mutants in comparison with the wild type, and identify changes in leaf cuticles caused by drought stress. FTIR spectra revealed both genotype- and treatment-dependent differences in the chemical make-up of Arabidopsis leaf cuticles. Drought stress caused specific changes in the integrated area of the CH3 peak, asymmetrical and symmetrical CH2 peaks, ester carbonyl peak and the peak area ratio of ester CO to CH2 asymmetrical vibration. CH3 peak positively correlated with the total wax accumulation. Thus, ATR-FTIR spectroscopy is a valuable tool that can advance our understanding of the role of cuticle chemistry in plant response to drought and allow selection of superior drought-tolerant varieties from large genetic resources.

Simple plant cell morphologies, such as cylindrical shoot cells, are determined by the extensibility pattern of the primary cell wall, which is thought to be largely dominated by cellulose microfibrils, but the mechanism leading to more complex shapes, such as the interdigitated patterns in the epidermis of many eudicotyledon leaves, is much less well understood. Details about the manner in which cell wall polymers at the periclinal wall regulate the morphogenetic process in epidermal pavement cells and mechanistic information about the initial steps leading to the characteristic undulations in the cell borders are elusive. Here, we used genetics and recently developed cell mechanical and imaging methods to study the impact of the spatio-temporal dynamics of cellulose and homogalacturonan pectin distribution during lobe formation in the epidermal pavement cells of Arabidopsis (Arabidopsis thaliana) cotyledons. We show that nonuniform distribution of cellulose microfibrils and demethylated pectin coincides with spatial differences in cell wall stiffness but may intervene at different developmental stages. We also show that lobe period can be reduced when demethyl-esterification of pectins increases under conditions of reduced cellulose crystallinity. Our data suggest that lobe initiation involves a modulation of cell wall stiffness through local enrichment in demethylated pectin, whereas subsequent increase in lobe amplitude is mediated by the stress-induced deposition of aligned cellulose microfibrils. Our results reveal a key role of noncellulosic polymers in the biomechanical regulation of cell morphogenesis.

ATR-FTIR spectroscopy in combination with uni- and multivariate analysis was used to quantify the spectral–chemical composition of the leaf cuticle of pea, investigating the effects of variety and heat stress. Field pea (Pisum sativum L.) is sensitive to heat stress and our goal was to improve canopy cooling and flower retention by investigating the protective role of lipid-related compounds in leaf cuticle, and to use results in the future to identify heat resistant genotypes. The objective was to use Attenuated Total Reflection (ATR)-Fourier Transform Infrared (FTIR) spectroscopy, a non-invasive technique, to investigate and quantify changes in adaxial cuticles of fresh leaves of pea varieties that were subjected to heat stress. Eleven varieties were grown under control (24/18 °C day/night) and heat stress conditions (35/18 °C day/night, for 5 days at the early flowering stage). These 11 had significant spectral differences in the integrated area of the main lipid region, CH2 region, CH3 peak, asymmetric and symmetric CH2 peaks, ester carbonyl peak, and the peak area ratio of CH2 to CH3 and ester carbonyl to CH2 asymmetric peak, indicating that cuticles had spectral–chemical diversity of waxes, cutin, and polysaccharides. Results indicated considerable diversity in spectral–chemical makeup of leaf cuticles within commercially available field pea varieties and they responded differently to high growth temperature, revealing their diverse potential to resist heat stress. The ATR-FTIR spectral technique can, therefore, be further used as a medium-throughput approach for rapid screening of superior cultivars for heat tolerance.

In the present study, FTIR spectroscopy and hyperspectral imaging was introduced as a non-destructive, sensitive-reliable tool for assessing the tripartite kernel-fungal endophyte environment interaction. Composition of coleorhizae of Triticum durum was studied under ambient and drought stress conditions. The OH-stretch IR absorption spectrum suggests that the water-deficit was possibly improved or moderated by kernel’s endophytic partner. The OH-stretch frequency pattern coincides with other (growth and stress) related molecular changes. Analysis of lipid (3100–2800 cm−1) and protein (1700–1550 cm−1) regions seems to demonstrate that drought has a positive impact on lipids. The fungal endosymbiont direct contact with kernel during germination had highest effect on both lipid and protein (Amide I and II) groups, indicating an increased stress resistance in inoculated kernel. Compared to the indirect kernel-fungus interaction and to non-treated kernels (control), direct interaction produced highest effect on lipids. Among treatments, the fingerprint region (1800–800 cm−1) and SEM images indicated an important shift in glucose oligosaccharides, possibly linked to coleorhiza-polymer layer disappearance. Acquired differentiation in coleorhiza composition of T. durum, between ambient and drought conditions, suggests that FTIR spectroscopy could be a promising tool for studying endosymbiont-plant interactions within a changing environment.

Pea (Pisum sativum L.) is a major legume crop grown in a semi-arid climate in Western Canada, where heat stress affects pollination, seed set and yield. Seed set and pod growth characteristics, along with in vitro percentage pollen germination, pollen tube growth and pollen surface composition, were measured in two pea cultivars (CDC Golden and CDC Sage) subjected to five maximum temperature regimes ranging from 24 to 36 °C. Heat stress reduced percentage pollen germination, pollen tube length, pod length, seed number per pod, and the seed-ovule ratio. Percentage pollen germination of CDC Sage was greater than CDC Golden at 36 °C. No visible morphological differences in pollen grains or the pollen surface were observed between the heat and control-treated pea. However, pollen wall (intine) thickness increased due to heat stress. Mid-infrared attenuated total reflectance (MIR-ATR) spectra revealed that the chemical composition (lipid, proteins and carbohydrates) of each cultivar's pollen grains responded differently to heat stress. The lipid region of the pollen coat and exine of CDC Sage was more stable compared with CDC Golden at 36 °C. Secondary derivatives of ATR spectra indicated the presence of two lipid types, with different amounts present in pollen grains from each cultivar.

Clubroot disease is a serious threat to canola production in western Canada and many parts of the world. Rcr1 is a clubroot resistance (CR) gene identified recently and its molecular mechanisms in mediating CR have been studied using several omics approaches. The current study aimed to characterize the biochemical changes in the cell wall of canola roots connecting to key molecular mechanisms of this CR gene identified in prior studies using Fourier transform infrared (FTIR) spectroscopy. The expression of nine genes involved in phenylpropanoid metabolism was also studied using qPCR. Between susceptible (S) and resistance (R) samples, the most notable biochemical changes were related to an increased biosynthesis of lignin and phenolics. These results were supported by the transcription data on higher expression of BrPAL1. The up-regulation of PAL is indicative of an inducible defence response conferred by Rcr1; the activation of this basal defence gene via the phenylpropanoid pathway may contribute to clubroot resistance conferred by Rcr1. The data indicate that several cell-wall components, including lignin and pectin, may play a role in defence responses against clubroot. Principal components analysis of FTIR data separated non-inoculated samples from inoculated samples, but not so much between inoculated S and inoculated R samples. It is also shown that FTIR spectroscopy can be a useful tool in studying plant-pathogen interaction at cellular levels.

In wheat (Triticum aestivum), it is commonly assumed that Al is detoxified by the release of organic anions into the rhizosphere, but it is also possible that detoxification occurs within the apoplast and symplast of the root itself. Using Al-resistant (ET8) and Al-sensitive (ES8) near-isogenic lines of wheat, we utilized traditional and synchrotron-based approaches to provide in situ analyses of the distribution and speciation of Al within root tissues. Some Al appeared to be complexed external to the root, in agreement with the common assumption. However, root apical tissues of ET8 accumulated 4- to 6-times more Al than ES8 when exposed to Al concentrations that reduce root elongation rate by 50 % (3.5 µM Al for ES8 and 50 µM for ET8). Furthermore, in situ analyses of ET8 root tissues indicated the likely presence of Al-malate and other forms of Al, predominantly within the apoplast. To our knowledge, this is the first time that X-ray absorption near edge structure (XANES) analyses have been used to examine the speciation of Al within plant tissues. The information obtained in the present study is important in developing an understanding of the underlying physiological mode of action for improved root growth in systems with elevated soluble Al.

Wheat (Triticum aestivum L.) is the largest cereal crop grown in Western Canada where drought during late vegetative and seed filling stages affects plant development and yield. To identify new physiochemical markers associated with drought tolerance, epidermal characteristics of the flag leaf of two wheat cultivars with contrasting drought tolerance were investigated. The drought resistant 'Stettler' had a lower drought susceptibility index, greater harvest index and water-use efficiency than the susceptible 'Superb'. Furthermore, flag leaf width, relative water content and leaf roll were significantly greater in Stettler than in Superb at moderate drought stress (MdS). Visible differences in epicuticular wax density on the adaxial flag leaf surfaces and larger bulliform cells were identified in Stettler as opposed to Superb. Mid-infrared attenuated total internal reflectance spectra revealed that Stettler flag leaves had increased asymmetric and symmetric CH2 but reduced carbonyl esters on its adaxial leaf surface compared to Superb under MdS. X-ray fluorescence spectra revealed a significant increase in total flag leaf Zn concentrations in Stettler in response to MdS. Such information on the microstructural and chemical features of flag leaf may have potential as markers for drought tolerance and thereby accelerate the selection and release of more drought-resistant cultivars.

Fusarium head blight (FHB) is a serious disease of wheat worldwide. Cultivar resistance to FHB depends on biochemical factors that confine the pathogen spread in spikes. Breeding for cultivar resistance is considered the most practical way to manage this disease. In this study, different spectroscopy and microscopy techniques were applied to discriminate resistance in wheat genotypes against FHB. Synchrotron-based spectroscopy and imaging techniques, including focal plane array infrared and X-ray fluorescence (XRF) spectroscopy were used to understand changes in biochemical and trace elements in rachis following FHB infection. Sumai3 and Muchmore were used to represent resistant and susceptible cultivars to FHB, respectively, in this study. The histological comparison of rachis showed substantial differences in the cell wall thickness between the cultivars after infection. Synchrotron-based infrared imaging emphasized substantial difference in biochemical composition of rachis samples between the two cultivars prior to visible symptoms; in the resistant Sumai3, infrared bands representing alkyl ester, cellulose and lignin vibrations as well as amide I, pectin, cellulose, hemicellulose, and aromatics group were stronger and more persistent compared to the susceptible cultivar. These bands may be the candidates of biochemical markers for FHB resistance. Focal plane array infrared imaging (FPA) spectra from the rachis epidermis and vascular bundles revealed a new band (1710 cm-1) related to the oxidative stress on the susceptible cultivar only. XRF spectroscopy data revealed differences in trace elemental composition between cultivars, and between non-inoculated and inoculated samples, with substantial increases observed for Ca, K, Mn, Fe, Zn, and Si in the resistant cultivar. These trace elements are related to cell wall stability, metabolic process, and plant defense mechanisms such as lignification pathway and callose deposition. The combination of cell wall elemental composition and lignification plays a role in the mechanism of type II host resistance to FHB. Biochemical profiling using the synchrotron-based spectroscopy holds potential for screening wheat genotypes for FHB resistance.

The effect of steam explosion pretreatment, process (die) temperature, feedstock particle size, and moisture content was evaluated on the physical quality of pellets produced from poplar wood and wheat straw. Following feedstock preparation, which involved either pretreatment and moisture conditioning (9 and 15%, wet basis) or grinding (0.8 and 3.2 mm hammer mill screens) and moisture conditioning, the materials were compressed in a plunger–die assembly with a force of 4000 N. The resulting pretreated pellets had a higher density and tensile strength than the untreated. Also, the pretreated pellets experienced a dimensional reduction after 14 days, whereas the untreated pellets expanded in the diametric and longitudinal axes. Pretreated wheat straw generally had a higher pellet density, higher tensile strength, and higher dimensional reduction than the pretreated poplar pellets. Conversely, the untreated poplar pellets had a higher pellet physical quality than the untreated wheat straw pellets. Increasing the die temperature (from 70 to 100 °C) and decreasing the feedstock particle size (from 3.2 to 0.8 mm) increased pellet physical quality. The effect of moisture content on pellet physical quality varied with the levels of other factors (die temperature and particle size). Using Fourier Transform Infrared Photoacoustic Spectroscopy, it was found that the lignocellulosic structure was disrupted by pretreatment. The resulting higher relative percentage, and availability, of lignin was attributed to the increased quality of the pretreated feedstock pellets.

Hardness is a kernel characteristic that influences both milling and processing characteristics of wheat. It is one characteristic that is used for segregating wheat to meet the needs for various products. Kernel virteousness is a visual marker for hardness and is the characteristic assessed during the grading process. The potential of classifying vitreous and non-vitreous durum wheat kernels, in crease-down position, using imaging systems based on real time soft X-rays or transmitted light was assessed in this study. Durum wheat kernels at 14, 15 and 16% moisture contents were used as samples in this study. Image features modeling gray level distribution, textural and shape moments were measured and used to develop a classification system for vitreous and non-vitreous durum wheat kernels. The classification accuracies were 76% for vitreous kernels and 82% for non-vitreous kernels at 16% moisture content using the soft X-ray system but for the transmitted light system, the classification accuracies were 86% for vitreous and 93% for non-vitreous kernels. Moisture content had no effect on classifying vitreous or non-vitreous kernels by the transmitted light system but the classification accuracies increased with moisture content for non-vitreous kernels by the soft X-ray system.

With climate change, pea will be more frequently subjected to heat stress in semi-arid regions like Saskatchewan during flowering. The pollen germination percentage of two pea cultivars was reduced by heat stress (36°C) with an important decrease in cultivar 'CDC Golden' compared to 'CDC Sage.' Lipids, protein and other pollen coat compositions of whole intact pollen grains of both pea cultivars were investigated using mid infrared (mid-IR) attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy. Curve fitting of ATR absorbance spectra in the protein region enabled estimation and comparison of different protein secondary structures between the two cultivars. CDC Sage had relatively greater amounts of α-helical structures (48.6-43.6%; band at 1654 cm(-1)) and smaller amounts of β-sheets (41.3-46%) than CDC Golden. The CDC Golden had higher amounts of β-sheets (46.3-51.7%) compared to α-helical structures (35.3-36.2%). Further, heat stress resulted in prominent changes in the symmetrical and asymmetrical CH2 bands from lipid acyl chain, ester carbonyl band, and carbohydrate region. The intensity of asymmetric and symmetric CH2 vibration of heat stressed CDC Golden was reduced considerably in comparison to the control and the decrease was higher compared to CDC Sage. In addition, CDC Golden showed an increase in intensity at the oxidative band of 3015 cm(-1). These results reveal that the whole pollen grains of both pea cultivars responded differently to heat stress. The tolerance of CDC Sage to heat stress (expressed as pollen germination percentage) may be due to its protein richness with α-helical structures which would protect against the destructive effects of dehydration due to heat stress. The low pollen germination percentage of CDC Golden after heat stress may be also due to its sensitivity to lipid changes due to heat stress.

There is a need for an objective and efficient method to detect insect infestations in the incoming grain in commercial grain-handling facilities. The potential of a soft X-ray method to detect infestations by monitoring feeding damage to kernels caused by the red flour beetle, Tribolium castaneum (Herbst), in wheat was determined in this study. Wheat kernels, artificially infested by T. castaneum eggs were X-rayed continuously for 16 days at 4 day interval for infestations by four larval stages. Algorithms were developed to extract a total of 57 features using histogram groups, textural features, and histogram and shape moments from the X-ray images of wheat kernels. Identification of uninfested and infested wheat kernels was determined using the DISCRIM procedure of the statistical classifiers and a four-layer back propagation neural network (BPNN). Uninfested and kernels infested by four larval instars were correctly identified with more than 73 and 86% classification accuracies by the statistical classifiers and BPNN, respectively, using 57 features. There was no significant difference between the statistical and neural network classifiers for the identification of uninfested and wheat kernels infested by T. castaneum.

Insect infestations in stored wheat affect the chemical characteristics and baking qualities of wheat flour, and insect-infested flours are unacceptable in the baking industry. The efficiency of the soft X-ray method to detect infestations caused by Cryptolestes ferrugineus (Stephens), Tribolium castaneum (Herbst), Plodia interpunctella (Hubner), Sitophilus oryzae (L.), and Rhyzopertha dominica (F.) in wheat kernels was determined in this study. Wheat kernels infested by different insects were prepared by artificial implantation of insect eggs or by introducing adult insects in wheat samples. Kernels infested by different stages of the insects were X-rayed until the adults emerged from the kernels. A total of 57 features using histogram groups, histogram and shape moments, and textural features were extracted from the X-ray images and a linear-function parametric classifier was used to identify the insect-infested kernels. The parametric classifier identified more than 84% of infestations due to ...

Background Fusarium head blight (FHB), a scab principally caused by Fusarium graminearum Schw., is a serious disease of wheat. The purpose of this study is to evaluate the potential of combining synchrotron based phase contrast X-ray imaging (PCI) with Fourier Transform mid infrared (FTIR) spectroscopy to understand the mechanisms of resistance to FHB by resistant wheat cultivars. Our hypothesis is that structural and biochemical differences between resistant and susceptible cultivars play a significant role in developing resistance to FHB. Results Synchrotron based PCI images and FTIR absorption spectra (4000–800 cm−1) of the floret and rachis from Fusarium-damaged and undamaged spikes of the resistant cultivar ‘Sumai3’, tolerant cultivar ‘FL62R1’, and susceptible cultivar ‘Muchmore’ were collected and analyzed. The PCI images show significant differences between infected and non-infected florets and rachises of different wheat cultivars. However, no pronounced difference between non-inoculated resistant and susceptible cultivar in terms of floret structures could be determined due to the complexity of the internal structures. The FTIR spectra showed significant variability between infected and non-infected floret and rachis of the wheat cultivars. The changes in absorption wavenumbers following pathogenic infection were mostly in the spectral range from 1800–800 cm−1. The Principal Component Analysis (PCA) was also used to determine the significant chemical changes inside floret and rachis when exposed to the FHB disease stress to understand the plant response mechanism. In the floret and rachis samples, PCA of FTIR spectra revealed differences in cell wall related polysaccharides. In the florets, absorption peaks for Amide I, cellulose, hemicellulose and pectin were affected by the pathogenic fungus. In the rachis of the wheat cultivars, PCA underlines significant changes in pectin, cellulose, and hemicellulose characteristic absorption spectra. Amide II and lignin absorption peaks, persistent in the rachis of Sumai3, together with increased peak shift at 1245 cm−1 after infection with FHB may be a marker for stress response in which the cell wall compounds related to pathways for lignification are increased. Conclusions Synchrotron based PCI combined with FTIR spectroscopy show promising results related to FHB in wheat. The combined technique is a powerful new tool for internal visualisation and biomolecular monitoring before and during plant-microbe interactions to understand both the differences between cultivars and their different responses to disease stress. Electronic supplementary material The online version of this article (doi:10.1186/s12870-014-0357-5) contains supplementary material, which is available to authorized users.

Dual energy X-ray imaging technique makes it possible to determine the make-up of a scanned object by exploiting differences in how the scanned material interacts with X-rays at different energies. The potential of classifying vitreousness in durum wheat using dual energy X-ray images is determined in this study. Durum wheat kernels at 12% moisture content were used as samples for this study. Algorithms were developed for the logarithmic subtraction of images and for feature extraction. Histogram groups and total gray values were extracted from the dual energy subtracted images. Statistical and neural network classifiers were used for identifying vitreous and non-vitreous kernels from the sample images. Neural network classifiers correctly classified vitreous and non-vitreous kernels with 96 and 98% accuracies, respectively. The correct classification accuracies using statistical classifiers were 89 and 97%, respectively for vitreous and non-vitreous kernels. Dual energy X-ray imaging is an effective method for determining wheat hardness in durum kernels

One of the challenges that need to be addressed to automate grain inspection is the machine detection of insect infestations in grains. In this study, the soft X-ray and NIR spectroscopy methods to detect insect infestations were evaluated for their potential for real-time application. Infested wheat kernels were prepared by artificially infesting Canada Western Red Spring wheat by Sitophilus oryzae adults. Single kernels of wheat uninfested and infested by larvae, pupae, and adults of S. oryzae were first scanned by X-rays. The same infested kernels were then mixed with uninfested bulk grain and scanned using a spectrophotometer. The infestation level in the soft X-ray method was quantified by counting the number of infested and unifested kernels whereas in the NIR spectroscopy method it was quantified by the mass of infested and unifested grain. The identification of infestations by both methods increased with the increase in the developmental stage of the insect from larvae to adult stage. The soft X-ray method has the advantage of potential application in grain inspection over NIR spectroscopy where the number of infested or insect-damaged kernels is an essential information. The NIR spectroscopy analyzing bulk samples has applications in grain management such as fumigation where the identification of insect species is critical and precise quantification of infestations is not vital.

Using soft X-ray it is possible to detect insect infestations in grain samples. Numerous studies have determined the potential of the soft x-ray method to identify insect-infested grain kernels by different types of insects. Only a few attempts have been made to determine the insect types and their developmental stages from infested grain samples that would help to decide management strategies. Mass loss in infested grain kernels depends on the insect type and its life stages. Hence, a correlation between the features obtained from the x-ray images of grain kernels and their mass may be an improved way of determining insect species and their developmental stages. In this study, area and total gray values extracted from the x-ray images of the kernels were correlated to their mass. Single kernels of Canada Western Red Spring wheat was scanned at 15.5 kV and 70 µA with kernels’ crease facing down and up or sideways. For kernels scanned with the crease down, correlation coefficients of over 0.70 were obtained for area and total gray values. However, for kernels with crease up or on the side a poor correlation (r2 = 0.35) was determined between total gray value and mass. This was due to the fact that real time x-ray images have less gray values for dense areas. Hence, all images were transformed into negative images and then analyzed. These images showed a good correlation (r2 above 0.70) between the features from the x-ray images and kernels’ mass for both crease down and up kernels. This relationship may also be used to identify foreign materials and mechanically damaged kernels in grain samples during identification of insect-infested grain kernels.

The potential of a soft X–ray method (15 kV and 65 .A) to detect internal seed infestations by the rice weevil (Sitophilus oryzae) in Canada Western Red Spring wheat was determined in this study. The infested kernels were identified by the presence of egg plugs and were scanned with a real–time fluoroscope every 5 to 7 d until the adults emerged from the kernels. A total of 57 features using histogram groups, textural features, and histogram and shape moments were extracted from the X–ray images of the wheat kernels. Parametric and non–parametric classifiers, and a 4–layer back propagation neural network classifier were used to identify uninfested and infested wheat kernels using histogram and textural features independently, and using all 57 features together. There was no significant difference between the classifiers for the identification of uninfested and infested wheat kernels. More than 95% of uninfested kernels and kernels infested by larval stages were correctly identified by all the classifiers. Wheat kernels infested by pupae–adults and insect–damaged kernels were identified with more than 99% accuracy by the classifiers.

The efficiency of a soft X-ray method (65 kV and 15 µA) to detect internal seed infestations by the rice weevil, Sitophilus oryzae in Canada Western Red Spring (CWRS) wheat was determined in this study. The infested kernels were identified by the presence of egg plugs and X-rayed every 5 to 7 d until the adults emerged from the kernels. A total of 57 features using histogram groups, histogram and shape moments, and textural features were extracted from the X-ray images. A fourlayer back propagation neural network correctly identified 99% of sound kernels and classed 1% as infested. About 97% of wheat kernels infested by larvae and all kernels infested by pupa and adult stages were correctly identified as infested.

Deterioration rates were determined for 15-19% moisture content (m.c., wet basis) wheat (Triticum aestivum L. cv. 'Barrie') stored at constant temperatures or with a step decrease in storage temperatures. Deterioration rates were determined by measuring germination capacity of the grain and respiration rates of grain and microorganisms. Safe storage time was defined as the time for germination to decrease to 90%. Safe storage times of 19% m.c. wheat stored at constant temperatures ranged from 2.5 d at 30 and 35 degrees C to 37 d at 10 degrees C. Deterioration rates of 19% m.c. wheat stored with a step decrease in storage temperatures (35-25, 30-20, 25-20, and 20-15 degrees C) were determined and safe storage times were satisfactorily predicted. Safe storage times of 17% m.c. wheat were 5, 7, and 15 d at 35, 30, and 25 degrees C, respectively. Respiration rates and germination percentages of 15 and 16% m.c. wheat stored at 25 degrees C remained constant for 70 d. The respiration rates of 17-19% m.c. wheat at 25 degrees C increased while the germination percentages decreased with storage time. Germination dropped from 98 to 92-89% when the dry matter losses were about 0.05% and visible mould occurred when the dry matter losses were about 0.1% in 17-19% m.c. wheat. Safe storage times of 17% m.c. wheat stored at 35-25 degrees C were compared with those determined in similar previous work with cultivars 'Domain' and 'Katepwa'. 'Domain' had the longest and 'Barrie' had the shortest storage times.