Application of artificial neural networks to classify Avena fatua and Avena sterilis based on seed traits: insights from European Avena populations primarily from the Balkan Region.

BACKGROUND: Avena fatua and A. sterilis are challenging to distinguish due to their strong similarities. However, Artificial Neural Networks (ANN) can effectively extract patterns and identify these species. We measured seed traits of Avena species from 122 locations across the Balkans and from some populations from southern, western, and central Europe (total over 22 000 seeds). The inputs for the ANN model included seed mass, size, color, hairiness, and placement of the awn attachment on the lemma. RESULTS: The ANN model achieved high classification accuracy for A. fatua and A. sterilis (R2 > 0.99, RASE < 0.0003) with no misclassification. Incorporating geographic coordinates as inputs also resulted in successful classification (R2 > 0.99, RASE < 0.000001) with no misclassification. This highlights the significant influence of geographic coordinates on the occurrence of Avena species. The models revealed hidden relationships between morphological traits that are not easily detectable through traditional statistical methods. For example, seed color can be partially predicted by other seed traits combined with geographic coordinates. When comparing the two species, A. fatua predominantly had the lemma attachment point in the upper half, while A. sterilis had it in the lower half. A. sterilis exhibited slightly longer seeds and hairs than A. fatua, while seed hairiness and mass were similar in both species. A. fatua populations primarily had brown, light brown, and black colors, while A. sterilis populations had black, brown, and yellow colors. CONCLUSIONS: Distinguishing A. fatua from A. sterilis based solely on individual characteristics is challenging due to their shared traits and considerable variability of traits within each species. However, it is possible to classify these species by combining multiple seed traits. This approach also has significant potential for exploring relationships among different traits that are typically difficult to assess using conventional methods.

Response of oat morphologies, root exudates, and rhizosphere fungal communities to amendments in a saline-alkaline environment.

The application of organic amendments to saline-alkaline soil has been recommended as an agricultural strategy to improve crop productivity and soil health. However, there has been limited research on how organic soil amendment strategies affect the health of oats and their associated rhizosphere fungal communities in saline-alkaline conditions. Thus, the objectives of this study were to understand the effects of oat cultivars with contrasting saline-alkaline tolerances and different amendments on plant morphologies, root exudates (soluble sugars and organic acids), and rhizosphere fungal communities in a saline-alkaline environment. Experiments were conducted on a saline-alkaline tolerant cultivar, Baiyan2, and a saline-alkaline sensitive cultivar, Caoyou1, under four different organic amendment strategies: 1. control (no amendment application), 2. bio-fertilizer application, 3. rotten straw application, and 4. a co-application of bio-fertilizer and rotten straw. Results showed that plant morphological characters of Baiyan2 were better than Caoyou1, and that soluble sugar and organic acid levels in the rhizosphere of Baiyan2 were significantly lower than Caoyou1. Compared to the control, oat root and plant development was significantly improved by the combined bio-fertilizer and rotten straw amendment. Bio-fertilizer application promoted malic and citric acid levels, contributing to a higher total organic acid level, and significantly increased the abundance of Rhizopus arrhizus and decreased the abundance of the fungal pathogens Alternaria, Cladosporium, Sarocladium and Heydenia of Ascomycota in both oat cultivars. All amendment treatments containing rotten straw, except the combined amendment in Baiyan2, significantly increased the relative abundance of Ascomycota (specifically Gibberella, Talaromyces, Fusarium, and Bipolaris) and decreased the relative abundance of R. arrhizus by reducing soluble sugar and organic acid levels. For the combined amendment in Baiyan2, there were no significant changes in Gibberella and Rhizopus between the control and amendment treatment. Our results suggest that co-application of bio-fertilizer and rotten straw, combined with a tolerant oat cultivar, is an effective method to increase crop productivity and enhance soil health in a saline-alkaline environment.

Characterising the morphological characters and carbohydrate metabolism of oat culms and their association with lodging resistance.

Lodging resistance can be improved by enhancing the mechanical strength of culms, and culm carbohydrates could improve this mechanical strength. Culm carbohydrates can regulate development of the culm and affect its toughness. The present study determines the relationship between lodging and carbohydrate content in oat culms. Field experiments were conducted in alpine regions in 2017 and 2018 using three oat varieties with different lodging resistance. Lodging-related morphological characteristics were directly determined and culm carbohydrate content and enzyme activity related to cellulose synthesis and sucrose metabolism were evaluated with ultraviolet spectrophotometry. Results showed that the lower the gravity height or the lower ratio of gravity height to plant height, the stronger the lodging resistance of the varieties. Higher culm nonstructural (NSC) and structural (SC) carbohydrate content contributed to the ability of culms to resist lodging, especially the content of cellulose and sucrose. PCA showed that sucrose metabolism and SC content were closely related to lodging resistance. Correlation analysis showed that the lodging index (LI) was significantly negatively correlated with NSC. Sucrose content was highly and significantly positively correlated with NSC. Additionally, the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) were highly and significantly positively correlated with sucrose and cellulose content. The relationship between field characters and oat lodging, as well as the regulatory mechanism of carbohydrate content on lodging resistance of the culm are discussed.

Morphological and molecular genetic variations of oat genotypes grown in Kermanshah, Iran.

Morphological traits and molecular markers are two common methods for genetic variation studies. Molecular markers, morphological traits methods and relationship between the two were used to study genetic variation among 43 oat genotypes and varieties. For this purpose, an augmented design was conducted in three replicates at 2008-2009 cropping season in the experimental field of Campus of Agriculture and Natural Resources of Razi University, Kermanshah, Iran. Four wild oat accessions (Avena sterilis) were added to evaluated genotypes in molecular experiment. Results showed a significant variation among genotypes for all morphological traits and they were classified based on this variation in four groups by WARD cluster analysis. In molecular experiment, 28 inter simple sequence repeat (ISSR) primers amplified 206 polymorph bands. Based on Jaccard similarity matrix, similarity among genotypes was varied from 0.23 to 0.66 and cluster analysis classified genotypes in seven groups by complete linkage method. The correlation between ISSR marker and morphological traits classifications was not significant. ISSR showed to be a helpful marker for genotype identity and separation as it put wild accessions in a group.

Alimentos integrais / Foods Integrals

Introdução: Alimento integral é aquele que não teve sua estrutura modificada no processo de industrialização e manteve as vitaminas, os minerais e as fibras. Objetivo: Verificar evidências do uso dos alimentos integrais na prevenção e tratamento de doenças. Métodos: Busca sistematizada da literatura, por meio de busca eletrônica de artigos que avaliem o uso de alimentos integrais na terapêutica médica. Resultados: Encontramos uma revisão sistemática com 10 estudos com pouca qualidade metodológica e de curta duração. Esse estudo evidenciou uma diminuição significativa do colesterol total e do LDL-colesterol (lipoproteína de baixa densidade), sem influência na glicemia, peso corpóreo, pressão arterial e triglicérides, no grupo suplementado com alimentos integrais. Encontramos um ensaio clínico randomizado com 18 meses de acompanhamento, no qual o grupo que ingeriu alimentos integrais teve perda de peso com diminuição significativa da circunferência abdominal, sem perda significativa de vitaminas, minerais e fibras. Conclusão: Pelos estudos apresentados, os efeitos redutores do colesterol e do LDL-colesterol estão demonstrados em estudos de curta duração. Há necessidade de mais estudos com boa qualidade metodológica para verificarmos em longo prazo todas as alterações metabólicas e consequentes benefícios circulatórios.

Histological analysis and 3D reconstruction of winter cereal crowns recovering from freezing: a unique response in oat (Avena sativa L.).

The crown is the below ground portion of the stem of a grass which contains meristematic cells that give rise to new shoots and roots following winter. To better understand mechanisms of survival from freezing, a histological analysis was performed on rye, wheat, barley and oat plants that had been frozen, thawed and allowed to resume growth under controlled conditions. Extensive tissue disruption and abnormal cell structure was noticed in the center of the crown of all 4 species with relatively normal cells on the outside edge of the crown. A unique visual response was found in oat in the shape of a ring of cells that stained red with Safranin. A tetrazolium analysis indicated that tissues immediately inside this ring were dead and those outside were alive. Fluorescence microscopy revealed that the barrier fluoresced with excitation between 405 and 445 nm. Three dimensional reconstruction of a cross sectional series of images indicated that the red staining cells took on a somewhat spherical shape with regions of no staining where roots entered the crown. Characterizing changes in plants recovering from freezing will help determine the genetic basis for mechanisms involved in this important aspect of winter hardiness.

Classification of oat and groat kernels using NIR hyperspectral imaging.

An innovative procedure to classify oat and groat kernels based on coupling hyperspectral imaging (HSI) in the near infrared (NIR) range (1006-1650 nm) and chemometrics was designed, developed and validated. According to market requirements, the amount of groat, that is the hull-less oat kernels, is one of the most important quality characteristics of oats. Hyperspectral images of oat and groat samples have been acquired by using a NIR spectral camera (Specim, Finland) and the resulting data hypercubes were analyzed applying Principal Component Analysis (PCA) for exploratory purposes and Partial Least Squares-Discriminant Analysis (PLS-DA) to build the classification models to discriminate the two kernel typologies. Results showed that it is possible to accurately recognize oat and groat single kernels by HSI (prediction accuracy was almost 100%). The study demonstrated also that good classification results could be obtained using only three wavelengths (1132, 1195 and 1608 nm), selected by means of a bootstrap-VIP procedure, allowing to speed up the classification processing for industrial applications. The developed objective and non-destructive method based on HSI can be utilized for quality control purposes and/or for the definition of innovative sorting logics of oat grains.

3D volumes constructed from pixel-based images by digitally clearing plant and animal tissue.

Construction of three-dimensional volumes from a series of two-dimensional images has been restricted by the limited capacity to decrease the opacity of tissue. The use of commercial software that allows colour-keying and manipulation of two-dimensional images in true three-dimensional space allowed us to construct three-dimensional volumes from pixel-based images of stained plant and animal tissue without generating vector information. We present three-dimensional volumes of (1) the crown of an oat plant showing internal responses to a freezing treatment, (2) a sample of a hepatocellular carcinoma from a woodchuck liver that had been heat-treated with computer-guided radiofrequency ablation to induce necrosis in the central portion of the tumour, and (3) several features of a sample of mouse lung. The technique is well suited to images from large sections (greater than 1 mm) generated from paraffin-embedded tissues. It is widely applicable, having potential to recover three-dimensional information at virtually any resolution inherent in images generated by light microscopy, computer tomography, magnetic resonance imaging or electron microscopy.

Using Arabidopsis thaliana as a model to study subzero acclimation in small grains.

The suitability of using Arabidopsis as a model plant to investigate freezing tolerance was evaluated by observing similarities to winter cereals in tissue damage following controlled freezing and determining the extent to which Arabidopsis undergoes subzero-acclimation. Plants were grown and frozen under controlled conditions and percent survival was evaluated by observing re-growth after freezing. Paraffin embedded sections of plants were triple stained and observed under light microscopy. Histological observations of plants taken 1 week after freezing showed damage analogous to winter cereals in the vascular tissue of roots and leaf axels but no damage to meristematic regions. The LT(50) of non-acclimated Arabidopsis decreased from about -6 degrees C to a minimum of about -13 degrees C after 7 days of cold-acclimation at 3 degrees C. After exposing cold-acclimated plants to -3 degrees C for 3 days (subzero-acclimation) the LT(50) was lowered an additional 3 degrees C. Defining the underlying mechanisms of subzero-acclimation in Arabidopsis may provide an experimental platform to help understand winter hardiness in economically important crop species. However, distinctive histological differences in crown anatomy between Arabidopsis and winter cereals must be taken into account to avoid misleading conclusions on the nature of winter hardiness in winter cereals.

Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa.

BACKGROUND: Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required. RESULTS: From an oat cDNA library 9792 single-pass EST sequences were obtained. The library was prepared from pooled RNA samples isolated from leaves of four-week old Avena sativa (oat) plants incubated at +4 degrees C for 4, 8, 16 and 32 hours. Exclusion of sequences shorter than 100 bp resulted in 8508 high-quality ESTs with a mean length of 710.7 bp. Clustering and assembly identified a set of 2800 different transcripts denoted the Avena sativa cold induced UniGene set (AsCIUniGene set). Taking advantage of various tools and databases, putative functions were assigned to 1620 (58%) of these genes. Of the remaining 1180 unclassified sequences, 427 appeared to be oat-specific since they lacked any significant sequence similarity (Blast E values > 10(-10)) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX E values < or = 10(-10)) to genes previously reported to be involved in cold stress related processes. 107 novel oat transcription factors were also identified, out of which 51 were similar to genes previously shown to be cold induced. The CBF transcription factors have a major role in regulating cold acclimation. Four oat CBF sequences were found, belonging to the monocot cluster of DREB family ERF/AP2 domain proteins. Finally in the total EST sequence data (5.3 Mbp) approximately 400 potential SSRs were found, a frequency similar to what has previously been identified in Arabidopsis ESTs. CONCLUSION: The AsCIUniGene set will now be used to fabricate an oat biochip, to perform various expression studies with different oat cultivars incubated at varying temperatures, to generate molecular markers and provide tools for various genetic transformation experiments in oat. This will lead to a better understanding of the cellular biology of this important crop and will open up new ways to improve its agronomical properties.

[Comparative studies of oat cultivars from Southern Brazil: effect of grain morphology on industrial yield]. / Estudo comparativo de cultivares de aveia (Avena sativa L.) do sul do Brasil: efeito da morfologia do grão no rendimento industrial.

The purpose of this work was to study the effect of grain morphology of oats on their industrial yield. The five cultivars studied: CTC3, UFRGS7, UFRGS14, UPF7 and UPF16 were grown in three localities with different soil and climate conditions, for two consecutive years. The parameters evaluated in the oat samples before and after dehulling were grain size and shape (by image analysis), comparing them to industrial yield, weight of a thousand kernels and hectoliter weight. The results showed that image analysis of oat samples (with hulls), does not have any relation to industrial yield, different from what was observed with groat samples (dehulled). Industrial yield varied according to genotype, locality and year, while area, minimum and maximum diameters and grain shape were only affected by the genetic factor. It was observed that longer grains (UPF16) had the highest industrial yield, differently to rounder and shorter grains (UFRGS14) which had a lower yield due to the ease of breakage during hulling; the smallest grains also gave a low industrial yield.

Estudo comparativo de cultivares de aveia (Avena sativa L. ) do sul do Brasil: efeito da morfologia do grão no rendimento industrial / Comparative studies of oat cultivars from Southern Brazil: effect of grain morphology on industrial yield

The purpose of this work was to study the effect of grain morphology of oats on their industrial yield. The five cultivars studied: CTC3, UFRGS7, UFRGS14, UPF7 and UPF16 were grown in three localities with different soil and climate conditions, for two consecutive years. The parameters evaluated in the oat samples before and after dehulling were grain size and shape (by image analysis), comparing them to industrial yield, weight of a thousand kernels and hectoliter weight. The results showed that image analysis of oat samples (with hulls), does not have any relation to industrial yield, different from what was observed with groat samples (dehulled). Industrial yield varied according to genotype, locality and year, while area, minimum and maximum diameters and grain shape were only affected by the genetic factor. It was observed that longer grains (UPF16) had the highest industrial yield, differently to rounder and shorter grains (UFRGS14) which had a lower yield due to the ease of breakage during hulling; the smallest grains also gave a low industrial yield

Gravitropic responses of the Avena coleoptile in space and on clinostats. I. Gravitropic response thresholds.

We conducted a series of gravitropic experiments on Avena coleoptiles in the weightlessness environment of Spacelab. The purpose was to test the threshold stimulus, reciprocity rule and autotropic reactions to a range of g-force stimulations of different intensities and durations The tests avoided the potentially complicating effects of earth's gravity and the interference from clinostat ambiguities. Using slow-speed centrifuges, coleoptiles received transversal accelerations in the hypogravity range between 0.l and 1.0 g over periods that ranged from 2 to 130 min. All responses that occurred in weightlessness were compared to clinostat experiments on earth using the same apparatus. Characteristic gravitropistic response patterns of Atuena were not substantially different from those observed in ground-based experiments. Gravitropic presentation times were extrapolated. The threshold at 1.0 g was less than 1 min (shortest stimulation time 2 min), in agreement with values obtained on the ground. The least stimulus tested, 0.1 g for 130 min, produced a significant response. Therefore the absolute threshold for a gravitropic response is less than 0.1 g.

Gravitropic responses of the Avena coleoptile in space and on clinostats. II. Is reciprocity valid?

Experiments were undertaken to determine if the reciprocity rule is valid for gravitropic responses of oat coleoptiles in the acceleration region below 1 g. The rule predicts that the gravitropic response should be proportional to the product of the applied acceleration and the stimulation time. Seedlings were cultivated on 1 g centrifuges and transferred to test centrifuges to apply a transverse g-stimulation. Since responses occurred in microgravity, the uncertainties about the validity of clinostat simulation of weightlessness was avoided. Plants at two stages of coleoptile development were tested. Plant responses were obtained using time-lapse video recordings that were analyzed after the flight. Stimulus intensities and durations were varied and ranged from 0.1 to 1.0 g and from 2 to 130 min, respectively. For threshold g-doses the reciprocity rule was obeyed. The threshold dose was of the order of 55 g s and 120 g s, respectively, for two groups of plants investigated. Reciprocity was studied also at bending responses which are from just above the detectable level to about 10 degrees. The validity of the rule could not be confirmed for higher g-doses, chiefly because the data were more variable. It was investigated whether the uniformity of the overall response data increased when the gravitropic dose was defined as (gm x t) with m-values different from unity. This was not the case and the reciprocity concept is, therefore, valid also in the hypogravity region. The concept of gravitropic dose, the product of the transverse acceleration and the stimulation time, is also well-defined in the acceleration region studied. With the same hardware, tests were done on earth where responses occurred on clinostats. The results did not contradict the reciprocity rule but scatter in the data was large.