Metabolic pathways and genes identified by RNA-seq analysis of barley near-isogenic lines differing by allelic state of the Black lemma and pericarp (Blp) gene

A pipeline for processing hyperspectral images, with a case of melanin-containing barley grains as an example

Analysis of hyperspectral images is of great interest in plant studies. Nowadays, this analysis is used more and more widely, so the development of hyperspectral image processing methods is an urgent task. This paper presents a hyperspectral image processing pipeline that includes: preprocessing, basic statistical analysis, visualization of a multichannel hyperspectral image, and solving classification and clustering problems using machine learning methods. The current version of the package implements the following methods: construction of a confidence interval of an arbitrary level for the difference of sample averages; verification of the similarity of intensity distributions of spectral lines for two sets of hyperspectral images on the basis of the Mann-Whitney U-criterion and Pearson's criterion of agreement; visualization in two-dimensional space using dimensionality reduction methods PCA, ISOMAP and UMAP; classification using linear or ridge regression, random forest and catboost; clustering of samples using the EM-algorithm. The software pipeline is implemented in Python using the Pandas, NumPy, OpenCV, SciPy, Sklearn, Umap, CatBoost and Plotly libraries. The source code is available at: https://github.com/igor2704/Hyperspectral_images. The pipeline was applied to identify melanin pigment in the shell of barley grains based on hyperspectral data. Visualization based on PCA, UMAP and ISOMAP methods, as well as the use of clustering algorithms, showed that a linear separation of grain samples with and without pigmentation could be performed with high accuracy based on hyperspectral data. The analysis revealed statistically significant differences in the distribution of median intensities for samples of images of grains with and without pigmentation. Thus, it was demonstrated that hyperspectral images can be used to determine the presence or absence of melanin in barley grains with great accuracy. The flexible and convenient tool created in this work will significantly increase the efficiency of hyperspectral image analysis.

Chemical composition analysis and transcriptomics reveal the R2R3-MYB genes and phenol oxidases regulating the melanin formation in black radish

Melanins are dark-brown to black-colored biomacromolecules which have been thoroughly studied in animals and microorganisms. However, the biochemical and molecular basis of plant melanins are poorly understood. We first characterized melanin from the black radish (Raphanus sativus var. niger) 'HLB' through spectroscopic techniques. p-Coumaric acid was identified as the main precursor of radish melanin. Moreover, a joint analysis of transcriptome and coexpression network was performed for the two radish accessions with black and white cortexes, 'HLB' and '55'. A set of R2R3-type RsMYBs and enzyme-coding genes exhibited a coexpression pattern, and were strongly correlated with melanin formation in radish. Transient overexpression of two phenol oxidases RsLAC7 (laccase 7) or RsPOD22-1 (peroxidase 22-1) resulted in a deeper brown color around the infiltration sites and a significant increase in the total phenol content. Furthermore, co-injection of the transcriptional activator RsMYB48/RsMYB97 with RsLAC7 and/or RsPOD22-1, markedly increased the yield of black extracts. Spectroscopic analyses revealed that these extracts are similar to the melanin found in 'HLB'. Our findings advance the understanding of structural information and the transcriptional regulatory mechanism underlying melanin formation in radish.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.

Polyphenol oxidase genes in barley (Hordeum vulgare L.): functional activity with respect to black grain pigmentation

Polyphenol oxidase (PPO) is an oxidoreductase. In damaged plant tissues, it catalyzes enzymatic browning by oxidizing o-diphenols to highly reactive o-quinones, which polymerize producing heterogeneous dark polymer melanin. In intact tissues, functions of PPO are not well understood. The aim of the study was to investigate the barley PPO gene family and to reveal the possible involvement of Ppo genes in melanization of barley grain, which is controlled by the Blp1 gene. Based on known barley Ppo genes on chromosome 2H (Ppo1 and Ppo2), two additional genes-Ppo3 and Ppo4-were found on chromosomes 3H and 4H, respectively. These genes have one and two exons, respectively, contain a conserved tyrosinase domain and are thought to be functional. Comparative transcriptional analyzes of the genes in samples of developing grains (combined hulls and pericarp tissues) were conducted in two barley lines differing by melanin pigmentation. The genes were found to be transcribed with increasing intensity (while grains mature) independently from the grain color, except for Ppo2, which is transcribed only in black-grained line i:BwBlp1 accumulating melanin in grains. Analysis of this gene's expression in detached hulls and pericarps showed its elevated transcription in both tissues in comparison with yellow ones, while it was significantly higher in hulls than in pericarp. Segregation analysis in two F2 populations obtained based on barley genotypes carrying dominant Blp1 and recessive ppo1 (I) and dominant Blp1 and recessive ppo1 and ppo2 (II) was carried out. In population I, only two phenotypic classes corresponding to parental black and white ones were observed; the segregation ratio was 3 black to 1 white, corresponding to monogenic. In population II, aside from descendants with black and white grains, hybrids with a gray phenotype - light hulls and dark pericarp - were observed; the segregation ratio was 9 black to 3 gray to 4 white, corresponding to the epistatic interaction of two genes. Most hybrids with the gray phenotype carry dominant Blp1 and a homozygous recessive allele of Ppo2. Based on transcription and segregation assays one may conclude involvement of Ppo2 but not Ppo1 in melanin formation in barley hulls.

Genotypic and environmental effects on quality and nutritional attributes of Moroccan barley cultivars and elite breeding lines

Although barley is mainly used for livestock feed and beverages, its use as human feed can enrich human diets with some health benefits. The development of new hulless varieties rich in β-glucans and micronutrients can enhance the use of barley as food, but little is known about the effects of the environment on these nutritional traits. In this study, we evaluated five Moroccan varieties and two elite breeding lines of barley at four locations in Morocco during the 2016-2017 and 2017-2018 cropping seasons. The results showed highly significant differences between genotypes for β-glucan, protein, iron, and selenium contents, as well as 1000 kernel weight, but not zinc content; significant to highly significant differences between environments for all traits except β-glucan content; and significant to highly significant interactions for all traits. The highest level of β-glucan content has reached 11.57% observed at the Sidi El Aydi site during the growing season 2017-2018 for the hulless variety Chifaa. This variety has shown the highest content of β-glucan (6.2-11.57%) over all environments except at Tassaout during the 2016-2017 seasons. The breeding line M9V5 has achieved significantly higher protein content at all the locations during the two growing seasons, ranging from 12.38 to 20.14%. Most hulless lines had significantly higher β-glucan and protein contents, but lower 1000 kernel weight. For micronutrients, the content ranges were 28.94 to 38.23 ppm for Fe, 28.78 to 36.49 ppm for Zn, and 0.14 to 0.18 ppm for Se, with the highest content for Fe and Zn shown by the breeding line M9V5 and Chifaa showing average contents of 33.39 ppm, 35.34 ppm, and 0.18 ppm for Fe, Zn, and Se, respectively. The GGE biplot confirmed the high and relatively stable content of β-glucan and acceptable micronutrient contents of the Chifaa variety and identified Marchouch as the most discriminant site to breed for biofortified barley varieties.

Profile of phenolic compounds and antioxidant activity of organically and conventionally grown black-grain barley genotypes treated with biostimulant

Beneficial dietary and pro-health values, have resulted in the increasing consumption importance of barley. Therefore, genotypes and cultivation methods are sought that guarantee high functional value of grain. The aim of the study was to assess the content of phenolic acids, flavonoids, chlorophylls, anthocyanidins, phytomelanin and antioxidant activity of grain of three barley genotypes depending on agricultural technology. Two of them are primary genotypes with dark grain pigmentation Hordeum vulgare L. var nigricans and H. vulgare L. var. rimpaui, the third is a modern cultivar 'Soldo' H. vulgare with yellow grain, which is the control sample. Evaluated the effect of foliar application of a amino-acids biostimulant on the functional properties of grain under the conditions of organically and conventionally cultivations. The results indicated a higher antioxidant activity and the concentration of phenolic acids, flavonoids and phytomelanin in the black-grain genotypes. Organic cultivation and application of amino acids had increased the content of phenolic compounds in grain. The antioxidant activity was correlated with the content of syringic acid, naringenin, quercetin, luteolin and phytomelanin. Organically cultivation and the foliar application of an amino acid biostimulant improved the functional properties of barley grain, in particular the original, black-grained genotypes.

Heavy Metals, Their Phytotoxicity, and the Role of Phenolic Antioxidants in Plant Stress Responses with Focus on Cadmium: Review

The current state of heavy metal (HM) environmental pollution problems was considered in the review: the effects of HMs on the vital activity of plants and the functioning of their antioxidant system, including phenolic antioxidants. The latter performs an important function in the distribution and binding of metals, as well as HM detoxification in the plant organism. Much attention was focused on cadmium (Cd) ions as one of the most toxic elements for plants. The data on the accumulation of HMs, including Cd in the soil, the entry into plants, and the effect on their various physiological and biochemical processes (photosynthesis, respiration, transpiration, and water regime) were analyzed. Some aspects of HMs, including Cd, inactivation in plant tissues, and cell compartments, are considered, as well as the functioning of various metabolic pathways at the stage of the stress reaction of plant cells under the action of pollutants. The data on the effect of HMs on the antioxidant system of plants, the accumulation of low molecular weight phenolic bioantioxidants, and their role as ligand inactivators were summarized. The issues of polyphenol biosynthesis regulation under cadmium stress were considered. Understanding the physiological and biochemical role of low molecular antioxidants of phenolic nature under metal-induced stress is important in assessing the effect/aftereffect of Cd on various plant objects-the producers of these secondary metabolites are widely used for the health saving of the world's population. This review reflects the latest achievements in the field of studying the influence of HMs, including Cd, on various physiological and biochemical processes of the plant organism and enriches our knowledge about the multifunctional role of polyphenols, as one of the most common secondary metabolites, in the formation of plant resistance and adaptation.

Features of Activity of the Phenylpropanoid Biosynthesis Pathway in Melanin-Accumulating Barley Grains

Barley (Hordeum vulgare L.) grain pigmentation is caused by two types of phenolic compounds: anthocyanins (which are flavonoids) give a blue or purple color, and melanins (which are products of enzymatic oxidation and polymerization of phenolic compounds) give a black or brown color. Genes Ant1 and Ant2 determine the synthesis of purple anthocyanins in the grain pericarp, whereas melanins are formed under the control of the Blp1 gene in hulls and pericarp tissues. Unlike anthocyanin synthesis, melanin synthesis is poorly understood. The objective of the current work was to reveal features of the phenylpropanoid biosynthesis pathway functioning in melanin-accumulating barley grains. For this purpose, comparative transcriptomic and metabolomic analyses of three barley near-isogenic lines accumulating anthocyanins, melanins, or both in the grain, were performed. A comparative analysis of mRNA libraries constructed for three stages of spike development (booting, late milk, and early dough) showed transcriptional activation of genes encoding enzymes of the general phenylpropanoid pathway in all the lines regardless of pigmentation; however, as the spike matured, unique transcriptomic patterns associated with melanin and anthocyanin synthesis stood out. Secondary activation of transcription of the genes encoding enzymes of the general phenylpropanoid pathway together with genes of monolignol synthesis was revealed in the line accumulating only melanin. This pattern differs from the one observed in the anthocyanin-accumulating lines, where - together with the genes of general phenylpropanoid and monolignol synthesis pathways - flavonoid biosynthesis genes were found to be upregulated, with earlier activation of these genes in the line accumulating both types of pigments. These transcriptomic shifts may underlie the observed differences in concentrations of phenylpropanoid metabolites analyzed in the grain at a late developmental stage by high-performance liquid chromatography. Both melanin-accumulating lines showed an increased total level of benzoic acids. By contrast, anthocyanin-accumulating lines showed higher concentrations of flavonoids and p-coumaric and ferulic acids. A possible negative effect of melanogenesis on the total flavonoid content and a positive influence on the anthocyanin content were noted in the line accumulating both types of pigments. As a conclusion, redirection of metabolic fluxes in the phenylpropanoid biosynthesis pathway occurs when melanin is synthesized.

A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley

Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M₃ lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.

Improving the quality of barley transcriptome de novo assembling by using a hybrid approach for lines with varying spike and stem coloration

De novo transcriptome assembly is an important stage of RNA-seq data computational analysis. It allows the researchers to obtain the sequences of transcripts presented in the biological sample of interest. The availability of accurate and complete transcriptome sequence of the organism of interest is, in turn, an indispensable condition for further analysis of RNA-seq data. Through years of transcriptomic research, the bioinformatics community has developed a number of assembler programs for transcriptome reconstruction from short reads of RNA-seq libraries. Different assemblers makes it possible to conduct a de novo transcriptome reconstruction and a genome-guided reconstruction. The majority of the assemblers working with RNA-seq data are based on the De Bruijn graph method of sequence reconstruction. However, specif ics of their procedures can vary drastically, as do their results. A number of authors recommend a hybrid approach to transcriptome reconstruction based on combining the results of several assemblers in order to achieve a better transcriptome assembly. The advantage of this approach has been demonstrated in a number of studies, with RNA-seq experiments conducted on the Illumina platform. In this paper, we propose a hybrid approach for creating a transcriptome assembly of the barley Hordeum vulgare isogenic line Bowman and two nearly isogenic lines contrasting in spike pigmentation, based on the results of sequencing on the IonTorrent platform. This approach implements several de novo assemblers: Trinity, Trans-ABySS and rnaSPAdes. Several assembly metrics were examined: the percentage of reference transcripts observed in the assemblies, the percentage of RNA-seq reads involved, and BUSCO scores. It was shown that, based on the summation of these metrics, transcriptome meta-assembly surpasses individual transcriptome assemblies it consists of.

Analysis of color and texture characteristics of cereals on digital images

The color of the grain shell of cereals is an important feature that characterizes the pigments and metabolites contained in it. The grain shell is the main barrier between the grain and the environment, so its characteristics are associated with a number of important biological functions: moisture absorption, grain viability, resistance to pre-harvest germination. The presence of pigments in the shell affects various technological properties of the grain. Color characteristics, as well as the appearance of the grain shell are an important indicator of plant diseases. In addition, the color of the grains serves as a classifying feature of plants. Genetic control of the color formation of both grains and other plant organs is exerted by genes encoding enzymes involved in the biosynthesis of pigments, as well as regulatory genes. For a number of pigments, these genes are well understood, but for some pigments, such as melanin, which causes the black color of grains in barley, the molecular mechanisms of biosynthesis are still poorly understood. When studying the mechanisms of genetic control of grain color, breeders and geneticists are constantly faced with the need to assess the color characteristics of their shell. The technical means of addressing this problem include spectrophotometers, spectrometers, hyperspectral cameras. However, these cameras are expensive, especially with high resolution, both spatial and spectral. An alternative is to use digital cameras that allow you to get high-quality images with high spatial and color resolution. In this regard, recently, in the field of plant phenotyping, methods for evaluating the color and texture characteristics of cereals based on the analysis of two-dimensional images obtained by digital cameras have been intensively developed. This mini-review is devoted to the main tasks related to the analysis of color and texture characteristics of cereals, and to methods of their description based on digital images.

Wheat, Barley, and Oat Breeding for Health Benefit Components in Grain

Cereal grains provide half of the calories consumed by humans. In addition, they contain important compounds beneficial for health. During the last years, a broad spectrum of new cereal grain-derived products for dietary purposes emerged on the global food market. Special breeding programs aimed at cultivars utilizable for these new products have been launched for both the main sources of staple foods (such as rice, wheat, and maize) and other cereal crops (oat, barley, sorghum, millet, etc.). The breeding paradigm has been switched from traditional grain quality indicators (for example, high breadmaking quality and protein content for common wheat or content of protein, lysine, and starch for barley and oat) to more specialized ones (high content of bioactive compounds, vitamins, dietary fibers, and oils, etc.). To enrich cereal grain with functional components while growing plants in contrast to the post-harvesting improvement of staple foods with natural and synthetic additives, the new breeding programs need a source of genes for the improvement of the content of health benefit components in grain. The current review aims to consider current trends and achievements in wheat, barley, and oat breeding for health-benefiting components. The sources of these valuable genes are plant genetic resources deposited in genebanks: landraces, rare crop species, or even wild relatives of cultivated plants. Traditional plant breeding approaches supplemented with marker-assisted selection and genetic editing, as well as high-throughput chemotyping techniques, are exploited to speed up the breeding for the desired genotуpes. Biochemical and genetic bases for the enrichment of the grain of modern cereal crop cultivars with micronutrients, oils, phenolics, and other compounds are discussed, and certain cases of contributions to special health-improving diets are summarized. Correlations between the content of certain bioactive compounds and the resistance to diseases or tolerance to certain abiotic stressors suggest that breeding programs aimed at raising the levels of health-benefiting components in cereal grain might at the same time match the task of developing cultivars adapted to unfavorable environmental conditions.

Melanin Pigment in Plants: Current Knowledge and Future Perspectives

The word "melanin" refers to a group of high molecular weight, black, and brown pigments formed through the oxidation and polymerization of phenolic compounds. This pigment is present in all kingdoms of living organisms, but it remains the most enigmatic pigment in plants. The poor solubility of melanin in particular solvents and its complex polymeric nature significantly constrain its study. Plant melanin synthesis is mostly associated with the enzymatic browning reaction that occurs in wounded plant tissues. This reaction occurs when, due to the disruption of cellular compartmentation, the chloroplast-located polyphenol oxidases (PPOs) release from the chloroplast and interact with their vacuolar substrates to produce o-quinones, which in turn polymerize to melanin. Furthermore, the presence of melanin in intact seed tissues has been demonstrated by diagnostic physicochemical tests. Unlike the well-studied enzymatic browning reaction, little is known about how melanin is formed in seeds. Recent data have shown that it is a tightly controlled genetic process that involves many genes, among which the genes encoding PPOs might be key. The present article aims to provide an overview of the current knowledge on melanin in plants and to discuss future perspectives on its study in light of recent findings.

Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases

Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.

Melanin formation in barley grain occurs within plastids of pericarp and husk cells

Melanins are a class of darkly pigmented biopolymers which are widely distributed among living organisms. The molecular and cellular mechanisms adopted by bacteria, fungi and animals to synthesize melanin, have been well described, but less is known regarding their production in plants. Here, a pair of barley near isogenic lines, bred to differ with respect to the pigmentation of the spike, was compared in order to understand the tissue and cellular location of melanin deposition. The melanic nature of the pigments purified from black spikes was confirmed by a series of solubility tests and Fourier transform infrared spectroscopy. An analysis of grains harvested at various stages of their development revealed that intracellular pigmented structures first appeared in the pericarp and the husk of black spike plants at early dough stage. The co-localization of these structures with red autofluorescence suggested that they form in chloroplast-derived plastids, here designated "melanoplasts". Differences in dynamics of plastid internal structure during grain ripening were detected between the lines by transmission electron microscopy. Both lines accumulated plastoglobuli inside plastids, which persisted in black grain pericarp tissue up to the hard dough stage, while neither plastoglobuli nor any plastids were observed in grain of the control line at this stage. The role of plastoglobuli in melanin synthesis is discussed.

Quantitative proteomics analysis reveals proteins and pathways associated with anthocyanin accumulation in barley

The aim of the present study was to explore the underlying mechanisms involved in anthocyanin biosynthesis in purple, blue, and white barley using quantitative proteomics analysis. We identified the differences in protein expression and related functions involved in anthocyanin biosynthesis in purple, blue, and white barley (named H, M, and L groups, respectively, based on their anthocyanin content) using TMT-liquid chromatography/mass spectroscopy-based proteomic methods. Totally, 297, 300, 254, and 1421 differentially expressed proteins (DEPs) were found in H vs. L, H vs. M, L vs. M, and H vs. L vs. M groups, respectively. Six clusters of proteins from the 1421 DEPs were mainly involved in carbon metabolism, amino acid and secondary metabolite biosynthesis, and metabolic pathways. Several proteins were validated using parallel reaction monitoring. The proteins involved in amino acid biosynthesis, carbon metabolism, metabolic pathways, and phenylpropanoid biosynthesis were responsible for the color differences in the three barley varieties.