In situ thermal modification of kafirin using infrared radiations and microwaves.

BACKGROUND: Kafirin is a prolamin protein located in the corneous endosperm of sorghum. The conventional thermal processing of kafirin reduces its solubility, which limits its utilization in the food industry. Therefore, the study was aimed to investigate the effect of in situ thermal modification of kafirin using two different electromagnetic thermal treatments, namely infrared (IR) and microwave (MW) radiation, on the physicochemical, structural, thermal, and antioxidant properties. RESULTS: The results demonstrated that both the thermal modifications improved yield, purity, and solubility of the kafirin with a decrease in hydrophobicity. However, IR-treated samples showed higher solubility (910.67 g kg-1 ) and lower hydrophobicity (387.67). The IR modifications also improved the ratio of α helix/ß sheets to a great extent. The alterations in the disulfide content were concomitant with the improvement in the thermal stability of kafirin. Sodium dodecyl sulfate polyacrylamide gel electrophoresis showed variations in the band intensities of ß- and γ-kafirin, indicating alterations in the kafirin subunits. Morphological examination of kafirin revealed surface withering and agglomeration. Notably, IR treatment improved the antioxidant activity more efficiently (from 32.11% to 74.05%). CONCLUSION: Although both the IR and MW treatments modified kafirin, the effect seemed to be more pronounced in IR modification. The IR-modified kafirin had better solubility and lesser hydrophobicity than MW-modified kafirin. The physicochemical and structural changes induced by IR treatment improved the biological activity of kafirin, in terms of antioxidant activity. Therefore, it was concluded that the in situ IR modification of kafirin can alter its characteristic properties, improving its potential as a food ingredient. © 2021 Society of Chemical Industry.

Light Induced Regulation Pathway of Anthocyanin Biosynthesis in Plants.

Anthocyanins are natural pigments with antioxidant effects that exist in various fruits and vegetables. The accumulation of anthocyanins is induced by environmental signals and regulated by transcription factors in plants. Numerous evidence has indicated that among the environmental factors, light is one of the most signal regulatory factors involved in the anthocyanin biosynthesis pathway. However, the signal transduction of light and molecular regulation of anthocyanin synthesis remains to be explored. Here, we focus on the research progress of signal transduction factors for positive and negative regulation in light-dependent and light-independent anthocyanin biosynthesis. In particular, we will discuss light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis in plants. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by transcription factors is discussed based on the significant progress.

G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story.

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.

Uncover the Nuclear Proteomic Landscape with Enriched Nuclei Followed by Label-Free Quantitative Mass Spectrometry.

Treated with light pulse or under certain diurnal conditions, photoreceptors can translocate into nucleus followed by conformation change. Many critical components of light signaling pathways also majorly function in nucleus. Hence, it is beneficial to establish a combined method to uncover and compare the nuclear proteomic landscape among the mutants of light signaling components. Here we describe an optimized method to isolate nucleus with seedlings growing under light/dark cycles for further characterizing the nuclear proteome with label-free quantitation by liquid chromatography mass spectrometry (LC-MS).

Analysis of a radiation-induced dwarf mutant of a warm-season turf grass reveals potential mechanisms involved in the dwarfing mutant.

Zoysia matrella [L.] Merr. is a widely cultivated warm-season turf grass in subtropical and tropical areas. Dwarf varieties of Z. matrella are attractive to growers because they often reduce lawn mowing frequencies. In this study, we describe a dwarf mutant of Z. matrella induced from the 60Co-γ-irradiated calluses. We conducted morphological test and physiological, biochemical and transcriptional analyses to reveal the dwarfing mechanism in the mutant. Phenotypically, the dwarf mutant showed shorter stems, wider leaves, lower canopy height, and a darker green color than the wild type (WT) control under the greenhouse conditions. Physiologically, we found that the phenotypic changes of the dwarf mutant were associated with the physiological responses in catalase, guaiacol peroxidase, superoxide dismutase, soluble protein, lignin, chlorophyll, and electric conductivity. Of the four endogenous hormones measured in leaves, both indole-3-acetic acid and abscisic acid contents were decreased in the mutant, whereas the contents of gibberellin and brassinosteroid showed no difference between the mutant and the WT control. A transcriptomic comparison between the dwarf mutant and the WT leaves revealed 360 differentially-expressed genes (DEGs), including 62 up-regulated and 298 down-regulated unigenes. The major DEGs related to auxin transportation (e.g., PIN-FORMED1) and cell wall development (i.e., CELLULOSE SYNTHASE1) and expansin homologous genes were all down-regulated, indicating their potential contribution to the phenotypic changes observed in the dwarf mutant. Overall, the results provide information to facilitate a better understanding of the dwarfing mechanism in grasses at physiological and transcript levels. In addition, the results suggest that manipulation of auxin biosynthetic pathway genes can be an effective approach for dwarfing breeding of turf grasses.

Modification of rapeseed protein by ultrasound-assisted pH shift treatment: Ultrasonic mode and frequency screening, changes in protein solubility and structural characteristics.

We investigated the effect of ultrasound-assisted pH shift treatment on the micro-particle, molecular, and spatial structure of rapeseed protein isolates (RPI). Various ultrasonic frequency modes (fixed, and sweep) was used. Protein characterization by the indexes: particle size, zeta potential, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), scanning electron microscopy (SEM), free sulfhydryl (SH), surface hydrophobicity (Ho), Fourier transform infrared Spectrum (FTIR) and fluorescence intensity was studied to elucidate the changes in solubility and structural attributes of RPI. The results showed that ultrasonic frequency and working modes substantially altered the structure, and modified the solubility of RPI. Ultra + pH mode at fixed frequency of 20 kHz had the best effect on the solubility of RPI. Under the condition of ultra + pH mode, 20 kHz at pH 12.5, solubility, compared to control, increased from 8.90% to 66.84%; and the change in molecular structure of RPI was characterized by smaller particles (from 330.90 to 115.77 nm), high zeta potential (from -17.95 to -14.43 mV, p < 0.05), and increased free sulfhydryl (from 11.63 to 24.50 µmol/g) compared to control. Likewise, surface hydrophobicity increased (from 2053.9 to 2649.4, p < 0.05), whilst ɑ-helix and random coil decreased (p < 0.05), compared to control. The fluorescence spectroscopy and FTIR spectroscopy showed that the secondary and tertiary structure of the RPI were altered. These observations revealed that changes in RPI structure was the direct factor affecting solubility. In conclusion, ultrasound assisted pH shift treatment was proven to be an effective method for the modification of protein, with promising application in food industry.

Preservation of hydrogen peroxide-induced oxidative damage in HepG-2 cells by rice protein hydrolysates pretreated with electron beams.

In this paper, electron beam irradiated rice protein hydrolysates (ERPHs) were assessed for their ability to prevent hydrogen peroxide-induced oxidative stress in human HepG-2 cells. The related mechanism was also studied by analyzing the structural changes. Cytotoxicity experiments showed that rice protein hydrolysates pretreated with electron beam irradiation (EBI) were not toxic to cells if appropriate concentrations were applied. Cell viability markedly increased when the cells were treated with ERPHs before H2O2 induction. Furthermore, the ERPHs effectively suppressed H2O2-induced ROS production and lipid peroxidation and increased the protein expression levels of the intracellular antioxidant enzymes SOD, GSH-Px and CAT in H2O2-stressed HepG-2 cells. Consequently, the loss of mitochondrial membrane potential and cell apoptosis was alleviated. Circular dichroism analysis showed that pretreatment of rice protein with EBI significantly changed the secondary structure (the conversion of α-helices to random coils), which is beneficial to the improvement of its antioxidative activity. ERPHs exhibited stronger antioxidative effects than those without irradiation, possibly because of the difference in molecular weight distribution and amino acid composition. These findings indicate an efficient way to produce peptides with better antioxidant activity.

Identification and Characterization of γ-Ray-Induced Mutations in Rice Cytoplasmic Genomes by Whole-Genome Sequencing.

Chloroplasts and mitochondria are semi-autonomous organelles and have their own genomes (cytoplasmic genomes). Physical radiations (e.g., γ-rays) have been widely used in artificial mutation induction for plant germplasm enhancement and for breeding new cultivars. However, little is known at the genomic level about which kind of cytoplasmic mutations and/or characteristics could be induced in plants. The present study aimed to investigate the type, number, and distribution of inheritable cytoplasmic mutations induced by γ-rays in rice (Oryza sativa L.). Six plants were selected from the 2nd generation (M2) populations after γ-ray (137Cs) irradiation of the rice cultivar Nipponbare, 2 each for the 3 irradiation doses (150, 250, and 350 Gy), and their genomes were sequenced on an Illumina platform. Together with the whole-genome sequencing data of 3 external Nipponbare control plants, single-base substitutions (SBSs) and insertions/deletions (InDels) in chloroplast (cp) and mitochondrial (mt) genomes were identified and analyzed in-depth using bioinformatic tools. The majority of SBSs and InDels identified were background mutations in the 6 M2 plants, and the number of induced mutations varied greatly among the plants. Most induced mutations were present in a heterogeneous state, reflecting the fact that multiple cp and mt copies existed in the progenitor cells. The induced mutations were distributed in different genomic regions in the 6 M2 plants, including exonic regions, but none of them was predicted to cause nonsynonymous mutations or frameshifts. Our study thus revealed, at the genomic level, characteristics of cytoplasmic mutations induced by γ-rays in rice.

Effect of high energy electron beam on proteolysis and antioxidant activity of rice proteins.

This research focused on the effects of electron beam irradiation (EBI) on the hydrolysis and antioxidant activity of rice proteins (RPs). The RPs were treated with 0, 5, 10, 20 and 30 kGy doses of EBI. The results showed that EBI pretreatment improved significantly (P < 0.05) the degree of hydrolysis, increasing the DH value by more than 15.09% at a dose of 30 kGy. In addition, radical scavenging results showed that EBI treatment had effects on antioxidant activity and could increase the DPPH and ABTS+ radical scavenging activity of rice protein hydrolysates (RPHs) by 32.06% and 79.11%, respectively (30 kGy). The CAA test also confirmed that EBI pretreatment could effectively improve the ability of RPHs to remove intracellular free radicals. Scanning electron microscopy indicated that EBI treatment destroyed microstructures and resulted in cracks and fragments of RPs. Circular dichroism analysis showed that EBI affected the secondary structure of RPs by destroying the α-helix structure. Changes in the UV visible spectra indicated unfolding of RPs by EBI. Amino acid and molecular weight distribution analysis revealed that EBI pretreatment could increase the ratio of antioxidant-related amino acids and produce smaller peptides. Therefore, EBI pretreatment is an efficient method to promote protein proteolysis due to its effect on the molecular conformation as well as on protein microstructure. Moreover, EBI treatment applied before enzymatic hydrolysis has the potential to prepare hydrolysates with high bioactivity.

Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions.

Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.

Effect of high-power sonication pretreatment on extraction and some physicochemical properties of proteins from chickpea, kidney bean, and soybean.

Impact of high-power sonication (HPS) as pretreatment in extraction and some physicochemical properties of proteins from soybean flakes, flour of soybean, chickpea, and kidney bean was evaluated. Soybean flakes and flours from soybean, chickpea, and kidney bean were dispersed in distilled water (1.10 w/v) and sonicated at two power densities (PD) of 2.5 and 4.5 W/cm3 for 5 min continuously. Proteins were extracted at pH range 8-8.5. PD 2.5 and 4.5 W/cm3 significantly increased protein extraction yields from soy flakes to 29.03% and 25.87%, respectively, compared to 15.28% for unsonicated controls, but did not increase for flours. Freeze-dried spent substrates at higher PD sonication aggregated in size. Free sulfhydryl content for both sonicated and unsonicated soy flakes and flour were similar but increased in chickpea and kidney bean when HPS of 4.5 W/cm3 was applied, indicating the unfolding of protein structure. The protein band patterns for sonicated and unsonicated legumes proteins were found to be similar, indicating no peptide profile alterations by HPS. However, circular dichroism analysis showed changes in secondary structure composition in extracted kidney bean protein causing unfolding and destabilizing the native structure. The secondary structure composition for soy flakes and flour protein and chickpea protein remained unchanged.

Genomic changes and biochemical alterations of seed protein and oil content in a subset of fast neutron induced soybean mutants.

BACKGROUND: Soybean is subjected to genetic manipulation by breeding, mutation, and transgenic approaches to produce value-added quality traits. Among those genetic approaches, mutagenesis through fast neutrons radiation is intriguing because it yields a variety of mutations, including single/multiple gene deletions and/or duplications. Characterizing the seed composition of the fast neutron mutants and its relationship with gene mutation is useful towards understanding oil and protein traits in soybean. RESULTS: From a large population of fast neutron mutagenized plants, we selected ten mutants based on a screening of total oil and protein content using near infra-red spectroscopy. These ten mutants were regrown, and the seeds were analyzed for oil by GC-MS, protein profiling by SDS-PAGE and gene mapping by comparative genomic hybridization. The mutant 2R29C14Cladecr233cMN15 (nicknamed in this study as L10) showed higher protein and lower oil content compared to the wild type, followed by three other lines (nicknamed in this study as L03, L05, and L06). We characterized the fatty acid methyl esters profile of the trans-esterified oil and found the presence of five major fatty acids (palmitic, stearic, oleic, linoleic, and linolenic acids) at varying proportions among the mutants. Protein profile using SDS-PAGE of the ten mutants did exhibit discernable variation between storage (glycinin and ß-conglycinin) and anti-nutritional factor (trypsin inhibitor) proteins. In addition, we physically mapped the position of the gene deletions or duplications in each mutant using comparative genomic hybridization. CONCLUSION: Characterization of oil and protein profile in soybean fast neutron mutants will assist scientist and breeders to develop new value-added soybeans with improved protein and oil quality traits.

Phosphoproteomics Reveals the Biosynthesis of Secondary Metabolites in Catharanthus roseus under Ultraviolet-B Radiation.

Ultraviolet (UV)-B radiation acts as an elicitor to enhance the production of secondary metabolites in medicinal plants. To investigate the mechanisms, which lead to secondary metabolites in Catharanthus roseus under UVB radiation, a phosphoproteomic technique was used. ATP content increased in the leaves of C. roseus under UVB radiation. Phosphoproteins related to calcium such as calmodulin, calcium-dependent kinase, and heat shock proteins increased. Phosphoproteins related to protein synthesis/modification/degradation and signaling intensively changed. Metabolomic analysis indicated that the metabolites classified with pentoses, aromatic amino acids, and phenylpropanoids accumulated under UVB radiation. Phosphoproteomic and immunoblot analyses indicated that proteins related to glycolysis and the reactive-oxygen species scavenging system were changed under UVB radiation. These results suggest that UVB radiation activates the calcium-related pathway and reactive-oxygen species scavenging system in C. roseus. These changes lead to the upregulation of proteins, which are responsible for the redox reactions in secondary metabolism and are important for the accumulation of secondary metabolites in C. roseus under UVB radiation.

Thermal Treatment Greatly Improves Storage Stability and Monodispersity of Pea Seed Ferritin.

Plant ferritin in holo form is considered as a novel, ideal iron supplement for human nutrition in the 21st century, but its self-degradation and self-association features limit its application on account of the presence of extension peptide (EP), a specific domain only found in plant ferritin. Although reported chemicals such as Phenylmethanesulfonyl fluoride (PMSF) can inhibit its self-degradation, they are not edible and toxic. In the present work, we found that thermal treatment of pea seed ferritin (PSF) in the range of 60 to 80 °C can prolong the storage time of PSF from 3 days to at least 10 days. In the meanwhile, the aggregated form can be inhibited upon such treatment, therefore promoting its monodispersity. More important, such treatment had little effect on the natural shell-like structure of holo PSF and its iron content. In contrast, thermal treatment at higher temperature (90 °C or above) resulted in a change in ferritin structure. These new findings pave the way to the application of plant ferritin as an iron supplement. PRACTICAL APPLICATION: Thermal treatment at 60 to 80 °C can prolong the storage stability of PSF from 3 days to at least 10 days and prevent it from self-aggregation without affecting the shell-like structure. It has been known that the stability of PSF is closely associated with the bioavailability of iron within PSF. From the standpoint of nutrition, the above-mentioned thermal treatment could be used as a cooking method in our daily life or in food industry to improve the bioavailability of ferritin iron, thereby being beneficial for exploration of plant ferritin as a novel, ideal iron supplement to fight against IDA.

Comparisons of controlled environment and vineyard experiments in Sauvignon blanc grapes reveal similar UV-B signal transduction pathways for flavonol biosynthesis.

UV-B radiation is an environmental challenge affecting a number of metabolic functions in plants. Plants protect themselves from this potentially damaging radiation through synthesising UV-absorbing compounds such as flavonoids. This study aims to investigate the effect of UV-B on flavonoid biosynthesis in Sauvignon blanc grapes. In particular, a comparison has been made between controlled environment (CE) and vineyard trials to better understand molecular mechanisms of low/high fluence UV-B responses and how the results relate to each other in the context of flavonoid biosynthesis. Following exposure to supplemental UV-B in the CE, both flavonols and gene expression exhibited UV-B induced response. Flavonols, particularly quercetin/kaempferol 3-O-glycosides were increased at distinct stages of berry development. All genes measured showed a significant developmental regulation. VvFLS4, VvCHS1, VvMYB12, VvHY5 and PR (VvTL1 and VvChi4A/4B) increased due to UV-B in the CE experiments. However, PR were not responsive to the natural UV-B fluence in vineyard but were significantly induced at later stages of development. Overall, despite very different conditions in the CE and vineyard the majority of UV-B induced responses are similar. Only PR activities in the CE cabinets reflect a higher fluence stress response that is not reflected in the natural lower UV-B fluence environment.

RNA-Seq transcriptomic analysis of the Morus alba L. leaves exposed to high-level UVB with or without dark treatment.

Ultraviolet-B (UVB) irradiation induces oxidative stress in plant cells due to the generation of excessive reactive oxygen species. Morus alba L. (M. abla) is an important medicinal plant used for the treatment of human diseases. Also, its leaves are widely used as food for silkworms. In our previous research, we found that a high level of UVB irradiation with dark incubation led to the accumulation of secondary metabolites in M. abla leaf. The aim of the present study was to describe and compare M. alba leaf transcriptomics with different treatments (control, UVB, UVB+dark). Leaf transcripts from M. alba were sequenced using an Illumina Hiseq 2000 system, which produced 14.27Gb of data including 153,204,462 paired-end reads among the three libraries. We de novo assembled 133,002 transcripts with an average length of 1270bp and filtered 69,728 non-redundant unigenes. A similarity search was performed against the non-redundant National Center of Biotechnology Information (NCBI) protein database, which returned 41.08% hits. Among the 20,040 unigenes annotated in UniProtKB/SwissProt database, 16,683 unigenes were assigned 102,232 gene ontology terms and 6667 unigenes were identified in 287 known metabolic pathways. Results of differential gene expression analysis together with real-time quantitative PCR tests indicated that UVB irradiation with dark incubation enhanced the flavonoid biosynthesis in M. alba leaf. Our findings provided a valuable proof for a better understanding of the metabolic mechanism under abiotic stresses in M. alba leaf.

An algal photoenzyme converts fatty acids to hydrocarbons.

Although many organisms capture or respond to sunlight, few enzymes are known to be driven by light. Among these are DNA photolyases and the photosynthetic reaction centers. Here, we show that the microalga Chlorella variabilis NC64A harbors a photoenzyme that acts in lipid metabolism. This enzyme belongs to an algae-specific clade of the glucose-methanol-choline oxidoreductase family and catalyzes the decarboxylation of free fatty acids to n-alkanes or -alkenes in response to blue light. Crystal structure of the protein reveals a fatty acid-binding site in a hydrophobic tunnel leading to the light-capturing flavin adenine dinucleotide (FAD) cofactor. The decarboxylation is initiated through electron abstraction from the fatty acid by the photoexcited FAD with a quantum yield >80%. This photoenzyme, which we name fatty acid photodecarboxylase, may be useful in light-driven, bio-based production of hydrocarbons.

Effect of high pressure and thermal processing on spoilage-causing enzymes in mango (Mangifera indica).

The aim of the present work was to model the effect of combined pressure-temperature processing on spoilage-causing enzymes in mango pulp; which conventionally are inactivated using high temperatures leading to inevitable quality losses. The inactivation of enzymes pectin methylesterase (PME), polyphenol oxidase (PPO) and peroxidase (POD) was studied in mango pulp within the pressure, temperature and hold-time ranges of 0.1 to 600MPa, 40 to 70°C and 1s to 90min, respectively. The enzyme inactivation was described as a dual process: initial change in activity during dynamic pressure build-up phase and subsequent decrease under isobaric-isothermal conditions. The former led to considerable increase in activities of all the three enzymes (p<0.05); however, the increased activity reduced with increased intensity of applied pressure-temperature. On the other hand, isobaric-isothermal conditions led to substantial inactivation (p<0.05), with 600MPa/70°C/20min treatment being most effective in reducing the activities of PME, PPO and POD to 32, 15 and 26%, respectively. The enzyme inactivation data was non-linear under isobaric-isothermal conditions and fitted to the nth-order reaction model, indicative of the occurrence of series of reactions possibly due to pressure-temperature interaction effects. The estimated reaction order 'n' was 0.815, 1.106 and 1.137 for PME, PPO and POD, respectively. The estimated reaction rate constant k (min-1) depicted PME to be the most baroresistant enzyme followed by POD and PPO. Temperature and pressure dependency of k was expressed in terms of activation energy and activation volume using the Arrhenius- and Eyring-type relations, respectively. An empirical model with good correlation between actual and predicted data (R2>0.90) was proposed to simulate the rate of enzyme inactivation under isobaric-isothermal conditions as a function of pressure and temperature.

Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves.

Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

Identification of candidate genes for the seed coat colour change in a Brachypodium distachyon mutant induced by gamma radiation using whole-genome re-sequencing.

Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. To identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing. After removing natural variations, 906, 1057, and 978 DNA polymorphisms were detected in 142-3, 421-2, and 1376-1, respectively. A total of 13 high-risk DNA polymorphisms were identified in mutant 142-3. Based on a comparison with DNA polymorphisms in 421-2 and 1376-1, candidate causal mutations for the seed coat colour change in 142-3 were selected. In the two independent Arabidopsis thaliana lines carrying T-DNA insertions in the AtCHI, seed colour change was observed. We propose a frameshift mutation in BdCHI1 as a causal mutation responsible for seed colour change in 142-3. The DNA polymorphism information for these mutant lines can be utilized for functional genomics in B. distachyon and cereal crops.