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Graphene-based materials (GBMs) have become potential soil pollutants due to their wide applications in agricultural environments. Although physiological mechanisms of plant responses to GBMs have been previously explored, the underlying molecular mechanisms remain unclear. In this paper, we analysed the physiological and transcriptomic changes of buckwheat (Fagopyrum spp.) roots exposed to 100 mg/L graphene oxide (GO) with different diameter. GO negatively affected root growth and higher diameters of GO caused more adverse effects on the root. In total 3 724 GO-responsive genes were identified in root by transcriptome analysis. 70 differentially expressed genes (DEGs) were involved in ROS detoxification, and 37 transporter-encoding genes were found to be involved in GO response. These transporters may regulate the uptake and transport of GO in buckwheat. The gene expression of 84 transcription factors (TFs) showed a response to GO stress in the root, which may regulate the transporters and reactive oxygen species (ROS) detoxification-related genes. Finally, the difference in the transcriptomic response of the root to the three GO materials with different diameters was investigated. 49 GO-responsive genes may be involved in the difference in the toxicity of GO with different diameters. This study provides new insights into the molecular mechanisms of plant roots to GBMs.

Abstract Background The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet. Results In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement. Conclusions We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.

Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) is a crop of significant interest due to its nutritional value and resilience to drought conditions. However, drought, particularly following flowering, is a major factor contributing to yield reduction. This research employed two distinct Tartary buckwheat genotypes to investigate the effects of post-anthesis drought on growth and physicochemical characteristics. The study aimed to elucidate the response of Tartary buckwheat to drought stress. The findings indicated that post-anthesis drought adversely impacted the growth, morphology, and biomass accumulation of Tartary buckwheat. Drought stress enhanced the maximum photosynthetic capacity (Fv/Fm) and light protection ability (NPQ) of the ‘Xiqiao-2’ genotype. In response to drought stress, ‘Dingku-1’ and ‘Xiqiao-2’ maintained osmotic balance by accumulating soluble sugars and proline, respectively. Notably, ‘Xiqiao-2’ exhibited elevated levels of flavonoids and polyphenols in its leaves, which helped mitigate oxidative damage caused by drought. Furthermore, rewatering after a brief drought period significantly improved plant height, stem diameter, and biomass accumulation in ‘Dingku-1’. Overall, ‘Xiqiao-2’ demonstrated greater long-term tolerance to post-anthesis drought, while ‘Dingku-1’ was less adversely affected by short-term post-anthesis drought.

Background: Eurotium cristatum (E. cristatum) is the probiotic fungus in Fu-brick tea, with which fermentation brings a unique flavor and taste and health-promoting effects. Tartary buckwheat leaves are rich in functional active substances such as flavonoids and phenolic compounds, yet are not effectively utilized. Methods: Tartary buckwheat leaves were processed into raw green tea first and subsequently fermented with E. cristatum to develop a novel fermented leaf tea. The tea quality was evaluated by the aspects of the sensory scores by E-tongue, the volatile compounds by HS-SPME-GC-MS, the non-volatile profile by biochemical and UPLC-MS/MS methods and the antioxidant activity by the colorimetric assay. Results: Fermented leaf tea displayed a golden yellow color, a unique “flower” aroma and a dark-tea taste, with an improved sensory acceptability. Fermentation raised the content of volatile heterocyclic and aromatic compounds, alkenes and other aromatic components, which produced a unique floral flavor. The proportion of sour, bitter and astringency accounting non-volatile compounds such as phenolic acids and amino acids decreased, while the proportion of umami and sweet accounting substances such as responsible amino acids increased. Fermented leaf tea displayed a relative stronger total antioxidant activity against ABTS. Conclusion: E. cristatum fermentation exerted positive effects on Tartary buckwheat leaf tea quality.

Buckwheat is a famous edible and medicinal coarse cereal which contain abundant of bioactive flavonoids, such as rutin. In this study, the composition and diversity of endophytic fungi in eight different buckwheat seeds were analyzed by high-throughput sequencing of ITS rDNA. Results showed that, the fungal sequences reads were allocated to 272 OTUs, of them, 49 OTUs were shared in eight buckwheat seeds. These endophytic fungi could be classified into 6 phyla, 19 classes, 41 orders, 79 families, 119 genera, and 191 species. At genus level, Alternaria sp. was the domain fungal endophyte. Besides, fungal endophytes belonged to the genera of Epicocum, Cladosporium, Botrytis, Filbobasidium, Stemphylium, and Vishniacozyma were highly abundant in buckwheat seeds. The total flavonoids and rutin contents in tartary buckwheat cultivars (CQ, XQ, CH, K2) were much higher than those in common buckwheat cultivars (HT, T2, T4, T8). For tartary buckwheat cultivars, the total flavonoids and rutin contents were ranging from 2.6% to 3.3% and 0.9% to 1.3%, respectively. Accordingly, the tartary buckwheat samples displayed stronger antioxidant activity than the common buckwheat. Spearman correlation heat map analysis was successfully found that certain fungal species from the genera of Alternaria, Botryosphaeria, Colletorichum and Diymella exhibited significant positive correlation with flavonoids contents. Results of this study preliminary revealed the fungi-plant interaction relationship at secondary metabolite level, and could provide novel strategy for increasing the flavonoids accumulation of buckwheat seeds, as well as improving their quality.

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Titanium has been reported to have positive effects on crop growth and production in various species. However, the impact of titanium on the Tartary buckwheat crops has not yet been studied. Therefore, an experiment was conducted to investigate the effect of spraying different concentrations of ionic titanium on the growth, photosynthesis, and uptake of mineral nutrients in Tartary buckwheat. The results showed that the application of titanium significantly improved dry matter accumulation, internode diameter, main stem node, root length, root average diameter, root surface area, root volume, grains per plant, and weight of grains per plant. Additionally, chlorophyll and photosynthetic parameters showed improvement regardless of the concentration of titanium used. The study found that titanium accumulation was mainly in leaves. The content of titanium in leaves showed a significant positive correlation with K, Ca, Mg, Mn, Cu, Zn, and B. This suggests a potential synergistic relationship between titanium and minerals in Tartary buckwheat leaves. Furthermore, the study also observed a significant increase in the total accumulation of P, K, Ca, Mg, Mn, Cu, Zn, and B in Tartary buckwheat plants. Overall, this study provides evidence for the positive effects of titanium on Tartary buckwheat and offers a theoretical foundation for practical production.

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an important pseudocereal crop with excellent edible, nutritional and medicinal values. However, the yield of Tartary buckwheat (TB) is very low due to old-fashioned cultivation techniques, particularly unreasonable application of nitrogen fertilizer. To improve the understanding on the theories of nitrogen use in TB, the effects of nitrogen application on growth, as well as chemical properties and microbial community of rhizosphere soil were investigated in this study. Nitrogen application could promote the plant height, stem diameter, nitrogen accumulation and yield of TB. The relative abundance and diversity of bacteria and fungi in the rhizosphere soil of TB were improved by nitrogen fertilizer. Nitrogen application increased the abundance of beneficial bacteria such as Lysobacter and Sphingomonas in rhizosphere soil, and decreased the abundance of pathogenic fungi such as Fusarium and Plectosphaerella. The results indicated that nitrogen application changed the distribution of microbial communities in TB rhizosphere soil. Furthermore, the specific enriched or depleted microorganisms in the rhizosphere soil of four TB varieties were analyzed at OTU level. 87 specific nitrogen-responsive genes with sequence variation were identified in four varieties by integrating genomic re-sequencing and transcriptome analysis, and these genes may involve in the recruitment of specific rhizosphere microorganisms in different TB varieties. This study provided new insights into the effects of nitrogen application on TB growth and rhizosphere microbial community, and improved the understanding on the mechanisms of TB root–microbe interactions.

Abstract Background Photoperiod is an important environmental cue interacting with circadian clock pathway to optimize the local adaption and yield of crops. Quinoa (Chenopodium quinoa) in family Amaranthaceae has been known as superfood due to the nutritious elements. As quinoa was originated from the low-latitude Andes, most of the quinoa accessions are short-day type. Short-day type quinoa usually displays altered growth and yield status when introduced into higher latitude regions. Thus, deciphering the photoperiodic regulation on circadian clock pathway will help breed adaptable and high yielding quinoa cultivars. Results In this study, we conducted RNA-seq analysis of the diurnally collected leaves of quinoa plants treated by short-day (SD) and long-day conditions (LD), respectively. We identified 19,818 (44% of global genes) rhythmic genes in quinoa using HAYSTACK analysis. We identified the putative circadian clock architecture and investigated the photoperiodic regulatory effects on the expression phase and amplitude of global rhythmic genes, core clock components and transcription factors. The global rhythmic transcripts were involved in time-of-day specific biological processes. A higher percentage of rhythmic genes had advanced phases and strengthened amplitudes when switched from LD to SD. The transcription factors of CO-like, DBB, EIL, ERF, NAC, TALE and WRKY families were sensitive to the day length changes. We speculated that those transcription factors may function as key mediators for the circadian clock output in quinoa. Besides, we identified 15 novel time-of-day specific motifs that may be key cis elements for rhythm-keeping in quinoa. Conclusions Collectively, this study lays a foundation for understanding the circadian clock pathway and provides useful molecular resources for adaptable elites breeding in quinoa.

Tartary buckwheat is a cereal crop that has both medicinal and food origins. However, the underlying factors that contribute to Tartary buckwheat’s flowering and seed-setting characteristics, effective grain formation, and physiological changes are still not well understood. This study aimed to investigate the flowering and seed-setting characteristics of different parts of Tartary buckwheat, as well as the grain-filling characteristics after flowering. To achieve this, Tartary buckwheat cultivars with high (QK3) and low (XQ2) seed-setting rates were selected for pot and field experiments. The study found that Tartary buckwheat undergoes flowering and seed setting simultaneously. Many wilted flowers and grains were observed 45 and 51 d after flowering. Compared to XQ2, QK3 exhibited a higher grain formation rate and seed-setting rate by 7.42% and 26.16%, respectively. Additionally, QK3 had a significantly lower grain abortion rate by 12.03%. The 1000-grain weight and average grain-filling rate of QK3 were 11.10% and 14.81% higher than those of XQ2, respectively. QK3 exhibited a faster maximum grain-filling rate (Rmax), reaching 18.38% faster than XQ2. Additionally, the dry matter average distribution rate in the main stem and branched grains of QK3 was 13.26% and 23.07% higher than that of XQ2, respectively. The sucrose concentration, SS, and SSS enzyme activities of QK3 were all higher than those of XQ2, by 0.29–25.99%, 5.22–11.62%, and 6.64–12.47%, respectively. Correlation analysis revealed a significant positive correlation between sucrose, soluble sugar, and starch concentration during the grain formation process and SS and SSS activities. This suggests that the levels of SS, SSS, soluble sugar, and sucrose in the grain play a crucial role in grain filling.

Abstract Background Transcription factors (TFs) play important roles in plants. Among the major TFs, GATA plays a crucial role in plant development, growth, and stress responses. However, there have been few studies on the GATA gene family in foxtail millet (Setaria italica). The release of the foxtail millet reference genome presents an opportunity for the genome-wide characterization of these GATA genes. Results In this study, we identified 28 GATA genes in foxtail millet distributed on seven chromosomes. According to the classification method of GATA members in Arabidopsis, SiGATA was divided into four subfamilies, namely subfamilies I, II, III, and IV. Structural analysis of the SiGATA genes showed that subfamily III had more introns than other subfamilies, and a large number of cis-acting elements were abundant in the promoter region of the SiGATA genes. Three tandem duplications and five segmental duplications were found among SiGATA genes. Tissue-specific results showed that the SiGATA genes were mainly expressed in foxtail millet leaves, followed by peels and seeds. Many genes were significantly induced under the eight abiotic stresses, such as SiGATA10, SiGATA16, SiGATA18, and SiGATA25, which deserve further attention. Conclusions Collectively, these findings will be helpful for further in-depth studies of the biological function of SiGATA, and will provide a reference for the future molecular breeding of foxtail millet.

Abstract Tartary buckwheat (TB) is an edible pseudocereal with good health benefits, but its adhering thick shell and bitter taste inhibit its consumption. In this study, the first hybrid rice-Tartary buckwheat (RTB) variety Mikuqiao18 (M18), bred by the pedigree selection of crossbreeding ‘Miqiao’ (MQ) with ‘Jingqiaomai2’ (JQ2), was selected for an agronomic and metabolomics analysis. Compared with JQ2, M18 demonstrated a significantly lower yield per plant owing to the decreased grain weight and similar full-filling grain number per plant. However, M18 had a similar kernel weight per plant because of the thinner shell. The sense organ test suggested that M18 had higher taste quality regardless of partial replacement of rice through the improvement of preponderant indicators related to cereal taste quality, including lower values of total protein, albumin, glutelin, globulin, pasting temperature, cool paste viscosity, and setback. Meanwhile, M18 contained high levels of flavonoids, including rutin and quercetin, but presented a positive summary appraisal of cooking with 25% rice. Additionally, 92 metabolites were positively identified by GC–MS, including 59 differentially expressed metabolites (DEMs) between M18 and JQ2. Typically, M18 exhibited lower levels of 20 amino acids and higher levels of 6 sugars and 4 polyols. These DEMs might partly explain the superior eating quality of M18. In addition, M18 was abundant in 4-aminobutyric acid, which is beneficial to human health. The current findings offer a theoretical foundation for breeding rice-Tartary buckwheat with high yield and quality and promoting the cultivation and consumption of rice-Tartary buckwheat as a daily functional cereal.

Abstract Foxtail millet (Setaria italica) is rich in nutrients and extremely beneficial to human health. We identified and comprehensively analyzed 89 MADS-box genes in the foxtail millet genome. According to the classification of MADS-box genes in Arabidopsis thaliana and rice, the SiMADS-box genes were divided into M-type (37) and MIKC-type (52). During evolution, the differentiation of MIKC-type MADS-box genes occurred before that of monocotyledons and dicotyledons. The SiMADS-box gene structure has undergone much differentiation, and the number of introns in the MIKC-type subfamily is much greater than that in the M-type subfamily. Analysis of gene duplication events revealed that MIKC-type MADS-box gene segmental duplication accounted for the vast majority of gene duplication events, and MIKC-type MADS-box genes played a major role in the amplification of SiMADS-box genes. Collinearity analysis showed highest collinearity between foxtail millet and maize MADS-box genes. Analysis of tissue-specific expression showed that SiMADS-box genes are highly expressed throughout the grain-filling process. Expression analysis of SiMADS-box genes under eight different abiotic stresses revealed many stress-tolerant genes, with induced expression of SiMADS33 and SiMADS78 under various stresses warranting further attention. Further, some SiMADS-box proteins may interact under external stress. This study provides insights for MADS-box gene mining and molecular breeding of foxtail millet in the future.

Oats (Avena sativa L.) are mostly used as a germplasm resource for forage. This experiment showed the differences in the nutrient composition and the forage quality of five wild leather oat populations from Israel and one cultivated leather oat population from China. It also showed the correlation of the indicators with the geo-environmental factors in the places of origin of the six populations that were analysed. Three replicated experiments were conducted during a three-year period from 2018.10 to 2020.03, mainly from 11 indicators of nutrient composition and forage quality. In this experiment, Spearman’s correlation was used to analyse the differences between different groups (p < 0.05), the relationship between components was analysed by principal component analysis (PCA), and the kinship relationship between six groups was also analysed based on the data of 11 components. In terms of nutrient content, the cultivated group Hu had significantly lower ash (8.92%), crude protein (11.96%), and soluble sugar content (10.51%) than the wild oat groups. In terms of forage quality, the lignin content (3.31%) of the Hu population was 2.3 times higher than that of Evolution Canyon, and the fibre content was 8 times higher than that of Sede Boqer. This indicates that wild oats have better nutritional value and palatability. Following the correlation analysis, it was found that the environmental factors of the origin had a significant effect on the indexes of ash, crude protein, and soluble sugar of oat straw, but had less effect on the content of crude fat, total phosphorus, and total potassium. Meanwhile, the annual rainfall and the number of rainfall days in the origin had a significant effect on the fibre content. In conclusion, the higher variability of wild oat populations due to the influence of different environmental and geographical factors may be a new possibility brought by forage oats.

Exogenous melatonin (MT) regulates plant growth and mitigates stress in response to stress. To analyze the machinery of exogenous melatonin, which improves salt and alkaline tolerance in oats, MT’s function was identified in the oat seed germination stage in our previous study. In this study, morphogenesis, photosynthetic physiology, hormone levels, and ion homeostasis were evaluated using the same MT treatment concentration. The results revealed that compared to the S45 treatment, the 100 μmol·L−1 MT treatment efficiently increased the seedling height and main root length of oat seedlings; promoted secondary root development; enhanced the root volume and root surface area; maintained a higher photosynthetic pigment content (carotenoids; chlorophyll a; chlorophyll b); raised the leaf photosynthetic rate (Pn), intercellular CO2 concentration (Ci), conductance to H2O (Gs), and transpiration rate (Tr); enhanced the light energy absorption and conversion of leaves; increased the leaf GA3, Tryptamine (TAM), and IAA contents; and decreased ABA levels. Hierarchical cluster analysis revealed that MT treatment also increased the contents of P, K, Ca, Mn, Cu, Mg, Fe, Zn, Mo, Cd, Al, Se, Ni, Co, and Ti; decreased the Na/K ratio; and maintained cellular ionic homeostasis in oat seedlings under saline–alkali stress, as compared with the untreated group. These findings showed that MT treatment enhanced the adaptation of oat to saline–alkali stress through regulating the physiological process of seedling growth. This suggests that MT plays a different role in improving saline–alkali tolerance in the germination and seedling stages of oat.

Eurotium cristatum which produces golden particles, is the dominant fungus playing a key role in the “flowering” process and in the quality of Fu-brick tea. It can produce a variety of active enzymes and active metabolites, which have multiple biological effects, such as improving the quality of tea, antibacterial, hypoglycemic, regulating intestinal flora, antioxidant and other effects. As an important resource microorganism, Eurotium cristatum has been widely used. In this paper, the basic biological characteristics, rich enzyme system, diverse active metabolites, safety of Eurotium cristatum, as well as the changes of substances and biological activities in the processing of tea, beans, cereals, and Chinese herbs by Eurotium cristatum fermentation are reviewed. The existing problems and future research directions are analyzed and prospected, in order to provide reference for its in-depth research and development.

Abstract Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. Results In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. Conclusions Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.

Abstract Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes.

Rapid industrialization and urbanization have caused serious cadmium (Cd) pollution in soil. Tartary buckwheat is an important pseudocereal crop with the potential ability to tolerate various stresses. However, the responses to Cd stress in this species are unclear. In this study, we assessed the phenotypic, cytological, physiological, and transcriptomic characteristics of Tartary buckwheat under the various concentrations of Cd treatments to investigate the responses and their regulatory pathways for the first time. The results showed Tartary buckwheat could tolerate the high Cd concentration of 50 mg/L under Cd stress. The average root diameters increased as a result of more cell layers of the endodermis and the bigger size of the pericycle. Cd primarily accumulated in roots and relatively less transferred to leaves. Antioxidant activities and malondialdehyde (MDA) accumulation varied in different tissues and different Cd concentrations of treatments. Meanwhile, Cd stress led to the formation of Casparian strips in roots and damaged the cytoderm and organelles. The weighted gene co-expression and interaction network analyses revealed that 9 core genes induced by Cd stress were involved in metal ion binding, Ca signal transduction, cell wall organization, antioxidant activities, carbohydrate metabolic process, DNA catabolic process, and plant senescence, which regulated a series of phenotypic, cytological, and physiological changes above. These results laid the foundation for a deep understanding of the responses to Cd toxicity in Tartary buckwheat. It’s also a critical reference for the functional characterization of genes for Cd tolerance.

Tartary buckwheat is highly attractive for the richness of nutrients and quality, yet post-embryonic seed abortion greatly halts the yield. Seed development is crucial for determining grain yield, whereas the molecular basis and regulatory network of Tartary buckwheat seed development and filling is not well understood at present. Here, we assessed the transcriptional dynamics of filling stage Tartary buckwheat seeds at three developmental stages by RNA sequencing. Among the 4249 differentially expressed genes (DEGs), genes related to seed development were identified. Specifically, 88 phytohormone biosynthesis signaling genes, 309 TFs, and 16 expansin genes participating in cell enlargement, 37 structural genes involved in starch biosynthesis represented significant variation and were candidate key seed development genes. Cis-element enrichment analysis indicated that the promoters of differentially expressed expansin genes and starch biosynthesis genes are rich of hormone-responsive (ABA-, AUX-, ET-, and JA-), and seed growth-related (MYB, MYC and WRKY) binding sites. The expansin DEGs showed strong correlations with DEGs in phytohormone pathways and transcription factors (TFs). In total, phytohormone ABA, AUX, ET, BR and CTK, and related TFs could substantially regulate seed development in Tartary buckwheat through targeting downstream expansin genes and structural starch biosynthetic genes. This transcriptome data could provide a theoretical basis for improving yield of Tartary buckwheat.

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

Saline–alkali stress is one of the major factors limiting oat seed germination. The regulatory role of melatonin (MT) as a naturally occurring active substance is well known, but the mechanism of MT-mediated intrinsic physiological regulation of oat seed germination under saline–alkali stress is unclear. Therefore, this study investigated (1) the variability of different MT seed soaking concentrations and times on the germination of oat seeds under saline–alkali stress, and (2) the possible physiological regulatory mechanisms of MT on the germination of oat seeds under saline–alkali stress. The results showed that seed vigor was significantly reduced under saline–alkali stress, and seed germination of oats was significantly inhibited; different concentrations of MT seed soaking treatments improved the germination rate, germination potential, germination index, vigor index, root length, germ length, fresh weight, and dry weight; and, overall, treatment improved seed germination and exhibited the phenomenon of “low promotion and high inhibition”. The 100 μmol·L−1 MT seed soaking treatment effectively enhanced the activities of seed antioxidant enzymes (SOD, POD, CAT, and APX) and nonenzymatic antioxidants (GSH and AsA), affected the AsA-GSH cycle, and effectively increased the contents of osmoregulatory substances (proline, protein, and soluble sugar) by reducing levels of H2O2, OH−, and MDA, thus enhancing the tolerance of oats to saline–alkali and promoting seed germination. In conclusion, MT has a positive effect on the saline–alkali tolerance of oat seeds.

In the present study, we sequenced and assembled the complete chloroplast genome of Fagopyrum leptopodum (Diels) Hedberg. The chloroplast genome of F. leptopodum was composed of 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The F. leptopodum chloroplast genome is 159,375 bp in length, with a GC content of 37.81%. Phylogenetic analysis based on the combined chloroplast gene dataset indicated that the F. leptopodum exhibited a close relationship with Fagopyrum luojishanense.

Abstract In this study, the mitogenomes of two Paxillus species were assembled, annotated and compared. The two mitogenomes of Paxillus involutus and P. rubicundulus comprised circular DNA molecules, with the size of 39,109 bp and 41,061 bp, respectively. Evolutionary analysis revealed that the nad4L gene had undergone strong positive selection in the two Paxillus species. In addition, 10.64 and 36.50% of the repetitive sequences were detected in the mitogenomes of P. involutus and P. rubicundulus, respectively, which might transfer between mitochondrial and nuclear genomes. Large-scale gene rearrangements and frequent intron gain/loss events were detected in 61 basidiomycete species, which revealed large variations in mitochondrial organization and size in Basidiomycota. In addition, the insertion sites of the basidiomycete introns were found to have a base preference. Phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies, indicating that mitochondrial genes were reliable molecular markers for analyzing the phylogenetic relationships of Basidiomycota. This study is the first report on the mitogenomes of Paxillus, which will promote a better understanding of their contrasted ecological strategies, molecular evolution and phylogeny of these important ectomycorrhizal fungi and related basidiomycete species.

Umami is an important widely-used taste component of food seasoning. Umami peptides are specific structural peptides endowing foods with a favorable umami taste. Laboratory approaches used to identify umami peptides are time-consuming and labor-intensive, which are not feasible for rapid screening. Here, we developed a novel peptide sequence-based umami peptide predictor, namely iUP-BERT, which was based on the deep learning pretrained neural network feature extraction method. After optimization, a single deep representation learning feature encoding method (BERT: bidirectional encoder representations from transformer) in conjugation with the synthetic minority over-sampling technique (SMOTE) and support vector machine (SVM) methods was adopted for model creation to generate predicted probabilistic scores of potential umami peptides. Further extensive empirical experiments on cross-validation and an independent test showed that iUP-BERT outperformed the existing methods with improvements, highlighting its effectiveness and robustness. Finally, an open-access iUP-BERT web server was built. To our knowledge, this is the first efficient sequence-based umami predictor created based on a single deep-learning pretrained neural network feature extraction method. By predicting umami peptides, iUP-BERT can help in further research to improve the palatability of dietary supplements in the future.

Abstract Background Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms underlying inflorescence architecture is pivotal for improving crop yield potential. Quinoa (Chenopodium quinoa Willd), a pseudo cereal originated from Andean region of South America, has been widely recognized as a functional super food due to its excellent nutritional elements. Increasing worldwide consumption of this crop urgently calls for its yield improvement. However, dissection of the regulatory networks underlying quinoa inflorescence patterning is lacking. Results In this study, we performed RNA-seq analysis on quinoa inflorescence samples collected from six developmental stages, yielding a total of 138.8 GB data. We screened 21,610 differentially expressed genes (DEGs) among all the stages through comparative analysis. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to categorize the DEGs into ten different modules. Subsequently, we placed emphasis on investigating the modules associated with none branched and branched inflorescence samples. We manually refined the coexpression networks with stringent edge weight cutoffs, and generated core networks using transcription factors and key inflorescence architecture related genes as seed nodes. The core networks were visualized and analyzed by Cytoscape to obtain hub genes in each network. Our finding indicates that the specific occurrence of B3, TALE, WOX, LSH, LFY, GRAS, bHLH, EIL, DOF, G2-like and YABBY family members in early reproductive stage modules, and of TFL, ERF, bZIP, HD-ZIP, C2H2, LBD, NAC, C3H, Nin-like and FAR1 family members in late reproductive stage modules, as well as the several different MADS subfamily members identified in both stages may account for shaping quinoa inflorescence architecture. Conclusion In this study we carried out comparative transcriptome analysis of six different stages quinoa inflorescences, and using WGCNA we obtained the most highly potential central hubs for shaping inflorescence. The data obtained from this study will enhance our understanding of the gene network regulating quinoa inflorescence architecture, as well will supply with valuable genetic resources for high-yield elite breeding in the future.

Background: Common buckwheat (Fagopyrum esculentum) is an important staple food crop in southwest China, where drought stress is one of the largest limiting factors that lead to decreased crop production. To reveal the molecular mechanism of common buckwheat in response to drought stress, we performed a comprehensive transcriptomics study to evaluate gene expression profiles of common buckwheat during PEG-mediated drought treatment. Results: In total, 45 million clean reads were assembled into 53,404 unigenes with an average length of 749 bp and N50 length of 1296 bp. A total of 1329 differentially expressed genes (DEGs) were identified by comparing well-watered and drought-treated plants, out of which 666 were upregulated and 663 were downregulated. Furthermore, we defined the functional characteristics of DEGs using GO and KEGG classifications. GO enrichment analysis showed that the DEGs were significantly overrepresented in four categories, namely, “oxidoreductase activity,” “oxidation–reduction process,” “xyloglucan:xyloglucosyl transferase activity,” and “apoplast.” Using KEGG pathway analysis, a large number of annotated genes were overrepresented in terms such as “plant hormone signal transduction,” “phenylpropanoid biosynthesis,” “photosynthesis,” and “carbon metabolism.” Conclusions: These results can be further exploited to investigate the molecular mechanism of common buckwheat in response to drought treatment and could supply with valuable molecular sources for abiotic-tolerant elite breeding programs in the future.How to cite: Wu Q, Zhao G, Bai X et al. Characterization of the transcriptional profiles in common buckwheat (Fagopyrum esculentum) under PEG-mediated drought stress. Electron J Biotechnol 2019;39. https://doi.org/10.1016/j.ejbt.2019.03.005. Keywords: Abiotic stress, Aluminum, Chlorophyll-binding proteins, Common buckwheat (Fagopyrum esculentum), Differentially expressed genes (DEGs), Drought stress, RNA sequencing, Transcription factor, Transferase, Triticum

Stem lodging can limit the grain yield of Tartary buckwheat (Fagopyrum tataricum), and creates difficulties in harvesting. A 2-year study was conducted to study the relationships between stem characteristics and lodging resistance in Tartary buckwheat. Six Tartary buckwheat cultivars with three stem types (short-stemmed XQ1 and CQ1; mid-length stemmed YQ1 and QK3; and tall-stemmed DAB and DN1) were used. The stem characteristics differed significantly among the three stem types. Mid-length stems had the thickest stem wall, the greatest numbers of large and small vascular bundles, and the lowest stem diameter/stem wall thickness ratio among the three stem types. Mid-length stems had the highest stem breaking strength (SBS) and stem puncture strength (SPS) among the three types of stem. The lignin content was significantly higher in mid-length stems than in tall and short stems. The activities of phenylalanine ammonia-lyase (PAL), tyrosine ammonia-lyase (TAL), and cinnamyl alcohol dehydrogenase (CAD), but not 4-coumarate: CoA ligase (4CL), differed significantly among the three stem types. In correlation analyses, SBS was significantly positively correlated with stem diameter, stem wall thickness, and the number of large and small vascular bundles, but significantly negatively correlated with stem diameter/stem wall thickness and lodging rate. The lignin content was significantly positively correlated with the activities of lignin-related enzymes and with SBS and SPS, and significantly negatively correlated with lodging rate. The present study provides preliminary insights into the relationship between stem traits and lodging resistance in Tartary buckwheat, laying a foundation for a further understanding of lodging resistance. Abbreviations SBS: stem breaking strength; SPS: stem puncture strength; PAL: phenylalanine ammonia-lyase; TAL: tyrosine ammonia-lyase; CAD: cinnamyl alcohol dehydrogenase; 4CL: 4-coumarate: CoA ligase.

Heavy truck tires are one of the main sources of road traffic noise. However, the mechanism and propagation of the noise generated by these tires have not been systematically investigated. To determine the noise of heavy truck tires with different structures and patterns, and to analyze the correlation between the indoor tire noise and coast-by tire noise, an integrated tire indoor noise test and a coast-by noise test were designed and successfully implemented. The indoor test was conducted on a drum inside a semi-anechoic chamber to simultaneously measure the near field and far field noise of the tires. The outdoor measurements were carried out using a coast-by test on the new ISO 10844 surface. A formula for quantitative analysis with appropriate corrections was developed to analyze the data with reasonable errors, which can be used to predict the coast-by noise through the indoor tire noise test accurately and effectively. The analysis shows that when trying to build the relationship between indoor and outdoor heavy truck tire noise, care should be taken to differentiate the tires with a load capacity index in excess of 121 and without any dual fitting indication from ordinary tires, due to the specified test procedure.

Photosynthesis is the basis for plant productivity, and improvement of photosynthetic efficiency is an important way to improve crop yield. However, the relationship between photosynthetic parameters and the yield of Tartary buckwheat (Fagopyrum tataricum) under rainfed conditions is unclear. A two-year field trial was conducted during 2016 and 2017 to assess the photosynthetic capacity of different leaves, dry matter accumulation, and yield of four Tartary buckwheat cultivars from flowering to maturity. The leaves of all cultivars aged gradually after flowering, and the leaf chlorophyll (Chl) and soluble protein (SP) contents, net photosynthetic rates (Pn), transpiration rates (Tr), and stomatal conductance (Gs) tended to decline. The Chl, SP, Pn, Tr, and Gs of cultivars (cvs.) XiQiao2 and QianKu3 were significantly higher than those of LiuKu3 and JiuJiang at each sampling time from 18 days after anthesis to maturity, but the intercellular CO2 content (Ci) showed the opposite trend. Cultivars XiQiao2 and QianKu3 produced more total dry matter (mean 17.1% higher), had higher harvest index (HI, mean 16.4% higher), and yield (mean 29.0% higher) than cvs. LiuKu3 and JiuJiang at maturity, and the difference was remarkably consistent. The yield of all the cultivars was positively correlated with leaf Chl, SP, Pn, Tr, and Gs, but negatively correlated with Ci. At late growth stages, the high-yielding cultivars maintained higher Chl, SP contents, Pn, Tr, and Gs, and showed higher dry matter accumulation and lower Ci than the low-yielding cultivars, consistent with their higher leaf photosynthetic capacity. The important factors determining the yield of Tartary buckwheat were maintaining higher leaf Chl and SP content and photosynthetic capacity and delaying aging during the grain formation stage. Enhanced rates of photosynthesis and dry matter accumulation led to higher post-anthesis accumulation of biomass with a positive impact on grain number and higher yield.

Tartary buckwheat (Fagopyrum tataricum) is considered a profitable crop that possesses medicinal properties, because of its flavonoid compounds. However, the dehulling issue is becoming the bottleneck for consumption of Tartary buckwheat seed. In this study, we investigated the relation between dehulling efficiency and content of lignin and cellulose in the seed hull. Moreover, the untargeted metabolomics analysis, including partial least squares discriminant analysis (PLS-DA) and principal component analysis (PCA), were performed to examine the pattern of metabolic changes in the hull of Tartary buckwheat seeds, XQ 1 and MQ 1, during seed development using gas chromatography mass spectrometry (GC-MS). In mature seed hull the accumulation of highest lignin and lowest cellulose were observed in the hull of MQ 1 seed, a dehulling-friendly variety with highest dehulling efficiency (93%), than that in other dehulling recalcitrant varieties, such as XQ 1 with a range of dehulling efficiency from 2% to 6%. During seed development, the total content of lignin and cellulose increased. MQ 1 and XQ 1 displayed a similar trend in the change of lignin and cellulose that the content was decreased in lignin and increased in cellulose. PCA result showed the metabolic differentiations between MQ 1 and XQ 1 during seed development. The results of our study suggest the compensatory regulation of lignin and cellulose deposition in the hull of mature and developing seed, and deviation of MQ 1 from the ratio of lignin to cellulose of other dehulling recalcitrant varieties may have been a contributing factor that resulted in the dehulling differentia.

The purpose of this study was to investigate the effects of yeast polysaccharide (YPS) on growth and flavonoid accumulation in sprout cultures of Fagopyrum tataricum (tartary buckwheat). Without obvious change in the appearance of the sprouts, the exogenous YPS notably stimulated the production of functional metabolites in F. tataricum sprouts, and the stimulation effect was concentration-dependent. With 400 mg/L of YPS applied to the sprout cultures on day 6, the total rutin and quercentin content was effectively increased to 42.8 mg/gdw, or about 1.4-fold in comparison with the control of 31.2 mg/gdw. Feeding with 800 mg/L of YPS on day 9, the sprouts biomass was increased by about 8% compared to the control culture (0.99 gdw/100 sprouts versus 0.92 gdw/100 sprouts). Moreover, the present study revealed that the accumulation of these bioactive metabolites resulted from the stimulation of the phenylpropanoid pathway by YPS treatment. It could be an effective strategy for improving the functional quality of the F. tataricum sprouts provided with YPS.

To mitigate the wastage of seed resources and reduce the usage of pesticides and fertilizers, seed coating agents have gained popularity. This study employs single-factor and multi-index orthogonal experimental design methods to investigate the seed coating formula and physical properties of Tartary buckwheat. The specific effects of each component on Tartary buckwheat seed germination are analyzed. The findings reveal that the seed coating agent formulated with 1.5% polyvinyl alcohol, 0.15% sodium alginate, 0.2% op-10, 0.1% polyacrylamide, 8% colorant, 3% ammonium sulfate, 1% potassium dihydrogen phosphate, and 0.15% carbendazim exhibits the most effective coating. It demonstrates optimal physical properties and promotes seed germination efficiently. The suspension rate of this seed coating agent reaches 91.12%, with a mere 2.13% coating shedding rate and 2.5% coating seed rot rate. Furthermore, it achieves a germination percentage of 99.17%, which is 20.84% higher than the lowest group. The germination potential and index are also significantly higher than the lowest group, with an increase of 20.84% and 26.56%, respectively. Additionally, the vitality index is 553.08, a 15.75% increase compared to the lowest group. The application of seed coating agents helps reduce seed resource loss, increase plant numbers, and ultimately enhance agricultural yields. This finding holds practical significance in agricultural production. [ABSTRACT FROM AUTHOR]

Aluminum (Al) toxicity is a considerable factor limiting crop yield and biomass in acidic soil. Tartary buckwheat growing in acidic soil may suffer from Al poisoning. Here, we investigated the influence of Al stress on the growth of tartary buckwheat seedling roots, and the alleviation of Al stress by silicon (Si), as has been demonstrated in many crops. Under Al stress, root growth (total root length, primary root length, root tips, root surface area, and root volume) was significantly inhibited, and Al and malondialdehyde (MDA) accumulated in the root tips. At the same time, catalase (CAT) and ascorbate peroxidase activities, polyphenols, flavonoids, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) free-radical scavenging ability were significantly decreased. After the application of Si, root growth, Al accumulation, and oxidative damage were improved. Compared to Al-treated seedlings, the contents of ·O2− and MDA decreased by 29.39% and 25.22%, respectively. This was associated with Si-induced increases in peroxidase and CAT enzyme activity, flavonoid compounds, and free-radical scavenging (DPPH and ABTS). The application of Si therefore has positive effects on Al toxicity in tartary buckwheat roots by reducing Al accumulation in the roots and maintaining oxidation homeostasis. [ABSTRACT FROM AUTHOR]

Under the background of emerging agricultural education, practice bases are an important place to train profession talented person that match social needs, so it is very important to build stable and long-term practice bases. At present, the main problems in the construction of practice bases for postgraduates in local colleges and universities are mainly focusing on construction and neglecting management, imperfect cooperation mechanism and lack of teaching management effectively. It is of great significance to build a long-term management mechanism to ensure the education quality of practice bases. Therefore, constructing the mode of " double integration and double promotion of production and education" with practice bases as the carrier and realizing the organic combination of industrial needs and postgraduate projects is an important idea for local colleges and universities to train professional degree postgraduates to " know agriculture, love agriculture, strengthen agriculture and promote agriculture", and it also provides a reference for the mechanism construction of postgraduate bases. [ABSTRACT FROM AUTHOR]