Quinoa greens as a novel plant food: a review of its nutritional composition, functional activities, and food applications.

Quinoa (Chenopodium quinoa Willd) is widely regarded as a versatile pseudo-cereal native to the Andes Mountains in South America. It has gained global recognition as a superfood due to its rich nutritional profile. While quinoa grains are well-known, there is an undiscovered potential in quinoa greens, such as sprouts, leaves, and microgreens. These verdant parts of quinoa are rich in a diverse array of essential nutrients and bioactive compounds, including proteins, amino acids, bioactive proteins, peptides, polyphenols, and flavonoids. They have powerful antioxidant properties, combat cancer, and help prevent diabetes. Quinoa greens offer comparable or even superior benefits when compared to other sprouts and leafy greens, yet they have not gained widespread recognition. Limited research exists on the nutritional composition and biological activities of quinoa greens, underscoring the necessity for thorough systematic reviews in this field. This review paper aims to highlight the nutritional value, bioactivity, and health potential of quinoa greens, as well as explore their possibilities within the food sector. The goal is to generate interest within the research community and promote further exploration and wider utilization of quinoa greens in diets. This focus may lead to new opportunities for enhancing health and well-being through innovative dietary approaches.

New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health.

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.

Interkingdom multi-omics analysis reveals the effects of nitrogen application on growth and rhizosphere microbial community of Tartary buckwheat.

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.

Identification of a new allele of BraA09g066480.3C controlling the wax-less phenotype of Chinese cabbage.

BACKGROUND: Epidermal wax covers the surfaces of terrestrial plants to resist biotic and abiotic stresses. Wax-less flowering Chinese cabbage (Brassica campestris L. ssp. chinesis var. utilis tsen et lee) has the charateristics of lustrous green leaves and flower stalks, which are of high commercial value. RESULTS: To clarify the mechanism of the wax deficiency, the wax-less flowering Chinese cabbage doubled-haploid (DH) line 'CX001' and Chinese cabbage DH line 'FT', obtained from isolated microspore culture, were used in the experiments. Genetic analysis showed that the wax-less phenotype of 'CX001' was controlled by a recessive nuclear gene, named wlm1 (wax-less mutation 1), which was fine-mapped on chromosome A09 by bulked segregant analysis sequencing (BSA-seq) of B.rapa genome V3.0. There was only one gene (BraA09g066480.3C) present in the mapping region. The homologous gene in Arabidopsis thaliana is AT1G02205 (CER1) that encodes an aldehyde decarboxylase in the epidermal wax metabolism pathway. Semi-quantitative reverse transcription PCR and transcriptome analysis indicated that BraA09g066480.3C was expressed in 'FT' but not in 'CX001'. BraA09g066480.3C was lost in the CXA genome to which 'CX001' belonged. CONCLUSION: The work presented herein demonstrated that BraA09g066480.3C was the causal gene for wax-less flowering Chinese cabbage 'CX001'. This study will lay a foundation for further research on the molecular mechanism of epidermal wax synthesis in flowering Chinese cabbage.

Transcriptome Analyses Revealed the Wax and Phenylpropanoid Biosynthesis Pathways Related to Disease Resistance in Rootstock-Grafted Cucumber.

Cucumbers (Cucumis sativus L.) are a global popular vegetable and are widely planted worldwide. However, cucumbers are susceptible to various infectious diseases such as Fusarium and Verticillium wilt, downy and powdery mildew, and bacterial soft rot, which results in substantial economic losses. Grafting is an effective approach widely used to control these diseases. The present study investigated the role of wax and the phenylpropanoid biosynthesis pathway in black-seed pumpkin rootstock-grafted cucumbers. Our results showed that grafted cucumbers had a significantly higher cuticular wax contents on the fruit surface than that of self-rooted cucumbers at all stages observed. A total of 1132 differently expressed genes (DEGs) were detected in grafted cucumbers compared with self-rooted cucumbers. Pathway enrichment analysis revealed that phenylpropanoid biosynthesis, phenylalanine metabolism, plant circadian rhythm, zeatin biosynthesis, and diterpenoid biosynthesis were significantly enriched. In this study, 1 and 13 genes involved in wax biosynthesis and the phenylpropanoid biosynthesis pathway, respectively, were up-regulated in grafted cucumbers. Our data indicated that the up-regulated genes in the wax and phenylpropanoid biosynthesis pathways may contribute to disease resistance in rootstock-grafted cucumbers, which provides promising targets for enhancing disease resistance in cucumbers by genetic manipulation.

Effects of Reduced Phosphate Fertilizer and Increased Trichoderma Application on the Growth, Yield, and Quality of Pepper.

Phosphorus utilization by crop plants is often limited, thereby resulting in large accumulations of residual phosphorus fertilizer in the soil. Trichoderma fungi function as natural decomposition agents that can contribute to increasing decomposition and promoting nutrient absorption in plants. In this study, we developed a novel fertilizer application strategy that reduces phosphate fertilizer and increases Trichoderma and examined its effects on the growth, nutrient absorption, and fruit quality of pepper (Capsicum annuum L.). We compared the efficacies of eight treatments: P100 = standard dose application of phosphorus fertilizer; P85 = 85% dose; P70 = 70% dose; P0 = no phosphorus fertilizer; and the TP100, TP85, TP70, and TP0 treatments, in which a Trichoderma mixture was added to the P100, P85, P70, and P0 treatments, respectively. The combined fertilizer application strategy stimulated plant growth, increased chlorophyll content, improved yield, and enhanced nutrient absorption. Additionally, the strategy improved pepper fruit quality by increasing the contents of soluble proteins, soluble sugars, vitamin C, capsaicin, and capsanthin. A comprehensive analysis indicated that the TP85 treatment was the optimal fertilization regime for pepper. This study provides a novel fertilizer application strategy for pepper that not only ensures good plant growth but also protects soil health.

Integrated Metabolome and Transcriptome Analysis Provides New Insights into the Glossy Graft Cucumber Fruit (Cucumis sativus L.).

Cucumber is an important vegetable crop, and grafts often affect the quality and wax loss in cucumber fruit and affect its value. However, their metabolites and molecular mechanisms of action remain unclear. Metabolome and transcriptome analyses were conducted on the fruit peels of self-rooted plants (SR) grafted with white seed pumpkin (WG). The results showed that there were 352 differential metabolites in the fruit peels of the SR and WG. The transcriptome analysis showed 1371 differentially expressed genes (DEGs) between the WG and SR. These differentially expressed genes were significantly enriched in plant hormone signal transduction, cutin, suberin, wax biosynthesis, phenylpropanoid biosynthesis, and zeatin biosynthesis. By analyzing the correlation between differential metabolites and differentially expressed genes, six candidate genes related to the synthesis of glycitein, kaempferol, and homoeriodictyol were identified as being potentially important. Key transcription factors belonging to the TCP and WRKY families may be the main drivers of transcriptional changes in the peel between the SR and WG. The results of this study have provided a basis for the biosynthesis and regulation of wax loss and quality in grafted cucumbers and represents an important step toward identifying the molecular mechanisms of grafting onto cucumber fruit.

Integrated Physiological and Transcriptomic Analyses Revealed Improved Cold Tolerance in Cucumber (Cucumis sativus L.) by Exogenous Chitosan Oligosaccharide.

Cucumber (Cucumis sativus L.), sensitive to cold stress, is one of the most economically important vegetables. Here, we systematically investigated the roles of exogenous glycine betaine, chitosan, and chitosan oligosaccharide in alleviating cold stress in cucumber seedlings. The results showed that 50 mg·L-1 chitosan oligosaccharide had the best activity. It effectively increases plant growth, chlorophyll content, photosynthetic capacity, osmotic regulatory substance content, and antioxidant enzyme activities while reducing relative electrical conductivity and malondialdehyde levels in cucumber seedlings under cold stress. To reveal the protective effects of chitosan oligosaccharide in cold stress, cucumber seedlings pretreated with 50 mg·L-1 chitosan oligosaccharide were sampled after 0, 3, 12, and 24 h of cold stress for transcriptome analysis, with distilled water as a control. The numbers of differentially expressed genes in the four comparison groups were 656, 1274, 1122, and 957, respectively. GO functional annotation suggested that these genes were mainly involved in "voltage-gated calcium channel activity", "carbohydrate metabolic process", "jasmonic acid biosynthetic", and "auxin response" biological processes. KEGG enrichment analysis indicated that these genes performed important functions in "phenylpropanoid biosynthesis", "MAPK signaling pathway-plant", "phenylalanine metabolism", and "plant hormone signal transduction." These findings provide a theoretical basis for the use of COS to alleviate the damage caused by cold stress in plant growth and development.

Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis).

BACKGROUND: The growth and development of leaves and petioles have a significant effect on photosynthesis. Understanding the molecular mechanisms underlying leaf and petiole development is necessary for improving photosynthetic efficiency, cultivating varieties with high photosynthetic efficiency, and improving the yield of crops of which the leaves are foodstuffs. This study aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). The data were used to construct a competitive endogenous RNA (ceRNA) network to obtain insights into the mechanisms underlying leaf and petiole development. RESULTS: The leaves and petioles of the 'PHL' inbred line of Chinese cabbage were used as research materials for whole transcriptome sequencing. A total of 10,646 differentially expressed (DE) mRNAs, 303 DElncRNAs, 7 DEcircRNAs, and 195 DEmiRNAs were identified between leaves and petioles. Transcription factors and proteins that play important roles in leaf and petiole development were identified, including xyloglucan endotransglucosylase/hydrolase, expansion proteins and their precursors, transcription factors TCP15 and bHLH, lateral organ boundary domain protein, cellulose synthase, MOR1-like protein, and proteins related to plant hormone biosynthesis. A ceRNA regulatory network related to leaf and petiole development was constructed, and 85 pairs of ceRNA relationships were identified, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA, and 2 DEmiRNA-DEcircRNA pairs. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaves and petioles were screened from transcriptome data, and their functions were explored through subcellular localization analysis and transgenic overexpression verification. BrLSH1, BrLSH2 and BrLSH3 were nuclear proteins, and BrLSH2 inhibited the growth and development of Arabidopsis thaliana. CONCLUSIONS: This study identifies mRNAs and non-coding RNAs that may be involved in the development of leaves and petioles in Chinese cabbage, and establishes a ceRNA regulatory network related to development of the leaves and petioles, providing valuable genomic resources for further research on the molecular mechanisms underlying leaf and petiole development in this crop species.

Study on morphological traits, nutrient compositions and comparative metabolomics of diploid and tetraploid Tartary buckwheat sprouts during sprouting.

Tartary buckwheat (TB) sprout is a kind of novel nutritional vegetable, but its consumption was limited by low biomass and thin hypocotyl. The tetraploid TB sprouts was considered to be able to solve this issue. However, the nutritional quality of tetraploid TB sprouts and differences between conventional (diploid) and tetraploid TB sprouts remain unclear. In this study, the morphological traits, nutrient compositions and metabolome changes of diploid and tetraploid TB sprouts were analyzed. The water, pigments and minerals contents of TB sprouts increased during sprouting, while the contents of total soluble protein, reducing sugar, cellulose, and total phenol decreased. Compared with diploid sprouts, tetraploid sprouts had higher biomass and thicker hypocotyl. Tetraploid sprouts had higher ash and carotenoid contents, but had lower phenol and flavonoid accumulation. 677 metabolites were identified in TB sprouts by UPLC-MS analysis, including 62 diseases-resistance metabolites and 43 key active ingredients. Some key bioactive metabolites, such as rimonabant, quinapril, 1-deoxynojirimycin and miglitol, were identified. 562 differential expressed metabolites (DEMs) were identified during sprouting with seven accumulation patterns, and five hormones were found to be involved in sprout development. Additionally, 209 DEMs between diploid and tetraploid sprouts were found, and some key bioactive metabolites were induced by chromosome doubling such as mesoridazine, amaralin, atractyloside A, rhamnetin and Qing Hau Sau. This work lays a basis for the development and utilization of TB sprouts and provides evidence for the selection of tetraploid varieties to produce sprouts with high biomass and quality.

Identification of the global diurnal rhythmic transcripts, transcription factors and time-of-day specific cis elements in Chenopodium quinoa.

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.

Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency.

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4, FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified.

Regulatory function of the endogenous hormone in the germination process of quinoa seeds.

The economic and health significance of quinoa is steadily growing on a global scale. Nevertheless, the primary obstacle to achieving high yields in quinoa cultivation is pre-harvest sprouting (PHS), which is intricately linked to seed dormancy. However, there exists a dearth of research concerning the regulatory mechanisms governing PHS. The regulation of seed germination by various plant hormones has been extensively studied. Consequently, understanding the mechanisms underlying the role of endogenous hormones in the germination process of quinoa seeds and developing strategies to mitigate PHS in quinoa cultivation are of significant research importance. This study employed the HPLC-ESI-MS/MS internal standard and ELISA method to quantify 8 endogenous hormones. The investigation of gene expression changes before and after germination was conducted using RNA-seq analysis, leading to the discovery of 280 differentially expressed genes associated with the regulatory pathway of endogenous hormones. Additionally, a correlation analysis of 99 genes with significant differences identified 14 potential genes that may act as crucial "transportation hubs" in hormonal interactions. Through the performance of an analysis on the modifications in hormone composition and the expression of associated regulatory genes, we posit a prediction that implies the presence of a negative feedback regulatory mechanism of endogenous hormones during the germination of quinoa seeds. This mechanism is potentially influenced by the unique structure of quinoa seeds. To shed light on the involvement of endogenous hormones in the process of quinoa seed germination, we have established a regulatory network. This study aims to offer innovative perspectives on the breeding of quinoa varieties that exhibit resistance to PHS, as well as strategies for preventing PHS.

Genome-wide identification and expression analysis of glutathione S-transferase gene family to reveal their role in cold stress response in cucumber.

The plant glutathione S-transferases (GSTs) are versatile proteins encoded by several genes and play vital roles in responding to various physiological processes. Members of plant GSTs have been identified in several species, but few studies on cucumber (Cucumis sativus L.) have been reported. In this study, we identified 46 GST genes, which were divided into 11 classes. Chromosomal location and genome mapping revealed that cucumber GSTs (CsGSTs) were unevenly distributed in seven chromosomes, and the syntenic regions differed in each chromosome. The conserved motifs and gene structure of CsGSTs were analyzed using MEME and GSDS 2.0 online tools, respectively. Transcriptome and RT-qPCR analysis revealed that most CsGST members responded to cold stress. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for differentially expressed CsGSTs under cold stress revealed that these genes responded to cold stress probably through "glutathione metabolism." Finally, we screened seven candidates that may be involved in cold stress using Venn analysis, and their promoters were analyzed using PlantCARE and New PLACE tools to predict the factors regulating these genes. Antioxidant enzyme activities were increased under cold stress conditions, which conferred tolerance against cold stress. Our study illustrates the characteristics and functions of CsGST genes, especially in responding to cold stress in cucumber.

Transcriptomic, cytological, and physiological analyses reveal the potential regulatory mechanism in Tartary buckwheat under cadmium stress.

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.

Genome-wide identification and transcriptome analysis of the heavy metal-associated (HMA) gene family in Tartary buckwheat and their regulatory roles under cadmium stress.

Heavy metal-associated (HMA) genes are those related to heavy metal transport and detoxification in plants. HMA genes have not been reported in Tartary buckwheat so far. In this study, we accessed the HMA genes of Tartary buckwheat by genome-wide identification for the first time. A total of 56 HMA genes were identified, including 36 ATX1 (antioxidant protein1) genes, 13 HIPP (heavy metal-associated isoprenylated plant protein) genes, and 7 P1B-ATPase (P1B-type adenosine triphosphatase) genes. These gene structures, motif compositions, chromosomal distribution, phylogenetic relationship, duplication events, interaction networks, cis-acting elements, and transcriptional expression under cadmium (Cd) stress were investigated. Among them, genes in HIPP and ATX1 subfamilies were more closely related. The 56 HMA genes were involved in the regulation of metal ion transport and homeostasis by binding metal ions, likely triggered by signals transducted by plant hormones. Fifteen of these HMA genes played regulatory roles under Cd stress. FtP1bA1 was identified to be a core gene involved in the defense regulation of Cd stress. Our results provide not only the first overview and characteristics of HMA genes in the whole genome of Tartary buckwheat but also a valuable reference for the functional analysis of HMA genes under Cd stress. Understanding changes in gene regulation induced by Cd stress lays the foundation for breeding resistant varieties.

Dynamic transcriptome analysis suggests the key genes regulating seed development and filling in Tartary buckwheat (Fagopyrum tataricum Garetn.).

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.

Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis).

Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.

Integrating transcriptome and physiological analyses to elucidate the molecular responses of buckwheat to graphene oxide.

With the increasing application of nanomaterials, evaluation of the phytotoxicity of nanoparticles has attracted considerable interest. Buckwheat is an economically pseudocereal crop, which is a potential model for investigating the response of plants to hazardous materials. In this study, the response of buckwheat to graphene oxide (GO) was investigated by integrating physiological and transcriptome analysis. GO can penetrate into buckwheat root and stem, and high concentrations of GO inhibited seedlings growth. High concentration of GO improved ROS production and regulated the activities and gene expression of oxidative enzymes, which implying GO may affect plant growth via regulating ROS detoxification. Root and stem exhibit distinct transcriptomic responses to GO, and the GO-responsive genes in stem are more enriched in cell cycle and epigenetic regulation. GO inhibited plant hormone biosynthesis and signaling by analyzing the expression data. Additionally, 97 small secreted peptides (SSPs) encoding genes were found to be involved in GO response. The gene expression of 111 transcription factor (TFs) and 43 receptor-like protein kinases (RLKs) were regulated by GO, and their expression showed high correlation with SSPs. Finally, the TFs-SSPs-RLKs signaling networks in regulating GO response were proposed. This study provides insights into the molecular responses of plants to GO.

Genome-wide identification and expression analysis disclose the pivotal PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN members that may be utilized for yield improvement of Chenopodium quinoa.

Quinoa (Chenopodium quinoa) is a prospective orphan crop that needs yield improvement. Previous studies indicate PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family genes are highly associated with the key agronomic traits of crops. Characterizing the pivotal PEBP genes will speed up the domestication and yield improvement of quinoa. Previous investigations on PEBP genes of Chenopodium species indicated that, the PEBP genes, despite in the same subclade, may have experienced functional diversification. Especially, the allotetraploidy (AABB) and numerous segmental duplications and chromosomal rearrangements in quinoa make it more difficult to understand the functions of PEBP genes. More recently, 6 quinoa FT subfamily genes were predicted to be related to flowering of quinoa. However, investigation on the whole PEBP family members is still lacking. In this study, we obtained 23 PEBP genes, including 5 MFT, 11 FTL and 7 TFL genes. We found 7 orthologous gene pairs, from sub-genome A and sub-genome B, respectively, showing collinearities with sugar beet. Evolution analysis on PEBP genes of two quinoa sub-genomes, sugar beet and relatives of diploid ancestors indicated that, the reasons for gene duplication events varied and 4 tandem duplications are the major reason for PEBP family expansion. Tissue-specific expression analysis suggested that expression patterns are mostly differing between orthologous gene pairs. Analysis on gene expressions at 6 stages suggested the possible positive roles of CqFTL1/CqFTL2, CqFTL5, CqFTL8, CqFTL6/CqFTL9 and CqTFL6/CqTFL7, and negative roles of CqTFL1/CqTFL2/CqTFL3, CqTFL4/CqTFL5 in inflorescence branching. Expression analysis in ABA-treated seed, in combination with the cis-acting element distribution analysis, indicated that CqMFT2, CqMFT3 and CqMFT4 may regulate seed germination via ABA signaling. Observations on responses to night break and photoperiod changes highlighted the roles of CqFTL5 and CqFTL8 under short day, and CqFTL6 under long day for quinoa flowering. Further, co-expression network analysis indicated that 64 transcription factors may act upstream of CqFTL5 and CqFTL8 to regulate flowering. Together, this study will help us identify the pivotal PEBP genes that may be utilized for quinoa breeding in future.