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Graphene oxide (GO) is widely used in various scientific fields, including biochemistry and environmental and plant science, because of its unique physicochemical properties. However, there is limi...

Summary Hemp (Cannabis sativa L.) is an annual and typically dioecious crop. Due to the therapeutic potential for human diseases, phytocannabinoids as a medical therapy is getting more attention recently. Several candidate genes involved in cannabinoid biosynthesis have been elucidated using omics analysis. However, the gene function was not fully validated due to few reports of stable transformation for Cannabis tissues. In this study, we firstly report the successful generation of gene‐edited plants using an Agrobacterium‐mediated transformation method in C. sativa. DMG278 achieved the highest shoot induction rate, which was selected as the model strain for transformation. By overexpressing the cannabis developmental regulator chimera in the embryo hypocotyls of immature grains, the shoot regeneration efficiency was substantially increased. We used CRISPR/Cas9 technology to edit the phytoene desaturase gene and finally generated four edited cannabis seedlings with albino phenotype. Moreover, we propagated the transgenic plants and validated the stable integration of T‐DNA in cannabis genome.

Flax (Linum usitatissimum L.) is an important industrial crop, and its seeds are rich in a variety of functional nutrition and health components. Therefore, flaxseed is not only an important raw ma...

Numerous candidate genes related to apomixis have been identified through transcriptomics; however, the molecular mechanism underlying apomixis remains unclear. Elucidation of the underlying mechanisms is essential to expand its application in crop breeding. Therefore, here, we employed the isobaric tags for a relative and absolute quantification labeling technology to investigate the protein expression in Boehmeria tricuspis generated through different reproductive modes at the functional megaspore stage. We identified 40 differential abundance proteins associated with apomeiosis, most of which were involved in "response to stress". Functional analysis suggested that lower levels of reactive oxygen species (ROS) play a role in inducing the development of apomeiosis. Proteins related to ROS regulation, cell wall modifications, and stability under heat stress play a crucial role in the development of diplosporic apomeiosis. Our results give evidence to the insight that stress can induce a switch from apomixis to sexuality by ROS content, and an increased composition of stress tolerance as well as secondary metabolites can buffer ROS effects. Precise coordination of these proteins involved in inter-related regulatory control mechanisms may act together in the transition from the sexual to apomixis development.

Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

Flax (Linum usitatissimum L.) is an important economic crop worldwide. The lignin content of flax stems directly determines the quality of flax fiber, and excessively high lignin content in the fiber leads to pollutant discharge by the textile industry. Flax seeds also contain lignans, a group of compounds that are structurally similar to lignin and highly beneficial for human health. The biosynthesis of lignan and lignin occurs in the same metabolic pathway. To elucidate the metabolic relationship between these two compounds and the regulatory nodes of their metabolic processes, third generation (Iso-Seq) and second generation (Illumina) sequencing technologies were used in this study to obtain the transcriptomes of a pair of flax cultivars with significant differences in lignan content. The results showed that the differentially expressed genes (DEGs) are significantly enriched in the lignin and lignan biosynthesis pathways. Ten genes with significant differences in expression (|Log2 FC|>4) were selected for quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The expression levels of these genes all were significantly different in Shuangya 4 and NEW at different stages of flax seed and stem development. We speculated that these genes were most likely closely related to the lignan and lignin metabolism. We also found that the lignan and lignin content are significantly negatively correlated with each other during flax seed and stem development. The findings of this study provide a scientific basis for the application of biotechnological methods to the development of new high-quality flax cultivars with high lignan and low lignin content.

Additional file 3:. Review history.

Additional file 2: Figure S1. The average proportion of reads with different alignment lengths by mapping the garlic reference in 84 accessions. Sequence reads generated from whole genome resequencing. Figure S2 Distribution of garlic variations. Track i indicates the density of SNPs from Genotype-by-sequencing (GBS), and track ii and iii indicate the density of SNPs and indels from whole-genome sequencing (WGS). Figure S3. The bulbs from three varieties, S41, S59, and S56, which were the accessions of OG, CG1, and CG2, respectively. Figure S4. Effective population size Ne of four garlic populations estimated using the GBS SNPs by the SMC++ method. Figure S5. A Venn figure shows the selective gene number by the population branch statistic (PBS, green), the θπ ratio (πOG/πCG, blue), and the test of cross-population composite likelihood ratio (XP-CLR, yellow). Figure S6. Comparison of gene expression level among three groups. Manhattan plot shows the P value for the difference of transcript abundance of each gene between two groups by ANOVA analysis. The y axis indicates the -log10(P value). Figure S7. Characterization of ELF4-like Asa2G00681.1. a, Expression level of Asa2G00681.1 in the bulbs under enlarging growth (blue column) and un-enlargement (orange column) in three varieties. b, Expression level of Asa2G00681.1 in the enlarging bulbs of three garlic groups based on the estimation of FPKM value. In the Figure a and b, the y axis indicates the FPKM value, and Ns indicates no significant difference, and ** and *** indicate a significant difference at the level of 0.01 and 0.001, respectively. c, Distribution of the ratio of nucleotide diversity (πCG/πOG) and FST values in the region of 202.0-204 Mb on chromosome 2. The grey line indicates the position of Asa2G00681.1. Figure S8. Correlation between the transcript abundance of five selective candidates and the clove weight traits in 81 accessions. The number in the top right panes (green dashed box) represents the correlation coefficient, and the red and blue circle indicates the negative and positive correlation, respectively; *** indicated a significance at 0.001 level. The column diagram in the diagonal panes shows the distribution of trait phenotype and expression FPKM value of genes, in which the red line indicates a distribution trend. The scatter plot in the bottom left panes (purple dashed box) shows the correlation between the transcript abundances and the clove weight traits in 81 accessions, where the red line indicates a trend. Figure S9. Number of heterozygous and homozygous deleterious mutations in 84 garlic accessions and three groups (OG, CG1, CG2). Each box represents the mean and interquartile range. Figure S10. Distribution of deleterious allele frequency in 84 garlic accessions. Figure S11. Correlation between the transcript abundance of three selective candidates and the clove number traits in 81 accessions. The number in the top right panes (green dashed box) represents the correlation coefficient, and the red and blue circles indicate negative and positive correlation, respectively; ** and *** indicate a significance at 0.01 and 0.001 level. The column diagram in the diagonal panes shows the distribution of trait phenotype and expression FPKM value of genes, in which the red line indicates a distribution trend. The scatter plot in the bottom left panes (purple dashed box) shows the correlation between the transcript abundances and the clove number traits in 81 accessions, where the red line indicates a trend. Figure S12. Comparison of deleterious mutations burden in the coding region of Asa2G00245.1 among OG, CG1 and CG2. Figure S13 Whole genome association analysis of the clove number trait in 230 garlic accessions. Purple arrows indicate the associated position with significant signal (P < 5.32 ×10−9). The gene under associated loci indicates that it is near to the associated signal (within 200 kb), and its expression shows the significant correlation with the clove number trait in 81 transcriptome-examined accessions, and is considered as the candidate of corresponding loci. *, **, and *** represent the significant association at the level of 0.05, 0.01, and 0.001, respectively. Figure S14. Expression level of Asa2G000503.1 in the enlarging bulbs of three garlic groups based on the estimation of FPKM value. *, and ** indicate the significant difference at the level of 0.05 and 0.01, respectively. Figure S15. Differentially expressed genes (DEGs) in the bulbs whose cloves are before enlargement and under enlarging-growth in three varieties, Ershuizao (a), Chalingzipisuan (b), and Yuanjiangyangsuan (c). Orange dots represent genes with more transcripts in the library of enlarging bulbs, green dots represent genes with fewer transcripts in the library of enlarging bulbs, and grey dots indicate genes whose expression are not changed significantly. d, Venn diagram of differentially expressed genes from three varieties. Figure S16. A putative model for clove enlarging growth is proposed according to the orthologous analysis, in which 38 and 7 differentially expressed genes are the homologous genes involved in the photoperiod and gibberellin signal pathway. Heatmap shows the expressed difference of candidates between the bulbs whose cloves are under enlarging-growth (EB) and un-enlargement (UB). Figure S17. Phylogenetic tree of FT and FT-like proteins from six species, including garlic (blue), onion (green), Arabidopsis (purple), rice (orange), potato (black), and tomato (pink). Figure S18. Comparison of the flowering time between wild (right) and Asa06G06199.1-overexpressed Arabidopsis (left). Figure S19. Phylogenetic relation of garlic BEL1-like Homeodomain (BELL) members and Arabidopsis and tomato homologs, AtATH1, AtPNY, AtPNF, and StBEL5. The proteins of garlic, Arabidopsis and tomato are indicated by blue, green, and pink circle. Figure S20. Phylogenetic tree of DELLA proteins from three species, including garlic (blue), Arabidopsis (green), and rice (orange). Figure S21. Distribution of the ratio of nucleotide diversity (πCG/πOG) and FST values in the region near to the bulb traits-related candidates, which underwent selection in either CG1 or CG2.

Background Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. Results We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58–19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. Conclusions We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

Ramie (Boehmeria nivea L.) is a perennial herb and an ideal raw material for plant protein feed. Thus, the selection and breeding of high-yielding varieties of forage ramie have a considerable influence on livestock husbandry development. Although yield and yield components provide important indices for evaluating germplasm resources and breeding new varieties, only a few studies have examined ramie forage yield traits. In this study, we assessed the growth rate, node number, node length, ramet number, plant height, dry-fresh weight ratio, and yield of 24 ramie varieties harvested at 12 time points during the middle period of growing season in Yuanjiang, China, from 2016 to 2017. We determined correlations among these traits and their effects on yield. The forage yield and its components showed high phenotypic diversity. Five components (namely, growth rate, node number, node length, ramet number, and plant height) showed significant positive correlations with forage yield, whereas dry-fresh weight ratio showed a significant negative correlation with yield. The principal component analysis revealed that a plant type with rapid growth, more nodes, strong ramets, and dense leaves can significantly improve forage yield. Ramet number and plant height were found to be the most important yield indices, with ramet number presenting a slightly stronger influence on yield. We established a regression equation to represent the relationship between yield components and yield. This study provides important information that will facilitate the breeding and germplasm screening of high-yielding forage ramie for an ideal plant type.

Background Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. Results There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. Conclusion We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.

Background: Flax ( Linum usitatissimum L.) is one of the most important economic crops in the world. The lignin content of flax stems directly determines the quality of flax fibers. Flax seeds contain lignans of highly beneficial for human health.Results: To elucidate the metabolic relationship between these compounds and the regulatory nodes of their metabolic processes, third generation (PacBio Iso-Seq) and second generation (Illumina) sequencing technologies were used to sequence the transcriptomes of a pair of flax cultivars with significant differences in lignan content. It was discovered that the differential expressed genes (DEGs) are significantly enriched in the lignin and lignan biosynthesis pathways. Furthermore, there are seven genes with significant differences in expression that were annotated as UDP-glucosyl transferases ( UGTs ). We found that lignan and lignin content is significantly negatively correlated with each other. SEM observations on flax bast fibers provided further evidence of this relationship.Conclusions: This is the first full-length transcriptome analysis on flax plants using third-generation sequencing technologies, and it is also the first study to observe a negative correlation between lignin and lignan content of flax plants. Furthermore, it was found that UGTs are likely to be regulatory node genes for lignan and lignin metabolism.

Jute (Corchorus spp.) is the second most important global natural fiber crop after cotton. Analyses of the genetic diversity and population structure of the germplasm are useful for improving Corchorus breeding. Recently, limited studies on genetic diversity and population structure in jute have been carried out. In the present study, the genetic diversity and population structure of 453 accessions in Corchorus olitorius L., including cultivars, landraces, genetic materials and wild germplasm, were analyzed using 39 SSR markers. The results showed that C. olitorius populations have moderate genetic diversity with an average gene diversity (he) value of 0.322 and polymorphic information content (PIC) value of 0.270 in all accessions. Regarding the geographic distribution, the average he and PIC values were highest in Kenya (0.332, 0.273), followed by Nepal (0.307, 0.259), and China (0.303, 0.253). Among the different germplasm types, the wild germplasm showed higher genetic diversity with an average he value of 0.362 and PIC value of 0.299. The population structure analysis revealed two populations, Pop1 and Pop2; Pop1 was further divided into three subpopulations, and Pop2 was further divided into two subpopulations. These populations were verified by FST statistics, principal coordinate analysis (PCoA) and neighbour-joining trees. This study contributes to the knowledge about levels and distribution of genetic diversity of C. olitorius worldwide and provides clues about the origin of C. olitorius.

Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.

Chinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

With the increasing production and wide application of carbon nanotubes (CNTs), they are inevitably released into the natural environment and ecosystems, where plants are the main primary producers. Hence, it is imperative to understand the toxic effects of CNTs on plants. The molecular mechanisms underlying the toxic effects of CNTs on plants are still unclear. Therefore, in the present study, we investigated the effects of high concentrations of multi-walled CNTs (MWCNTs) on Arabidopsis. Root elongation and leaf development were severely inhibited after MWCNT exposure. Excess production of H2O2, O2-, and malondialdehyde was observed, indicating that MWCNTs induced oxidative stress. The antioxidant system was activated to counter MWCNTs-induced oxidative stress. Combinatorial transcriptome and m6A methylome analysis revealed that MWCNTs suppressed auxin signaling and photosynthesis. Reactive oxygen species metabolism, toxin metabolism, and plant responses to pathogens were enhanced to cope with the phytotoxicity of MWCNTs. Our results provide new insights into the molecular mechanisms of CNT phytotoxicity and plant defense responses to CNTs.