Drought stress results in significant crop yield losses. Comparative transcriptome analysis between tolerant and sensitive species can provide insights into drought tolerance mechanisms in jute. We ...present a comprehensive study on drought tolerance in two jute species-a drought tolerant species (Corchorus olitorius L., GF) and a drought sensitive species (Corchorus capsularis L., YY). In total, 45,831 non-redundant unigenes with average sequence length of 1421 bp were identified. Higher numbers of differentially expressed genes (DEGs) were discovered in YY (794) than in GF (39), implying that YY was relatively more vulnerable or hyper-responsive to drought stress at the molecular level; the two main pathways, phenylpropanoid biosynthesis and peroxisome pathway, significantly involved in scavenging of reactive oxygen species (ROS) and 14 unigenes in the two pathways presented a significant differential expression in response to increase of superoxide. Our classification analysis showed that 1769 transcription factors can be grouped into 81 families and 948 protein kinases (PKs) into 122 families. In YY, we identified 34 TF DEGs from and 23 PK DEGs, including 19 receptor-like kinases (RLKs). Most of these RLKs were downregulated during drought stress, implying their role as negative regulators of the drought tolerance mechanism in jute.
•Cotyledons were used as explants in the rapid shoot regeneration method in hemp.•TDZ applied in MS medium were found to be capable of inducing in vitro shoots from cotyledons superior than BA and ...ZT.•Younger cotyledons (2–3 DAP) produced significantly higher regeneration frequency than elder ones (5–6 DAP).•The regeneration method was suitable while partly genotype dependent.•The method may afford an alternative method for micropropagation and germplasm conservation, and the in vitro plantlets may be suitable to set up a transformation system.
Hemp (Cannabis sativa) is an annual multipurpose crop that is distributed worldwide. An efficient regeneration protocol is needed for hemp genetic transformation, micropropagation, and germplasm conservation. We describe here a rapid protocol for in vitro shoot regeneration that uses cotyledons as explants. We concluded that TDZ in MS medium is more efficient in inducing in vitro shoots from cotyledons than BA and ZT. The best result, 51.7% induction frequency and 3.0 shoots per shoot explant, was recorded in MS medium containing 0.4mgl−1 TDZ and 0.2mgl−1 NAA (T4N2). The in vitro shoots grew to the height of 1.5–2cm in 3–4 weeks after culture initiation. At that time, approximately 80% of the shoots were rooted well in half-strength Ms medium combined with 0.5–2mgl−1 IBA for 4–5 weeks before acclimation. It was observed that younger cotyledons (2–3 days after planting (DAP) were more useful as explants than older ones (5–6 DAP) because they had a significantly higher regeneration frequency. We cultured 3 DAP cotyledons of eight cultivars in T4N2 medium to test the efficiency. The regeneration frequency varied from 35.7% to 54.8%, which indicated that this regeneration protocol was effective, although partly genotype dependent. We regard this protocol as an alternative method for micropropagation and germplasm conservation, and the in vitro plantlets may be suitable to set up a transformation system.
Cannabis sativa, a dioecious plant that has been cultivated worldwide for thousands of years, is known for its secondary metabolites, especially cannabinoids, which possess several medicinal effects. ...In this study, we investigated the autopolyploidization effects on the biosynthesis and accumulation of these metabolites, transcriptomic and metabolomic analyses were performed to explore the gene expression and metabolic variations in industrial hemp autotetraploids and their diploid progenitors. Through these analyses, we obtained 1,663 differentially expressed metabolites and 1,103 differentially expressed genes. Integrative analysis revealed that phenylpropanoid and terpenoid biosynthesis were regulated by polyploidization. No substantial differences were found in the cannabidiol or tetrahydrocannabinol content between tetraploids and diploids. Following polyploidization, some transcription factors, including nine bHLH and eight MYB transcription factors, affected the metabolic biosynthesis as regulators. Additionally, several pivotal catalytic genes, such as flavonol synthase/flavanone 3-hydroxylase, related to the phenylpropanoid metabolic pathway, were identified as being modulated by polyploidization. This study enhances the overall understanding of the impact of autopolyploidization in C. sativa and the findings may encourage the application of polyploid breeding for increasing the content of important secondary metabolites in industrial hemp.
Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated ...flax is widely used in the food and textile industry. It is of great significance to elucidate the genetic characteristics of flax collections for accelerating the process of breeding improvement in this dual purpose crop. With the development of next-generation sequencing, we can use new methods, such as SLAF-seq (specific-locus amplified fragment sequencing), to decode unknown genomes of species. In this study, a high-through sequencing of flax collections using SLAF-seq was conducted. The evolutionary tendency was defined and candidate genes associated with agronomic traits of flax species were identified by Genome-Wide Association Studying (GWAS).
A flax collection consisting of 224 varieties were sequenced by SLAF-seq. In total, 346,639 SLAF tags were developed from all accessions, with an average sequencing depth of 7.19 for each accession. A total of 584,987 SNPs (single nucleotide polymorphism) with an MAF > 0.05 were identified from these SLAFs. The population structure division and phylogenetic analysis indicated a strong divergence among three kinds of flax groups. The genome-wide variation uncovered that oil flax had the highest genetic diversity and was considered to be the ancestor of fiber flax and oil-fiber flax. Sixteen associated peak SNPs for six traits were obtained by GWAS of oil-related traits using EMMAX (efficient mixed-model association eXpedited). Candidate genes and their related pathway were evaluated. A new GWAS was developed for fiber properties using the GLM (General linear model) model and a number of loci were identified.
To our knowledge, this is the first study on discovery multiple loci for important agronomic traits of flax species using GWAS strategy. These results will provide the highest possibility of incorporating both high fiber and good oil traits in a single variety.
Reductions in bleeding rates and bulk shrinkage of grouting repair materials comprise the key to solving the leakage of earth-rock dams. In this paper, an anti-seepage grouting material for ...earth-rock dam was developed by introducing mineral admixtures and graphene oxide (GO) nano sheets into low-cost clay-cement grouting materials and by adding polycarboxylate superplasticizers (PCs) to improve slurry viscosity. The experimental results show that the shear stress and viscosity of the slurry increase with the increase in GO concentration, and the slurry has a certain thixotropy. GO can provide a platform to promote the formation of hydration products and fill the pores of clay particles due to its high specific surface area and low volume; in this paper, the microstructure of clay-cement-graphene oxide (CCGO) grouting materials were improved. Therefore, the bleeding rate, bulk shrinkage rate, setting time and unconfined compressive strength (UCS) of the sample were macroscopically improved. In particular, the bleeding rate and bulk shrinkage rate were shown to be 0% when the content of GO reached 1.08 g/kg. Thus, the grouting anti-seepage and reinforcement performance of CCGO grouting materials were improved.
Soil salinity, a major environmental stress, reduces agricultural productivity by restricting plant development and growth. Jute (Corchorus spp.), a commercially important bast fiber crop, includes ...two commercially cultivated species, Corchorus capsularis and Corchorus olitorius. We conducted high-throughput transcriptome sequencing of 24 C. capsularis and C. olitorius samples under salt stress and found 127 common differentially expressed genes (DEGs); additionally, 4489 and 492 common DEGs were identified in the root and leaf tissues, respectively, of both Corchorus species. Further, 32, 196, and 11 common differentially expressed transcription factors (DTFs) were detected in the leaf, root, or both tissues, respectively. Several Gene Ontology (GO) terms were enriched in NY and YY. A Kyoto Encyclopedia of Genes and Genomes analysis revealed numerous DEGs in both species. Abscisic acid and cytokinin signal pathways enriched respectively about 20 DEGs in leaves and roots of both NY and YY. The Ca2+, mitogen-activated protein kinase signaling and oxidative phosphorylation pathways were also found to be related to the plant response to salt stress, as evidenced by the DEGs in the roots of both species. These results provide insight into salt stress response mechanisms in plants as well as a basis for future breeding of salt-tolerant cultivars.
Flax (
L.) is an important cash crop, and its agronomic traits directly affect yield and quality. Molecular studies on flax remain inadequate because relatively few flax genes have been associated ...with agronomic traits or have been identified as having potential applications. To identify markers and candidate genes that can potentially be used for genetic improvement of crucial agronomic traits, we examined 224 specimens of core flax germplasm; specifically, phenotypic data for key traits, including plant height, technical length, number of branches, number of fruits, and 1000-grain weight were investigated under three environmental conditions before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome-wide association study (GWAS) for these five agronomic traits. Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the important agronomic traits. Our analyses identified a total of 42 SNP loci that showed significant correlations with the five important agronomic flax traits. Next, candidate genes were screened in the 10 kb zone of each of the 42 SNP loci. These SNP loci were then analyzed by a more stringent screening via co-identification using both a general linear model (GLM) and a mixed linear model (MLM) as well as co-occurrences in at least two of the three environments, whereby 15 final candidate genes were obtained. Based on these results, we determined that
and
are candidate genes for plant height,
and
are candidate genes for the number of branches,
and
are candidate genes for the number of fruits, and
is a candidate gene for the 1000-seed weight. We propose that the identified SNP loci and corresponding candidate genes might serve as a biological basis for improving crucial agronomic flax traits.
Abstract
Background
Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown.
Results
Here ...we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication.
Conclusions
This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop.
Flax is a crucial fiber crop that exhibits excellent textile properties and serves as a model plant for investigating phloem fiber development. The regulation of multiple genes significantly ...influences fiber development, notably involving NAC (NAM, ATAF1/2, CUC2) transcription factors in forming the fiber secondary cell wall (SCW). Overexpression of LuNAC61 in flax resulted in sparse top meristematic zone leaves and significantly reduced stem cellulose content. Scanning electron microscopy and staining observations revealed a significant reduction in fiber bundles. β-Glucuronidase (GUS) staining analysis demonstrated high activity of the LuNAC61 promoter in the bast fibers of the flax stem. Additionally, several members of the LuPLATZ and LuCesA families exhibited significant coexpression with LuNAC61. Subcellular localization indicated the presence of LuPLATZ24 protein in the nucleus and cytoplasm, LuNAC61 protein exclusively in the nucleus, and LuCesA10 in the nucleus and endoplasmic reticulum. LuPLATZ24 positively regulates LuNAC61, whereas LuNAC61 negatively affects LuCesA10, suggesting the involvement of a metabolic network in regulating flax fiber development. In conclusion, this study provides a critical opportunity for a comprehensive and in-depth analysis of the mechanisms governing flax fiber development and the potential use of biotechnology to enhance flax fiber yield.
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.
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.
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.
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