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Soil and water contamination from heavy metals and metalloids is one of the most discussed and caused adverse effects on food safety and marketability, crop growth due to phytotoxicity, and environmental health of soil organisms. A hydroponic investigation was executed to evaluate the influence of citric acid (CA) on copper (Cu) phytoextraction potential of jute (Corchorus capsularis L.). Three-weeks-old seedlings of C. capsularis were exposed to different Cu concentrations (0, 50, and 100 μM) with or without the application of CA (2 mM) in a nutrient growth medium. The results revealed that exposure of various levels of Cu by 50 and 100 μM significantly (p < 0.05) reduced plant growth, biomass, chlorophyll contents, gaseous exchange attributes, and damaged ultra-structure of chloroplast in C. capsularis seedlings. Furthermore, Cu toxicity also enhanced the production of malondialdehyde (MDA) which indicated the Cu-induced oxidative damage in the leaves of C. capsularis seedlings. Increasing the level of Cu in the nutrient solution significantly increased Cu uptake by the roots and shoots of C. capsularis seedlings. The application of CA into the nutrient medium significantly alleviated Cu phytotoxicity effects on C. capsularis seedlings as seen by plant growth and biomass, chlorophyll contents, gaseous exchange attributes, and ultra-structure of chloroplast. Moreover, CA supplementation also alleviated Cu-induced oxidative stress by reducing the contents of MDA. In addition, application of CA is helpful in increasing phytoremediation potential of the plant by increasing Cu concentration in the roots and shoots of the plants which is manifested by increasing the values of bioaccumulation (BAF) and translocation factors (TF) also. These observations depicted that application of CA could be a useful approach to assist Cu phytoextraction and stress tolerance against Cu in C. capsularis seedlings grown in Cu contaminated sites.

Summary Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

Jute ( Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production 1 . Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species 2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis , respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute. High-quality draft genomes have been generated for the two commercially cultivated jute species, Corchorus olitorius and Corchorus capsularis . Transcriptome analyses revealed key regulatory and structural genes involved in fibre formation.

Population structure and relationship analysis is of great importance in the germplasm utilization and association mapping. Jute, comprised of white jute (C. capsularis L) and dark jute (C. olitorius L), is second to cotton in its commercial significance in the world. Here, we assessed the genetic structure and relationship in a panel of 159 jute accessions from 11 countries and regions using 63 SSRs. The structure analysis divided the 159 jute accessions from white and dark jute into Co and Cc group, further into Co1, Co2, Cc1 and Cc2 subgroups. Out of Cc1 subgroup, 81 accessions were from China and the remaining 10 accessions were from India (2), Japan (5), Thailand, Vietnam (2) and Pakistan (1). Out of Cc2 subgroup, 35 accessions were from China, and the remaining 3 accessions were from India, Pakistan and Thailand respectively. It can be inferred that the genetic background of these jute accessions was not always correlative with their geographical regions. Similar results were found in Co1 and Co2 subgroups. Analysis of molecular variance revealed 81% molecular variation between groups but it was low (19%) within subgroups, which further confirmed the genetic differentiation between the two groups. The genetic relationship analysis showed that the most diverse genotypes were Maliyeshengchangguo and Changguozhongyueyin in dark jute, BZ-2-2, Aidianyehuangma, Yangjuchiyuanguo, Zijinhuangma and Jute 179 in white jute, which could be used as the potential parents in breeding programs for jute improvement. These results would be very useful for association studies and breeding in jute.

Background Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3- O -methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress. Results In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius . Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis ; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius ). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs , CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants. Conclusions This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus , Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.

Background Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute ( Corchorus capsularis L.) is an important industrial raw material fiber crop because of its elite characteristics. However, construction of a high-density genetic map and identification of QTLs has been limited in white jute due to a lack of sufficient molecular markers. The specific locus amplified fragment sequencing (SLAF-seq) strategy combines locus-specific amplification and high-throughput sequencing to carry out de novo single nuclear polymorphism (SNP) discovery and large-scale genotyping. In this study, SLAF-seq was employed to obtain sufficient markers to construct a high-density genetic map for white jute. Moreover, with the development of abundant markers, genetic dissection of fiber yield traits such as plant height was also possible. Here, we present QTLs associated with plant height that were identified using our newly constructed genetic linkage groups. Results An F 8 population consisting of 100 lines was developed. In total, 69,446 high-quality SLAFs were detected of which 5,074 SLAFs were polymorphic; 913 polymorphic markers were used for the construction of a genetic map. The average coverage for each SLAF marker was 43-fold in the parents, and 9.8-fold in each F 8 individual. A linkage map was constructed that contained 913 SLAFs on 11 linkage groups (LGs) covering 1621.4 cM with an average density of 1.61 cM per locus. Among the 11 LGs, LG1 was the largest with 210 markers, a length of 406.34 cM, and an average distance of 1.93 cM between adjacent markers. LG11 was the smallest with only 25 markers, a length of 29.66 cM, and an average distance of 1.19 cM between adjacent markers. ‘SNP_only’ markers accounted for 85.54% and were the predominant markers on the map. QTL mapping based on the F 8 phenotypes detected 11 plant height QTLs including one major effect QTL across two cultivation locations, with each QTL accounting for 4.14–15.63% of the phenotypic variance. Conclusions To our knowledge, the linkage map constructed here is the densest one available to date for white jute. This analysis also identified the first QTL in white jute. The results will provide an important platform for gene/QTL mapping, sequence assembly, genome comparisons, and marker-assisted selection breeding for white jute.

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.

Lignin is a versatile plant metabolite challenging high-end industrial applications of several plant products including jute. Application of developmental mutant in regulation of lignification in jute may open up door for much awaited jute based diversified products. In the present study, a novel dark jute ( Corchorus olitorius L.) mutant with low lignin (7.23%) in phloem fibre being compared to wild-type JRO 204 (13.7%) was identified and characterised. Unique morphological features including undulated stem, petiole and leaf vein distinguished the mutant in gamma ray irradiated mutant population. Histological and biochemical analysis revealed reduced lignification of phloem fibre cells of the plant. RT-PCR analysis demonstrated temporal transcriptional regulation of CCoAMT1 gene in the mutant. The mutant was found an extremely useful model to study phloem fibre developmental biology in the crop besides acting as a donor genetic stock for low lignin containing jute fibre in dark jute improvement programme.

The study is aimed to evaluate the antioxidant and hepatoprotective activity of an ethanolic extract from Corchorus depressus (CDEE). The total phenolic and flavonoid content of CDEE was determined using standard curve of gallic acid and quercetin, respectively. In vitro antioxidant activity was determined by 2,2-diphenyl-1-picryl hydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzo-thiazoline-6-sulfonic acid) diammonium salt radicals and hydrogen peroxide methods. The CDEE possessed strong antioxidant activity in vitro. The pre-treatment of CDEE to CCl4 treated rats prevented hepatocyte damage as evidenced by estimating various biochemical parameters and histopathological observations. CDEE significantly prevented CCl4 induced elevation of aspartate aminotransferase, alanine aminotransaminase, alkaline phosphatase, total bilirubin and CCl4 induced decrease in total protein level in Wistar rats. The CDEE treated rat liver anti-oxidant parameters superoxide dismutase, catalase, monodialdehyde and glutathione were significantly antagonized for the pro-oxidant effect of CCl4. Histopathological studies also supported the protective effect of CDEE. This study partially validated the folk and traditional use of snail in liver disorder through CCl4-induced rat experimental model.

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.