De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis).

BACKGROUND: WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS: A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS: A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.

Effect of Citric Acid on Growth, Ecophysiology, Chloroplast Ultrastructure, and Phytoremediation Potential of Jute (Corchorus capsularis L.) Seedlings Exposed to Copper Stress.

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.

Influence of phosphorus on copper phytoextraction via modulating cellular organelles in two jute (Corchorus capsularis L.) varieties grown in a copper mining soil of Hubei Province, China.

Soil in mining areas is typically highly contaminated with heavy metals and lack essential nutrients for plants. Phosphorus reduces oxidative stress, improves plant growth, composition, and cellular structure, as well as facilitates the phytoremediation potential of fibrous crop plant species. In this study, we investigated two jute (Corchorus capsularis) varieties HongTieGuXuan and GuBaChangJia cultivated in copper (Cu)-contaminated soil (2221 mg kg-1), under different applications of phosphorus (0, 30, 60, and 120 kg ha-1) at both anatomical and physiological levels. At the same Cu concentration, the tolerance index of HongTieGuXuan was higher than that of GuBaChangJia, indicating that HongTieGuXuan may be more tolerant to Cu stress. Although the normal concentration of P (60 kg ha-1) in the soil improved plant growth, biomass, chlorophyll content, fibre yield and quality, and gaseous exchange attributes. However, high concentration of P (120 kg ha-1) was toxic to both jute varieties affected morphological and physiological attributes of the plants under same level of Cu. Moreover, Cu toxicity increased the oxidative stress in the leaves of both jute varieties was overcome by the activities of antioxidant enzymes. Furthermore, the high concentration of Cu altered the ultrastructure of chloroplasts, plastoglobuli, mitochondria, and many other cellular organelles in both jute varieties. Thus, phytoextraction of Cu by both jute varieties increased with the increase in P application in the Cu-contaminated soil. This suggests that P application enhanced the phytoremediation potential jute plants and can be cultivated as fibrous crop in Cu-contaminated sites.

Aquaponics: a sustainable alternative to conventional agriculture in Egypt - a pilot scale investigation.

Conventional agriculture has been widely used to overcome food scarcity in Egypt, but in turn created new environmental, social, and economic problems. Aquaponics has a huge potential as a sustainable solution since it demonstrates promising results for urban food development while providing new entrepreneurship and start-up opportunities. Although it presents a big opportunity especially for developing countries like Egypt, it still requires further studies and researches to fully overcome foreseen challenges. This study discusses the possibility of implementing aquaponics as an alternative to conventional agriculture in Egypt through a comparison between aquaponics and conventional agriculture. The first section of this investigation analyzes the economic feasibility of aquaponics in terms of capital and operational expenditure costs. Then, an experimental comparative study is carried out examining two pilot-scale aquaponics systems (Deep water Culture system and Integrated Aqua-Vegaculture system), where crop quality (vitamins, heavy metals, and pesticides residues) of the two systems has been compared among each other, as well as to that of the commercially available organic food available in supermarkets. Results indicated that both systems produce high-quality safe organic food. The economic feasibility analysis indicated that Integrated Aqua-Vegaculture System is producing more crops with a wider variety of almost 20% less capital expenditure and operational expenditure costs. Fish production for both systems was close, yet slightly higher in Deep Water Culture. Although, on the short term, aquaponics entails relatively high capital and operational expenditure costs compared with conventional agriculture; yet, on the long term, it is more profitable, while saving up to 85% of the water wasted by conventional farming techniques. Finally, the study discusses the main limitations, drawbacks, and future of aquaponics in Egypt where public awareness and a new mindset are needed to highlight the link between agriculture and sustainability.

Effects of peat on plant growth and lead and zinc phytostabilization from lead-zinc mine tailing in southern China: Screening plant species resisting and accumulating metals.

In order to investigate the toxicity-resistance of eighteen Chinese native plants in lead (Pb)-zinc (Zn) mine tailings, we categorized their resistance to Pb and Zn, and tested their potential for phytoremediation effectiveness of Pb and Zn. Fourteen woody plant species belonging to 12 families, and 4 herbaceous species belonging to 4 families, were grown in pots with mixtures of 100% tailing +0% peat (CK), 90% tailing +10% peat (A1), and 80% tailing + 20% peat (A2), respectively. Plant height and biomass, chlorophyll content, and Pb and Zn contents of non-rhizosphere spoil mixtures and plant tissues were measured. Fifteen of the plants grew in all three spoil mixtures. Both A1 and A2 had higher plant height and biomass increment and chlorophyll contents than CK. The content of Pb and Zn in plant shoots and roots was CK > A1 > A2. The value of BCF less than 0.1, compared to 1, was a more precise classification basis for plants excluding metals. Screening for Pb and Zn resistant plants and their bioremediation potential produced the following candidate species: Sapium sebiferum, Salix matsudana, Hibiscus cannabinus, Corchorus capsularis, Ricinus communis, and Populus nigra. These species were highly Pb and Zn tolerant species, with notable growth characteristics and capacities to bioaccumulate Pb and Zn from the mine tailings. Compared to CK, the removal of Pb and Zn from non-rhizosphere spoil increased by an average of 9.64% and 9.6%, respectively in A1, but decreased in A2. The results indicated candidate species and 10% peat addition in the tailing were significant in phytoremediation of Pb and Zn regarding environmental safety.

Morphological, Histobiochemical and Molecular Characterisation of Low Lignin Phloem Fibre (llpf) Mutant of Dark Jute (Corchorus olitorius L.).

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.

High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing.

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 F8 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 F8 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 F8 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.

A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.).

We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2x = 14) using an F6 recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as colocalized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest colocalized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those of fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.

Retting of jute grown in arsenic contaminated area and consequent arsenic pollution in surface water bodies.

Arsenic (As) toxicity of ground water in Bengal delta is a major environmental catastrophe. Cultivation of jute, a non edible crop after summer rice usually reduces arsenic load of the soil. However, during retting of jute As is present in the crop and thus increase its amount in surface water bodies. To test this hypothesis, a study was carried out in ten farmers' field located in As affected areas of West Bengal, India. As content of soil and variou the jute plant were recorded on 35 and 70 days after sowing (DAS) as well as on harvest date (110 DAS). During the study period, due to the influence of rainfall, As content of surface (0-150 mm) soil fluctuates in a narrow range. As content of jute root was in the range of 1.13 to 9.36 mg kg(-1). As content of both root and leaf attained highest concentration on 35 DAS and continuously decreased with the increase in crop age. However, in case of shoot, the As content initially decreased by 16 to 50% during 35 to 70 DAS and on 110 DAS the value slightly increased over 70 DAS. Retting of jute in pond water increased the water As content by 0.2 to 2.0 mg L(-1). The increment was 1.1 to 4 times higher over the WHO safe limit (0.05 mg L(-1)) for India and Bangladesh. Microbiological assessment in this study reveals the total bacterial population of pre and post retting pond water. Bacterial strains capable in transforming more toxic As-III to less toxic AS-V were screened and six of them were selected based on their As tolerance capacity. Importantly, identified bacterial strain Bacterium C-TJ19 (HQ834294) has As transforming ability as well as pectinolytic activity, which improves fibre quality of jute.

Genome size variation in Corchorus olitorius (Malvaceae s.l.) and its correlation with elevation and phenotypic traits.

In this study, we report genome size variations in Corchorus olitorius L. (Malvaceae s.l.), a crop species known for its morphological plasticity and broad geographical distribution, and Corchorus capsularis L., the second widely cultivated species in the genus. Flow cytometric analyses were conducted with several tissues and nuclei isolation buffers using 69 accessions of C. olitorius and 4 accessions of C. capsularis, representing different habitats and geographical origins. The mean 2C nuclear DNA content (± SD) of C. olitorius was estimated to be 0.918 ± 0.011 pg, with a minimum of 0.882 ± 0.004 pg, and a maximum of 0.942 ± 0.004 pg. All studied plant materials were found to be diploid with 2n = 14. The genome size is negatively correlated with days to flowering (r = -0.29, p < 0.05) and positively with seed surface area (r = 0.38, p < 0.05). Moreover, a statistically significant positive correlation was detected between genome size and growing elevation (r = 0.59, p < 0.001) in wild populations. The mean 2C nuclear DNA content of C. capsularis was estimated to be 0.802 ± 0.008 pg. In comparison to other economically important crop species, the genome sizes of C. olitorius and C. capsularis are much smaller, and therewith closer to that of rice. The relatively small genome sizes will be of general advantage for any efforts into genomics or sequencing approaches of these species.

Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis.

Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 µg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future.

Development of a transgenic hairy root system in jute (Corchorus capsularis L.) with gusA reporter gene through Agrobacterium rhizogenes mediated co-transformation.

Transgenic hairy root system is important in several recalcitrant plants, where Agrobacterium tumefaciens-mediated plant transformation and generation of transgenic plants are problematic. Jute (Corchorus spp.), the major fibre crop in Indian subcontinent, is one of those recalcitrant plants where in vitro tissue culture has provided a little success, and hence, Agrobacterium-mediated genetic transformation remains to be a challenging proposition in this crop. In the present work, a system of transgenic hairy roots in Corchorus capsularis L. has been developed through genetic transformation by Agrobacterium rhizogenes harbouring two plasmids, i.e. the natural Ri plasmid and a recombinant binary vector derived from the disarmed Ti plasmid of A. tumefaciens. Our findings indicate that the system is relatively easy to establish and reproducible. Molecular analysis of the independent lines of transgenic hairy roots revealed the transfer of relevant transgenes from both the T-DNA parts into the plant genome, indicating the co-transformation nature of the event. High level expression and activity of the gusA reporter gene advocate that the transgenic hairy root system, thus developed, could be applicable as gene expression system in general and for root functional genomics in particular. Furthermore, these transgenic hairy roots can be used in future as explants for plantlet regeneration to obtain stable transgenic jute plants.

Characterization of a lignified secondary phloem fibre-deficient mutant of jute (Corchorus capsularis).

BACKGROUND AND AIMS: High lignin content of lignocellulose jute fibre does not favour its utilization in making finer fabrics and other value-added products. To aid the development of low-lignin jute fibre, this study aimed to identify a phloem fibre mutant with reduced lignin. METHODS: An x-ray-induced mutant line (CMU) of jute (Corchorus capsularis) was morphologically evaluated and the accession (CMU 013) with the most undulated phenotype was compared with its normal parent (JRC 212) for its growth, secondary fibre development and lignification of the fibre cell wall. KEY RESULTS: The normal and mutant plants showed similar leaf photosynthetic rates. The mutant grew more slowly, had shorter internodes and yielded much less fibre after retting. The fibre of the mutant contained 50 % less lignin but comparatively more cellulose than that of the normal type. Differentiation of primary and secondary vascular tissues throughout the CMU 013 stem was regular but it did not have secondary phloem fibre bundles as in JRC 212. Instead, a few thin-walled, less lignified fibre cells formed uni- or biseriate radial rows within the phloem wedges of the middle stem. The lower and earliest developed part of the mutant stem had no lignified fibre cells. This developmental deficiency in lignification of fibre cells was correlated to a similar deficiency in phenylalanine ammonia lyase activity, but not peroxidase activity, in the bark tissue along the stem axis. In spite of severe reduction in lignin synthesis in the phloem cells this mutant functioned normally and bred true. CONCLUSIONS: In view of the observations made, the mutant is designated as deficient lignified phloem fibre (dlpf). This mutant may be utilized to engineer low-lignin jute fibre strains and may also serve as a model to study the positional information that coordinates secondary wall thickening of fibre cells.