Lignin, the second most abundant biopolymer on Earth, imparting rigidity to plant cell walls but poses a challenge in the processing of lignocellulosic biomass such as jute (Corchorus spp.). Compared to other bast fibers such as flax and ramie, jute fiber has a very high lignin content (13.3

Background Crotalaria juncea, a member of Fabaceae family, offers significant agricultural, commercial, and environmental benefits. The bast fibres from C. juncea stems are utilised across diverse industries for the production of ropes, threads, twines, fishing nets, and paper. This fast-growing legume enhances soil fertility through nitrogen fixation when applied as green manure. It exhibits a late-acting self-incompatibility trait, promoting outcrossing and resulting in a heterogeneous plant population. The maternally inherited chloroplast sequence is ideal for species identification, understanding the evolution of self-incompatible species, and analysing population dynamics. Results The chloroplast genome of C. juncea was identified using whole-genome skimming data. The chloroplast genome was 152,635 base pairs in length and contained 36.62% GC content. It comprises 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis revealed significant collinearity and synteny between the chloroplast genomes of C. juncea and other Crotalaria spp. Despite conserved codon usage and repetitive sequences distributions across Crotalaria spp., most protein-coding genes exhibited higher Ka/Ks values, suggesting positive evolutionary selection with adaptive significance. Phylogenetic analysis of shared chloroplast genes, compared to the whole chloroplast genome, yielded superior clade resolution within the Fabaceae family. The analysis also identified highly diverse genes-clpP, matK, ndhF, and rpoC2-based on nucleotide diversity estimation, underscoring their potential utility for species identification within the Crotalaria genus and broader Fabaceae family members. Conclusions This study presents a comprehensive analysis of the C. juncea chloroplast genome. The variable sequence and gene features offer substantial potential for applications in species- and population-level identification, phylogenetic studies, and the exploration of adaptive evolution in C. juncea and other Fabaceae species.

The genetic basis of topsoil-foraging root system architecture (RSA) contrary to a steep-cheap-deep root ideotype typical of most annual crops, and how it has evolved in jute (Corchorus olitorius) during its domestication as a bast-fibre crop are unknown. For jute is cross-incompatible with wild Corchorus species, we used an F2-F2:3 population founded by a bast fibre-shy mutant with impaired fibre development, RSA and nitrate reductase activity (NRA) and its corresponding wild-type (WT). To detect quantitative trait loci (QTL) for 11 RSA-related traits, leaf and root NRA and shoot biomass, we generated the whole-plant transcriptomes and constructed a genome-integrated genetic map comprising genic and genomic single nucleotide polymorphisms (SNPs). We identified a total of 154 QTL anchoring 107 unique SNP loci, with 140 exerting small effects. Seventy-five percent of these were identified as multi-trait QTL associated with 42 SNP loci, suggesting a well-coordinated pleiotropic control of RSA and NRA. By analyzing the mutant to WT ratios of the QTL number, additive effects and phenotypic variance explained over the 14 traits, we show that additive effects contributed to tweaking the RSA. We identified QTL with regulatory roles and reconstructed a multidimensional QTL gene interaction network governing the jute RSA characterized by a low root to shoot ratio (RSR). This study reveals gradual domestication of topsoil-foraging RSA in jute driven by coordinated action of many small-effect QTL, with an interplay of above- and below-ground NR activities modulated by key regulatory genes. This knowledge will help maintain the delicate balance of RSA and NRA during jute varietal improvement. A topsoil-foraging root system architecture in jute has coevolved with nitrogen-use efficiency during its domestication by the coordinated action of many small-effect QTL, with an interplay of above- and below-ground nitrate reductase activities.

Though, lignocellulosic bast fibre of jute (genus- Corchorus ) is ranked as the world’s second most important fibre crop after cotton, higher lignin and lower cellulose content cause it to lose quality which requires improvement. The genes associated with fibre quality were reportedly discovered in lignin and cellulose biosynthetic pathways. The objective of this study was to clarify the function of the genes and/ enzymes involved in lignin and cellulose pathway in olitorius jute. Two popular olitorius jute varieties (JRO-524 and JBO-1) were selected to compare their yield and quality performances, biochemical and histochemical parameters, gene sequencing and expression studies. Variations were found in fibre yield parameters. The fine-JBO-1 fibre had more bundle strength than course-JRO-524. In the JBO-1 bark tissue, acid-detergent-lignin-content, lignin-biosynthetic enzyme- PAL and CAD activities were significantly reduced compared to JRO-524 at 30-Days-after-germination(DAG) and 60-DAG, while cellulose content of JBO-1 was significantly elevated than JRO-524 at 60-DAG. Histochemical analysis revealed higher lignified fibre-cell-bundles of JRO-524. Partial CDS of monolignol-F5H gene of two varieties were sequenced. By qRT-PCR data analysis, it was found that in the JBO-1 bark tissue, monolignol-C3H gene exhibited significantly under-expression at both 30-DAG and 60-DAG whereas monolignol-F5H and cellulose-biosynthetic-gene-CES displayed significant over-expression at 30-DAG and under-expression at 60-DAG compared to JRO-524. Current research indicated that jute's fine fibre is attributed with greater bundle strength, reduced lignin content, decreased lignin-biosynthetic enzymes activity, higher cellulose content, lower C3H gene expression at both 30 and 60-DAG, reduced F5H expression at 60-DAG and increased Ces expression at 30-DAG.

The rhizosphere soil microbiomes, which are essential for plant development, stress adaptability, and general soil health, are greatly impacted by agricultural management practices, particularly those involving nutrient applications. This study evaluated the long-term effects of nutrient management practices on soil physicochemical properties, microbial communities, enzyme activities, and biological soil health in a rice-lentil-jute cropping system. The treatments included a control, inorganic fertilizers (recommended dose of fertilizers), and Soil Test Crop Response based integrated nutrient management (combination of inorganic fertilizer based on soil test-based fertilizer prescription equations, farmyard manure (FYM), and bioinoculants). When compared to both control and inorganic treatments, integrated nutrient management (INM) enhanced soil organic carbon, available nitrogen, phosphorus, and potassium. Microbial populations, comprising of bacteria, actinomycetes, fungi, Azotobacter, and phosphate-solubilizing microorganisms, along with soil enzymatic activities, showed marked increases under INM. Metagenomic analysis of the hypervariable V3-V4 region of 16S rRNA indicated that the bacterial community in the rice-lentil-jute cropping sequence was dominated by Proteobacteria, with 58 phyla having over 1% abundance. The INM treatment increased the Shannon diversity index by 12.6% compared to the control, reflecting improved microbial diversity, richness, and resilience, which are critical for enhancing crop productivity and stress tolerance. The Biological Soil Health Index (BSHI) was highest in the INM treatment, with average contributions from Azotobacter (22.7%), Bacteroidota (12.1%), Actinobacteriota (21.9%), very labile organic carbon (23.1%), and labile organic carbon (20.2%) to BSHI. In summary, ten years of INM enhanced soil health and bacterial community structure and composition, leading to sustainable crop yields in rice-based cropping system. These findings highlight the necessity of integrating balanced nutrient management in long-term agricultural practices.

The lignocellulosic fibers obtained from dark jute are of superior strength, but their coarseness often limits their industrial value, and fiber quality estimation processes further complicate plant selection. Therefore, the current investigation was undertaken to identify some high-yielding and fine-fiber-producing dark jute cultivars among a diverse panel based on morphological and anatomical characteristics. Furthermore, the role of lignin and some genes associated with its biosynthesis pathway, which influence fiber quality attributes, were investigated. The pooled analysis of variance over 2 years demonstrated significant variations among the genotypes across the evaluated traits. The genetic parameters, principal component analysis, and correlation studies signified that the assessment of mid-diameter alongside plant height and basal diameter could enhance the selection efficiency for high-fiber-yielding cultivars. Among the bark anatomical traits, the area of the fiber wedge, lumen area, and number of fiber cells per bundle demonstrated the best estimates of fiber yield and quality. The lignin content (%) and the activities of the phenylalanine ammonia-lyase (PAL) and cinnamyl alcohol dehydrogenase (CAD) enzymes revealed significant differences among the genotypes under evaluation, with a positive association between them for fiber strength and fineness. The upregulated activity of the genes PAL, CAD, and 4-coumarate-CoA ligase (4CL) in the genotype BCCO 105 than in its fine fiber-producing counterpart (OIN 95) depicted a critical role of these enzymes leading to disparity in fiber qualities. The high-fiber yielders (BCCO 105, OIN 123) and fine-fiber producing genotypes (OIN 95, OIN 128, BCCO 115, BCCO 120) detected in the present study will not only enrich the breeding materials for future fiber quality enhancements but also fulfill the quest for a superior fiber producing dark jute cultivar that can be utilised in the industrial sector efficiently.

Leaf litter, abundant in lignocellulosic materials, is difficult to degrade, hindering efficient composting in agriculture. This study focused on isolating and identifying Bacillus species with strong cellulolytic activity to improve leaf litter decomposition under subtropical agro-climatic conditions. Three bacterial strains, B1S, B1M, and B1D were isolated from composted leaf litter and characterized through morphological, biochemical, and enzymatic analyses. B1S, identified as Bacillus stercoris, exhibited the highest total cellulase (0.818 ± 0.026 fpu/ml) and endoglucanase (25.674 ± 2.085 CMCase/mL) activities. B1D showed the highest β-glucosidase activity (3.561 ± 0.088 IU/mL). Optimal cellulase activity for B1S occurred at pH 5.0 and 37 °C. Inoculating compost piles with a mix of these strains significantly reduced composting time from 100 to 50 days, with a cellulose degradation rate of 45.18

Recent advances in genome editing tools and CRISPR-Cas technologies have enabled plant genome engineering reach new heights. The current regulatory exemptions for certain categories of genome edited products, such as those derived from SDN-1 and SDN-2, which are free of any transgene, have significantly accelerated genome editing research in a number of agricultural crop plants in different countries. Although CRISPR-Cas technology is becoming increasingly popular, it is still important to carefully consider a number of factors before planning and carrying conducting CRISPR-Cas studies. To attempt genome editing in a plant, a high-quality genome sequence and a repeatable tissue culture protocol for in vitro regeneration are essential. One of the most important steps in plant genome editing is the designing of a CRISPR construct, which involves selecting the appropriate Cas protein, sgRNA sequence, and appropriate regulatory sequence to trigger expression. Computational tools and algorithms play a crucial role in construct design and gRNA selection to minimize off-target effects and also to optimize their delivery techniques. Researchers may need to select appropriate software tools capable of analyzing post-editing detection of mutation events and other DNA sequence abnormalities to identify off-target effects. To fully fulfill the potential of plant genome editing, continued advances in computational biology are essential to meet the challenges it faces today.

The extraction of bast fibres such as jute from plant stems involves the removal of pectin, hemicellulose, and other noncellulosic materials through a complex microbial community. A consortium of pectinolytic bacterial strains has been developed and commercialized to reduce the retting time and enhance fibre quality. However, there are currently no studies on jute that describe the structural changes and sequential microbial colonization and pectin loss that occur during microbe-assisted water retting. This study investigated the stages of microbial colonization, microbial interactions, and sequential degradation of pectic substances from jute bark under controlled and conventional water retting. The primary occurrence during water retting of bast fibres is the bacterially induced sequential breakdown of pectin surrounding the fibre bundles. The study also revealed that the pectin content of the jute stem significantly decreases during the retting process. These findings provide a strong foundation for improving microbial strains for improved pectinolysis with immense industrial significance, leading to a sustainable jute-based “green” economy.

The biology of gametophytic late-acting self-rejection of pollen in pre-zygotic ovules is relatively unknown in the Fabaceae family of plants. Our understanding of the genetic basis of late-acting self-incompatibility (LSI) is limited due to a lack of sequence data and candidate genes. Crotalaria juncea, a Fabaceae family member that produces commercially important phloem fiber, possesses LSI. Due to a lack of selfed seeds, it is difficult to maintain genetic purity in germplasm and develop breeding lines for improved fiber quality and yield. To investigate candidate genes for LSI in C. juncea, a high-quality de novo transcriptome was generated. It facilitated the identification of genes from the self-incompatibility-related ribonuclease (RNase) family, specifically a Class III T2/RNase gene with sequence properties similar to S-RNase proteins. Based on conserved amino acid motifs, histidine residues, and a high isoelectric point (pI ≥9.0), Cjun_RNS3.1 was identified as an S-RNase homologue (non-S-RNase) or relic S-RNase gene. Unlike typical S-RNases found in known SI plant systems, evolutionary analysis of the Cjun_RNS3.1 protein revealed its ancestral origin. The expression of Cjun_RNS3.1 and other T2/RNase genes revealed differential expression patterns in the pistils of LSI and self-compatible Crotalaria species. The upregulation of the Cjun_RNS3.1 gene during the different stages of pollen tube development indicates that it may be involved in the LSI. In summary, the sunn hemp transcriptome is the first genomic resource reported from a Fabaceae family plant with the LSI trait. A non-S-RNase gene with an ancestral evolutionary origin and a diverse function was found, which could be related to gametophytic LSI. This could be used as a model system to investigate the molecular basis of LSI in the Fabaceae family and help develop C. juncea breeding lines for fibre improvement.

Developing sustainable agricultural practices is currently becoming an increasingly relevant challenge. As the worldwide population rises and climate change affects agriculture globally, new and sustainable approaches must be adopted to ensure food security. In this editorial, we invite contributions to a BMC Plant Biology collection on ‘Sustainable agriculture,’ covering research on the environmental and socioeconomic factors that affect sustainable agricultural practices and their management.

Developing sustainable agricultural practices is currently becoming an increasingly relevant challenge. As the worldwide population rises and climate change affects agriculture globally, new and sustainable approaches must be adopted to ensure food security. In this editorial, we invite contributions to a BMC Plant Biology collection on 'Sustainable agriculture,' covering research on the environmental and socioeconomic factors that affect sustainable agricultural practices and their management.

Lack of genomic resources in sunn hemp (Crotalaria juncea L.), a leguminous bast fiber crop, is one of the major constraints for germplasm characterization and genetic analysis. We identified non-redundant sets of a variety of molecular markers from the de novo flower-bud transcriptome of sunn hemp. These molecular markers included 1683 simple sequence repeats, 4759 intron length polymorphism markers primarily from protein-coding genes, and 3309 single nucleotide polymorphism allele-specific markers. All of these marker resources have been integrated into a simple database for easy access. To evaluate marker efficiency and polymorphism information content of the sampled primers, a subset of SSR and intron length polymorphism markers were validated in sunn hemp germplasm accessions to obtain average PIC values of 0.26–0.32. The SSR genotyping profiles also aided in the genetic distance matrix-based clustering of sunn hemp germplasm accessions. The ability of these molecular markers to successfully amplify in cross-genera bast fiber crops further demonstrated their effectiveness in genotyping. Thus, the current study describes the identification of previously undisclosed endogenous molecular markers in sunn hemp, which have potential applications in genetic studies and breeding in sunn hemp for bast fiber improvement.

Heat stress has a significant impact on the climatic adaptation of flax, a cool-season economic crop. Genome-wide DNA methylation patterns are crucial for understanding how flax cultivars respond to heat adversities. It is worth noting that the DNA methylome in flax has yet to be investigated at the nucleotide level. Although heat stress above 40°C caused oxidative damage in flax leaves, 5-azacytidine, a hypomethylating agent, reduced this effect by 15%-24%. Differences in the expression of the LuMET1 (DNA methyltransferase) gene suggested that DNA methylation/demethylation may play a major role in the flax heat stress response. Thus, whole-genome bisulfite sequencing-derived DNA methylation profiles in flax, with or without heat stress and 5-azaC, were developed and analyzed here. In response to heat stress, a high percentage of significant differentially methylated regions (DMRs), particularly hypomethylated DMRs, were identified in the CHH nucleotide sequence context (H = A/T/C). Some of these DMRs overlapped with transposable element insertions. The majority of DMRs were discovered in intergenic regions, but several DMR loci were also found near genes relevant to heat stress response and epigenetic processes. These DMRs, in particular, are linked to CpG islands, implying a possible role in promoter methylation and gene silencing. The DMRs discovered in this study are crucial for understanding and identifying the key players in heat stress response in flax, which will help in developing climate-smart flax varieties.

Background Chickpea ( Cicer arietinum L.) is the second most widely grown pulse and drought (limiting water) is one of the major constraints leading to about 40–50% yield losses annually. Dehydration responsive element binding proteins (DREBs) are important plant transcription factors that regulate the expression of many stress-inducible genes and play a critical role in improving the abiotic stress tolerance. Transgenic chickpea lines harbouring transcription factor, Dehydration Responsive Element-Binding protein 1A from Arabidopsis thaliana ( AtDREB1a gene) driven by stress inducible promoter rd29a were developed, with the intent of enhancing drought tolerance in chickpea . Performance of the progenies of one transgenic event and control were assessed based on key physiological traits imparting drought tolerance such as plant water relation characteristics, chlorophyll retention, photosynthesis, membrane stability and water use efficiency under water stressed conditions. Results Four transgenic chickpea lines harbouring stress inducible AtDREB1a were generated with transformation efficiency of 0.1%. The integration, transmission and regulated expression were confirmed by Polymerase Chain Reaction (PCR), Southern Blot hybridization and Reverse Transcriptase polymerase chain reaction (RT-PCR), respectively. Transgenic chickpea lines exhibited higher relative water content, longer chlorophyll retention capacity and higher osmotic adjustment under severe drought stress (stress level 4), as compared to control. The enhanced drought tolerance in transgenic chickpea lines were also manifested by undeterred photosynthesis involving enhanced quantum yield of PSII, electron transport rate at saturated irradiance levels and maintaining higher relative water content in leaves under relatively severe soil water deficit. Further, lower values of carbon isotope discrimination in some transgenic chickpea lines indicated higher water use efficiency. Transgenic chickpea lines exhibiting better OA resulted in higher seed yield, with progressive increase in water stress, as compared to control. Conclusions Based on precise phenotyping, involving non-invasive chlorophyll fluorescence imaging, carbon isotope discrimination, osmotic adjustment, higher chlorophyll retention and membrane stability index, it can be concluded that AtDREB1a transgenic chickpea lines were better adapted to water deficit by modifying important physiological traits. The selected transgenic chickpea event would be a valuable resource that can be used in pre-breeding or directly in varietal development programs for enhanced drought tolerance under parched conditions.

Global cultivation of flax fibre and oilseed is sparse due to poor climatic adaptability. Abiotic stresses, such as drought, salinity, and heat stress are the major limiting factors of flax cultivation. Varieties tolerant to biotic and abiotic stresses are the need of the hour with a sustainable high and stable yield. Exploring candidate genes to provide wider climatic adaptability in flax is of paramount importance. The present study delineates a detailed annotation of 164 Linum usitatissimum NAC-domain transcription factor genes (LuNACs) that are scattered across all 15 chromosomes. Phylogeny-wise majority of the LuNAC proteins were categorized into recognized NAC groups. Few LuNACs remain distinct, suggesting their species-specific expansion. Analysis of the LuNAC gene and protein domain architectures established their conserved nature and support the phylogenetic grouping. The homologs of LuNAC genes revealed their expansion because of whole-genome duplication events. Potential target sites of miRNA families, including the miRNA164, were identified in LuNAC genes, suggesting that a complex regulatory mechanism might be associated with abiotic stress tolerance in flax. In silico gene expression, deep GO analysis, functional inference from homologs, and RT-qPCR of selected LuNAC genes revealed their functional involvement in growth and development and in response to diverse abiotic stresses in flax. The LuNAC003 gene from the senescence-related subfamily was responsive to multiple stress conditions. All the above findings on LuNAC genes may promote them as candidate genes for further functional studies or utilize them in flax genetic improvement programs for improved fibre and seed oil productions, even under adverse environmental conditions.

Retting of bast fibres requires removal of pectin, hemicellulose and other non-cellulosic materials from plant stem tissues by a complex microbial community. A microbial retting consortium with high-efficiency pectinolytic bacterial strains is effective in reducing retting-time and enhancing fibre quality. We report comprehensive genomic analyses of three bacterial strains (PJRB 1, 2 and 3) of the consortium and resolve their taxonomic status, genomic features, variations, and pan-genome dynamics. The genome sizes of the strains are ~3.8 Mb with 3729 to 4002 protein-coding genes. Detailed annotations of the protein-coding genes revealed different carbohydrate-degrading CAZy classes viz. PL1, PL9, GH28, CE8, and CE12. Phylogeny and structural features of pectate lyase proteins of PJRB strains divulge their functional uniqueness and evolutionary convergence with closely related Bacillus strains. Genome-wide prediction of genomic variations revealed 12461 to 67381 SNPs, and notably many unique SNPs were localized within the important pectin metabolism genes. The variations in the pectate lyase genes possibly contribute to their specialized pectinolytic function during the retting process. These findings encompass a strong foundation for fundamental and evolutionary studies on this unique microbial degradation of decaying plant material with immense industrial significance. These have preponderant implications in plant biomass research and food industry, and also posit application in the reclamation of water pollution from plant materials.