Dark jute (Corchorus olitorius L.) can absorb lead (Pb) in the roots and translocate it to the shoots, making it a potential candidate for phytoremediation of Pb-contaminated soils. However, the genetic and molecular mechanisms regulating this process remain unclear. In this study, VA-50, a dwarf dark jute accession that accumulates Pb only in roots, and 18BS-81, a tall, late-flowering accession capable of transferring Pb to its shoots, were selected as parents. An F2population from their cross was used to map QTL intervals and identify candidate genes related to Pb accumulation and tolerance. Thirty extreme sensitive and resistant F2individuals were subjected to Bulk Segregant Analysis (BSA) under 400 mu mol/L Pb stress, together with transcriptome analysis of the parents. BSA-seq identified 668,436 high-quality SNPs and overlapping SNP and InDel signals revealed six candidate regions on chromosome 5 spanning 0.46 Mb. Transcriptome data were also used to screen 142 genes within this region, from which six candidate genes were selected. COS05g_00848 and COS05g_00849 encode lipoxygenases (LOX), COS05g_00890 encodes a mitochondrial ADP/ATP carrier protein, COS05g_00801 encodes PTZ00169 protein, while COS05g_01275 and COS05g_01276 lack predicted protein families, suggesting novel functions. These genes are associated with lipid oxidation pathways linked to glycerolipid and glycerophospholipid metabolism, which support membrane stability and mitigate Pb toxicity in sensitive cellular components. This study integrates BSA-seq and RNA-seq to identify candidate genes regulating Pb accumulation and tolerance in dark jute, providing a foundation for genetic improvement of dark jute for phytoremediation applications.

The U6 promoter plays a pivotal role in the CRISPR/Cas9 system by driving the transcription of single guide RNA (sgRNA), which directs Cas9 to achieve precise genome editing. Endogenous U6 promoters typically exhibit superior transcriptional activation efficiency compared to exogenous counterparts, thereby enhancing the efficacy of genome editing. However, the endogenous U6 promoter in kenaf (Hibiscus cannabinus L.) remains uncharacterized. In this study, we conducted a homologous search of the kenaf genome using the Arabidopsis U6 (AtU6-26) RNA sequence as a reference, identifying two candidate promoters, HcU6-1 and HcU6-14. Promoter fragments were amplified from the genomic DNA of kenaf cultivar 'Fuhong 952' and subsequently cloned into a GUS fusion expression vector. Histochemical staining revealed transcriptional activity for both promoters, with HcU6-14 demonstrating significantly stronger activity. To evaluate editing efficiency, we constructed a CRISPR/Cas9 vector containing HcALS sgRNA, driven by either the kenaf U6-14P promoter or the cotton U6-9P (GbU6-9P) promoter. Kenaf hairy roots were regenerated via Agrobacterium rhizogenes K599-mediated transformation. Sequencing analysis of ALS gene fragments from these hairy roots confirmed successful targeted editing when using the kenaf U6-14P promoter, whereas no base mutations were detected with the cotton U6 promoter. These findings highlight the superior editing efficiency of the kenaf U6 promoter and provide a critical foundation for advancing functional genomics research in kenaf.

White-fruited bitter melon (Momordica charantia L.) is a rare species of Momordica charantia L, valued for its pearl-like white pericarp. However, limited research is available regarding its supporting cultivation techniques and fruit quality. Two-season field trials were performed using ‘Kuzhongle’ as scion to evaluate the applicability of luffa rootstocks and seasonal variation in rootstock-mediated effects. Three luffa inbred lines (SS07, SS11, SS26) were screened in spring, and the superior SS26 was further compared with the commercial rootstock ’Yinzhen No.1’ in autumn. All rootstocks thickened stems, shortened internodes and promoted female flower formation in spring, with genotypically divergent influences on fruit quality. SS26 exhibited the highest survival rate and significantly enhanced soluble solid content, water content, crude protein content and vitamin C content, while reducing crude fiber content and total acid content. Seasonal comparison revealed consistent quality-modulating effects of SS26 across seasons, except for crude fiber, with a comprehensive performance comparable to the commercial rootstock. Overall, luffa rootstocks consistently modulate vegetative and flowering traits within a season, whereas their impacts on fruit quality show genotypic differences. SS26 exhibits stable and superior grafting performance, providing important material support for bitter gourd rootstock breeding research.

Banana (Musa spp.) fruit morphology is a key determinant of yield and quality, yet modeling its 3D structural dynamics across genotypes remains difficult. To address this challenge, we developed a generic, biomass-driven 3D structural model for banana fruit fingers that quantitatively links growth and morphology. Field experiments were conducted over two growing seasons in Hainan, China, using three representative genotypes. Morphological traits, including outer and inner arc length, circumference, and pedicel length, along with dry (W-d) and fresh weight (W-f), were measured every 10 days after flowering until 110 days. Quantitative relationships between morphological traits and W-f, as well as between W-d and W-f, were fitted using linear or Gompertz functions with genotype-specific parameters. Based on these functions, a parameterized 3D reconstruction method was implemented in Python, combining biomass-driven growth equations, curvature geometry, and cross-sectional interpolation to simulate the fruit's bending, tapering, and volumetric development. The resulting dynamic 3D models accurately reproduced genotype-specific differences in curvature, length, and shape with average fitting R-2 > 0.95. The proposed biomass-driven 3D structural model provides a methodological framework for integrating banana fruit morphology into functional-structural plant models.

Dark jute (Corchorus olitorius L.) can absorb lead (Pb) in the roots and translocate it to the shoots, making it a potential candidate for phytoremediation of Pb-contaminated soils. However, the genetic and molecular mechanisms regulating this process remain unclear. In this study, VA-50, a dwarf dark jute accession that accumulates Pb only in roots, and 18BS-81, a tall, late-flowering accession capable of transferring Pb to its shoots, were selected as parents. An F₂ population from their cross was used to map QTL intervals and identify candidate genes related to Pb accumulation and tolerance. Thirty extreme sensitive and resistant F₂ individuals were subjected to Bulk Segregant Analysis (BSA) under 400 μmol/L Pb stress, together with transcriptome analysis of the parents. BSA-seq identified 668,436 high-quality SNPs and overlapping SNP and InDel signals revealed six candidate regions on chromosome 5 spanning 0.46 Mb. Transcriptome data were also used to screen 142 genes within this region, from which six candidate genes were selected. COS05g_00848 and COS05g_00849 encode lipoxygenases (LOX), COS05g_00890 encodes a mitochondrial ADP/ATP carrier protein, COS05g_00801 encodes PTZ00169 protein, while COS05g_01275 and COS05g_01276 lack predicted protein families, suggesting novel functions. These genes are associated with lipid oxidation pathways linked to glycerolipid and glycerophospholipid metabolism, which support membrane stability and mitigate Pb toxicity in sensitive cellular components. This study integrates BSA-seq and RNA-seq to identify candidate genes regulating Pb accumulation and tolerance in dark jute, providing a foundation for genetic improvement of dark jute for phytoremediation applications.

Dark jute (Corchorus olitorius L.) is a high-biomass fiber crop with potential value for phytoremediation, but the genetic basis of whole-plant cadmium (Cd) accumulation and tolerance remains poorly understood. Identifying loci and candidate genes associated with Cd-related traits can support molecular improvement of dark jute for cultivation in Cd-affected environments. In this study, we integrated bulked segregant analysis sequencing (BSA-seq) with time-course RNA sequencing (RNA-seq), Cd phenotyping, and qRT-PCR validation to investigate Cd accumulation and tolerance in dark jute. A Cd-tolerant, low-accumulating accession (CO57) and a Cd-sensitive, high-accumulating accession (CO83) were used to generate an F₂ population for extreme-phenotype bulking. Time-course RNA-seq of the tolerant parent revealed substantial Cd-responsive transcriptional reprogramming, with 3,784-4,167 differentially expressed genes (DEGs) detected across root control-versus-Cd comparisons and 2,216-3,532 DEGs detected across aboveground tissue comparisons. Overlap analysis showed 1,207 shared DEGs between root and aboveground DEG sets. GO classification and KEGG pathway annotation provided functional context for the Cd-responsive gene set, indicating the involvement of cellular regulation, metabolic responses, stress response, transport, detoxification, sulfur metabolism, glutathione-related metabolism, and protein degradation pathways. For BSA-seq, 50 extremely low-accumulating and 50 extremely high-accumulating F₂ individuals were pooled, yielding 625,354 high-quality SNPs. ΔSNP-index analysis detected five candidate intervals spanning 7.13 Mb and containing 662 annotated genes. By integrating positional evidence, Cd-responsive expression patterns, and functional annotations, seven candidate genes were prioritized, including genes encoding ABC transporter-like proteins, a NAC-domain transcription factor, and two PLAC8-domain proteins annotated as Cd-resistance-related proteins. qRT-PCR analysis supported the expression patterns of the prioritized candidates. These results identify candidate genomic intervals and prioritized genes associated with whole-plant Cd accumulation and tolerance in dark jute. The study provides a genetic and transcriptomic framework for future functional validation, marker development, and phytoremediation-oriented improvement of dark jute.

Caffeic acid O-methyltransferase (COMT) catalyzes the penultimate methylation in monolignol biosynthesis, controlling lignin composition and abiotic-stress tolerance. Kenaf (Hibiscus cannabinus L.), a fast bast-fiber crop rich in lignin, is valued for its mechanical strength and resilience to salinity. However, the COMT gene family has not yet been systematically characterized in this species. Here, we integrated phylogenetics, synteny, promoter and transcriptome analyses to create a comprehensive profile of kenaf COMT genes. Genome-wide screening identified 81 HcCOMT genes. Phylogenetic reconstruction with COMTs from Arabidopsis thaliana and Gossypium hirsutum resolved 10 distinct clades. Synteny analysis revealed 2 collinear blocks with Arabidopsis and 14 with cotton, whereas intraspecific duplication events indicated recent lineage-specific expansion. Promoter analysis identified numerous cis-elements responsive to light, phytohormones and abiotic stress, suggesting complex transcriptional regulation. Transcriptome mining uncovered 6 candidate genes with pronounced tissue specificity and salt responsiveness; qRT-PCR confirmed these patterns in root, stem and leaf tissues under 200 mM NaCl: HcCOMT28 and HcCOMT29 were repressed in the leaf, whereas HcCOMT11, HcCOMT12, HcCOMT13, and HcCOMT17 were up-regulated, consistent with altered lignin deposition patterns. Our findings provide a comprehensive genomic resource delineating the structure, evolution, and salt-responsive expression of the kenaf COMT family, and establish a foundation for elucidating the molecular mechanisms underlying lignin-mediated salt tolerance and for breeding elite kenaf cultivars with tailored fiber properties.

Pepper (Capsicum annuum L.) fruits at immature stage (IS) display colors that range from dark green to light green and white. Due to the influence of genetic factors and consumption habits, white-fruited pepper germplasms are rare in nature and depend on artificial creation. However, the unclear complex genetic basis, coupled with the absence of developed functional markers cosegregation with white fruit trait, has impeded the efficiency of breeding white- fruited peppers. Herein, an F2 segregation population consisting of 3,000 individuals is derived from a cross between B1-2 with white fruit and D50 with dark green fruit at IS. Using bulked segregant analysis, a previously reported gene CaGLK ( Capana10g000333 ) is identified as a candidate that is responsible for white/green fruit color. A single nucleotide polymorphism (SNP) (G/A) at the position of the last base of the second intron of CaGLK, resulting in alternative splicing at the junction of the second intron and the third exon, causing the exclusion of 31 bp in cDNA sequence of B1-2, is associated with white fruit trait. A KASP marker is developed and shown to distinguish white-fruited pepper from the F2 population. The distinguishing efficiency of this marker reached up to 78.3% when tested in a natural population. This first report of a new allele CaGLKA that controlled white color provided a new handle to develop pepper cultivars with white color fruit.

WD40 repeat proteins play crucial roles in various biological processes, including stress responses, development, and signaling. In this study, we identified and characterized 142 WD40 genes (CsWDR) in cucumber (Cucumis sativus), using the Hidden Markov Model to detect WD40 domains. These genes exhibited considerable variation in protein length and domain structure, with some containing additional functional domains such as UTPB, zinc finger, and F-box. Phylogenetic analysis revealed seven distinct clusters of CsWDR proteins, suggesting functional divergence, including roles in stress tolerance. Gene Ontology analysis highlighted their involvement in metabolic processes, stress responses, and protein binding, with most localized to the nucleus. Expression profiling revealed distinct patterns across tissues and developmental stages, with significant responses to temperature and light conditions. Notably, the CsWDR36 gene, associated with parthenocarpy in cucumber, was further investigated. Two transcripts, CsWDR36-1 and CsWDR36-2, were identified, differing in the number of WD40 motifs. Real-time PCR showed higher expression of both genes in flowers, especially male flowers, with increased expression following flowering, suggesting a role in early fruit development. These findings provide insights into the functional diversity of CsWDR genes and their potential roles in cucumber development and stress response.

ER Bodies accumulate atypical myrosinases that hydrolyzes glucosinolates, generating chemically reactive products toxic to pathogens and herbivores. NAI2 is an ER Body component that facilitates ER body formation, similar to the ER Body, its homologous proteins are shown only in Brassicaceae. A new type of endoplasmic reticulum-derived vesicles, NAIP vesicles—which are related to the ER Body—have been found in recent years, and NAIPs (NAI2-interact proteins) not only play a critical and redundant role in ER Body formation, but also could assemble other proteins to coordinate or promote cargo recruitment to drive the formation of the NAIP vesicle. Unlike NAI2, homologous proteins of NAIPs are shown in all kinds of plants with 3 or 4 members, which increases the difficulty in studying the biological function of NAIP vesicles. Here, we optimized the CRISPR/Cas9 system for concurrent editing of multiple target genes by designing suitable multiple targeting sequences and ingeniously utilizing enzymatic sites for the linkage of various promoters. Additionally, appropriate methodologies were employed to construct CRISPR/Cas9 expression vectors and introduce them into tomato, resulting in knocking off three members of the NAIP vesicle-associated gene family. Noteworthy, this CRISPR/Cas9 system has potential applications for functional studies of the functionally redundant genes in eudicot plants. We also found that slnaip1/2/3s mutants were shorter in the youth age compared to the wild type, which provides a favorable clue for the subsequent identification of NAIP vesicles in other plants.

Luffa is a genus of tropical and subtropical vines in the Cucurbitaceae family, recognized as an important cultivated commercial vegetable. However, the seeds of the luffa species are considered hard-seeded, and the processes governing seed germination remain understudied. The 9-cis-epoxycarotenoid dioxygenase (NCED) genes, which are critical for seed germination, have not been well characterized in Luffa. In this study, we identified four LaNCED genes in Luffa acutangula and four LcNCED genes in Luffa cylindrica, distributed across four chromosomes in each species. Phylogenetic analysis classified these genes into two subgroups. Gene structure and motif composition analyses revealed both similarities and differences among the NCEDs. Cis-element analysis further revealed that these NCEDs may be involved in growth regulation by modulating the phytohormonal network and responding to stress stimuli. Expression profiling of LcNCED genes during seed germination showed a decrease in LcNCED2 levels, coinciding with an increase in α-amylase activity throughout the germination process. Subcellular localization assays demonstrated that LcNCED2 is localized in the chloroplast. Furthermore, transient overexpression of LcNCED2 in tobacco leaves led to a significant increase in ABA content. Our findings provide a comprehensive genomic characterization of the NCED family in Luffa cylindrica and Luffa acutangula and reveal the functional role of LcNCED2 in regulating ABA levels, which may play a critical role in seed germination.

The ARF (Auxin response factor), GH3 (Gretchen Hagen 3), and Aux/IAA (Auxin/indole-3-acetic acid) gene families are key components in auxin signaling pathway and function as regulators of growth in plants. However, this research is rarely reported in jute, which severely limits the understandings of mechanisms involved in fiber development. In this study, 13 ARF, 12 GH3 and 20 Aux/IAA putative genes were identified in the whole genome of jute. Exon-intron structures revealed the high conservation among these auxin-related gene family members. Chromosomal localization and synteny analysis showed that segmental duplication contributed to the expansion of CcARF, CcGH3 and CcIAA gene families. Phylogenetic and conserved motif analysis revealed that they have distinct functional and CcARF, CcGH3 and CcIAA-specific domains, respectively. The expression pattern analysis based on RNA-seq and qRT-PCR indicated that 7 CcARF, 5 CcGH3, and 14 CcIAA genes showed higher expression in stem barks than leaves at the vigorous vegetative growth stage in an elite cultivar Huangma 179 with normal plant height, respectively, suggesting they might regulate the development of bast fiber. Moreover, the expression of 5 CcARF, 4 CcGH3, and 12 CcIAA genes was differentially expressed in stem barks of a typical GA3 sensitive dwarf germplasm in comparison to Huangma 179. The cis-element analysis showed that promoters of 4 CcARF, 3 CcGH3, and 7 CcIAA genes had 1 to 3 cis-elements involved in gibberellin-responsiveness, giving a hint that they could respond to endogenous gibberellin accumulation in Huangma 179 and form a complicated network to regulate hormone regulatory network and plant height. This study provides useful information for functional analysis of ARF, GH3, and Aux/IAA genes, which would be taken as candidates for genetic improvement of bast fiber quality in jute.

Jute (Corchorus capsularis L.) is the second most important natural plant fiber source after cotton. However, developing an efficient gene editing system for jute remains a challenge. In this study, the transgenic hairy root system mediated by Agrobacterium rhizogenes strain K599 was developed for Meifeng 4, an elite jute variety widely cultivated in China. The transgenic hairy root system for jute was verified by subcellular localization and bimolecular fluorescence complementation (BiFC) assays. The CHLOROPLASTOS ALTERADOS 1 (CcCLA1) gene, which is involved in the development of chloroplasts, was targeted for editing at two sites in Meifeng 4. Based on this hairy root transformation, the gRNA scaffold was placed under the control of cotton ubiquitin GhU6.7 and -GhU6.9 promoters, respectively, to assess the efficiency of gene editing. Results indicated the 50.0% (GhU6.7) and 38.5% (GhU6.9) editing events in the target 2 alleles (gRNA2), but no mutation was detected in the target 1 allele (gRNA1) in transgenic-positive hairy roots. CcCLA1 gene editing at gRNA2 under the control of GhU6.7 in Meifeng 4 was also carried out by Agrobacterium tumefaciens-mediated transformation. Two CcCLA1 mutants were albinic, with a gene editing efficiency of 5.3%. These findings confirm that the CRISPR/Cas9 system, incorporating promoter GhU6.7, can be used as a gene editing tool for jute.

Protein phosphatase 2 C (PP2C) gene family is known for regulating a variety of abiotic stresses in plants. However, little is currently understood about this gene family in jute. In this study, a total of 60 CcPP2C genes were identified in jute, which were named from CcPP2C1 to CcPP2C60 according to the order of their physical coordinates. These CcPP2C proteins contained about 162-1324 amimo acids. Their isoelectric points varied in the range of 4.51-9.45, and their molecular weights varied from 18.307 to 146.906 kDa. The evolutionary tree of PP2Cs in jute and Arabidopsis indicated that PP2Cs can be divided into 12 branches. Sixty-seven collinear gene pairs were identified between 42 CcPP2Cs and 62 AtPP2Cs by analyzing the whole genome collinearity data of jute and Arabidopsis. The analyses of conserved motifs in these CcPP2C proteins and cis-elements in the promoters revealed that CcPP2Cs might play an extensive role in responses to various abiotic stresses in jute. Particularly, the expression patterns of CcPP2Cs in group A under salt treatments showed that CcPP2C51 was up-regulated under various stress treatments. And CcPP2C51 was localized in the nucleus and cell membrane. In Arabidopsis, the overexpression of CcPP2C51 positively regulated the salt-tolerance genes. Also, the overexpression of CcPP2C51 improved the salt tolerance of jute regenerated roots. This study revealed the origin and evolution of PP2C genes in jute, and provides potential possibilities for molecular breeding of jute.

Background Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. Results In this study, we investigated the satellite repeat signature in five okra ( Abelmoschus esculentus ) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. Conclusions Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Rocketing labor cost is a major challenge threatening agricultural sustainability and food security worldwide. The replacement of manual pruning of horticultural plants with chemical pruning has long been a goal for saving cost and reducing virus spreading. Here, guided by the structure-function relationship of allelochemical benzoic acid derivatives, we have identified 4-(2-phenylethynyl)-benzoicacid (PEBA) as a highly bioactive compound. PEBA arrested tomato seed germination at a concentration as low as 0.5 mu M, and effectively suppressed lateral branching at 10-100 mu M. In field conditions, a foliar spraying of 25 mu M PEBA altered tomato plant architecture by repressing emergence and elongation of lateral buds, without significantly affecting plant growth and final fruit yield. Moreover, PEBA could also inhibit seed germination in cereals, albeit at a lower efficacy. The application of 500 mu M and 750 mu M PEBA profoundly curbed preharvest sprouting in wheat and rice. Acute toxicity analysis using silkworm and Trichogramma chilonis revealed that PEBA posed a low risk of toxicity. The persistence analysis further indicated that residue levels of PEBA in various plant organs were very low following applications. The inhibitory effect of PEBA on tomato seed germination was associated with the suppression of GA1 accumulation and reactive oxygen species generation, while its effect on lateral bud outgrowth were related to perturbations in the plant hormones and the modulation of genes involved in secondary metabolism and those encoding ABC transporters. Collectively, our findings demonstrate the potential of PEBA as a potent plant growth regulator with significant value for chemical pruning.

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA(3) treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA(3) treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.