Background: As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results: In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions: This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

Highland barley is one of the few crops that can be grown at high elevations, making it a key resource within the Tibet Plateau. Weeds are a significant threat to highland barley production, and new herbicides and tolerant barley varieties are needed to control this ever-growing problem. A better understanding of existing herbicide resistance mechanisms is therefore needed. In this study, transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in two highland barley genotypes with differing sensitivities to the herbicide pyroxsulam. We identified several stress-responsive metabolites, including flavonoids and antioxidants, which accumulated to significantly higher levels in the pyroxsulam-resistant genotype. Additionally, we found key genes in both the flavonoid biosynthesis pathway and the antioxidant system that were up-regulated in pyroxsulam-resistant barley. This work significantly expands on the current understanding of the molecular mechanisms underlying differing pyroxsulam tolerance among barley genotypes and provides several new avenues to explore for breeding or engineering tolerant barley.

DOI 10.15835/nbha50212705 Grafting has been widely used to defense soil borne diseases and nematodes in vegetables production. However, the underlying mechanism of grafting-improved disease resistance is largely unknown. In this study, grafting cv. ‘Ledu’ scion to cv. ‘Jingxin No. 5’ rootstocks improved the resistance of pepper to Phytophthora capsici. To gain insights into the regulatory networks related to grafting, we performed transcriptome analysis of grafting and control pepper plants with or without P. capsici inoculation. RNA-seq analysis revealed that P. capsici infection largely re-programmed the pepper transcriptome and differentially expressed genes (DEGs) functionally annotated to metabolism processes including photosynthesis, response to stimulus, enzyme activity, and transcription were significantly enriched. Furthermore, the expression levels of most DEGs induced by P. capsici infection, such as genes functionally related to plant hormone signal transduction, plant-pathogen interaction, photosynthesis, reactive oxygen species, tend to recover to the control levels in grafting pepper plants, which help pepper maintain moderate plant defense response and considerable accumulation level of assimilation product, therefore fine-turning the dynamic balance between pepper growth-defense tradeoffs. Taken together, our results suggest the dynamic transcriptional programming in grafting pepper that underpin P. capsici disease and providing insight that the fine-tuning balance between growth and defense of grafting pepper.

The cereal cyst nematode, Heterodera avenae, is one of the most economically important pathogens impacting the worldwide production of cereals and is widely distributed in more than 16 regions in China. The present study used the numbers of nematodes inside the plant roots to evaluate the resistance/susceptibility of different subpopulations of barley Hordeum vulgare (QH2R, QH6R and TB2R) to H. avenae under field and pot conditions. Nematode development in two highly resistant varieties was also evaluated by in vivo experiment and microscopic observation. Analyses of 186 selected varieties showed the numbers of susceptible varieties identified with the number of females/cysts per plant (NFP) method were significantly higher than those identified with the Pf/Pi ratio (PPR) method, which indicated that the NFP method rather than the PPR method is more reliable to evaluate the resistance of barley. The field and pot experiment results indicated that the QH2R subpopulation had lower females/cysts numbers than QH6R and TB2R subpopulations, and eight HR varieties (Sunong 7617, Sunong 7635, Dongyuan 87-14, Rudong 14-46, Rudong 87-57, Rudong 87-8-45, Rudong 88-14-2, and Rudong 88-67-1) were identified in QH2R, with the NFP numbers below 4.2. Further microscopic observation of nematode development suggested that H. avenae often penetrated less into highly resistant varieties (Sunong 7635 and Dongyuan 87-14) and more frequently failed to develop into females than the susceptible barleys. The promising resistant varieties identified in the present research might be helpful for breeders to develop CCN-resistant cultivars and control H. avenae populations effectively at low costs.

Broad bean wilt virus 2 (BBWV2) represents a major constraint on pepper cultivation, yet the molecular basis of host resistance remains poorly understood. To address this gap, we investigated the antiviral defense responses of the Xunhua pepper landrace by integrating transcriptomic, metabolomic, and physiological analyses. BBWV2 infection markedly altered multiple physiological parameters, including soluble sugar content, peroxidase (POD) activity, alanine aminotransferase (ALT) activity, and jasmonic acid (JA) levels, reflecting perturbations in energy metabolism, oxidative stress, and hormonal regulation. Transcriptome profiling revealed persistent activation of the MAPK signaling cascade, characterized by the upregulation of MPK7, MAPKKK18, WRKY22, PR1, and ACS1–6, alongside the consistent downregulation of MPK4, WRKY24, PYL1–4, and CTR1, suggesting viral interference with immune signaling. Metabolomic analyses indicated pronounced enrichment in flavonoid, phenylpropanoid, and lignan biosynthetic pathways. Notably, antiviral metabolites such as aristolochic acid B, angelicin, and 7-demethylsuberosin accumulated progressively in parallel with the induction of biosynthetic genes including CHS, CHI, and PAL, supporting a coordinated transcriptional–metabolic defense response. Integrative analysis further highlighted a putative MAPK–transcription factor–metabolite regulatory axis, which may be disrupted by BBWV2 to undermine host immunity. This study provides a comprehensive overview of the antiviral responses in pepper, underscoring the critical contributions of MAPK signaling, secondary metabolic pathways, and physiological regulation. The key candidate genes and metabolites identified herein represent promising targets for future resistance breeding and functional validation. The online version contains supplementary material available at 10.1186/s12870-025-08040-1.

Background: Highland barley is one of the few crops that can be grown at high elevations, making it a key resource within the Tibet Plateau. Weeds are a significant threat to highland barley production and new herbicides and tolerant barley varieties are needed to control this ever-growing problem. Results: A better understanding of existing herbicide resistance mechanisms is therefore needed. In this study, transcriptomic and metabolomic analyses were used to identify molecular and physiological changes in two highland barley genotypes with differing sensitivities to pyroxsulam. We identified several stress-responsive metabolites, including flavonoids and antioxidants, which accumulated to significantly higher levels in the pyroxsulam-resistant genotype. Additionally, we found key genes in both the flavonoid biosynthesis pathway and the antioxidant system were up-regulated in pyroxsulam-resistant barley. Conclusions: This work significantly expands on the current understanding of the molecular mechanisms underlying differing pyroxsulam tolerance among barley genotypes and provides several new avenues to explore for breeding or engineering tolerant barley.