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.

This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89–99.56%) and Basidiomycota (0.33–25.78%). In healthy endosphere samples, Glomeromycota (0.08–1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04–1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47–35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48–91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases in wheat. Due to the large-scale and widely-distributed planting pattern of wheat, the directional selection pressure of the pathogen is very strong. Therefore, it is urgent to pyramid more stripe rust resistance genes in wheat cultivars to enhance resistance durability and ensure wheat production safety. In this study, two quantitative trait loci (QTL) for adult plant resistance (APR) to stripe rust, QYr.nafu-2BL and QYr.nafu-3BS, were validated and introgressed from wheat line P9897 into three Chinese elite wheat cultivars, Chuanmai 42, Xiangmai 25, and Zhengmai 9023, through marker validation. The three Chinese elite varieties were used as the female parent to cross with wheat line P9897, and they were selfed to the F6 generation. A total of 114 lines were then selected based on field agronomic traits and stripe rust resistance. Four markers (Xcfd73, Xgwm120, Xbarc87 and Xbarc133) linked with the QTL’s regions were employed to screen the 114 F6 lines. Subsequently, 27 lines combining two target QTL from P9897 were selected. The combination of agronomic traits and disease resistance results showed that 13 of these selected lines had favorable application prospects. The promising lines selected in this study could enrich the genetic resources of wheat stripe rust resistance genes, as well as provide material support and a theoretical basis for the prevention and control of wheat stripe rust in China.

The rate of chemical fertilizers’ utilization by crops does not exceed 40%. Environmental pollution and resource waste caused by the excessive application of chemical fertilizers have led to increased interested in using organic fertilizers as replacements for chemical ones. The present study investigated the impact of the combined application of chemical and organic fertilizers on the growth and nutrient utilization efficiency of highland barley (Hordeum vulgare L.). Compared to the application of 100% chemical fertilizers (OFR0), the substitution of chemical fertilizer with 40% organic fertilizer (OFR40) resulted in a significant increase in root length by 4% and improved the nutrient absorption capacity. The crop yields at harvest were not diminished in the combined fertilizer group compared to the OFR0 treatment group, while simultaneously achieving a 60% reduction in chemical fertilizer application. However, a complete substitution with 100% organic fertilizer (OFR100) resulted in a lower yield. This suggests that appropriate proportions of organic fertilizer replacement can maintain yield by increasing root length and enhancing the crop’s nutrient absorption capacity. In order to elucidate the mechanisms by which organic fertilizer modulates crop growth and nutrient utilization efficiency, combined transcriptomic and metabolomic analysis revealed that as the concentration of organic fertilizer increased, the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) shifted from secondary metabolite synthesis toward nitrogen metabolism. In addition, the gene expression and enzymatic activity of NR (nitrate reductase), GS (glutamine synthetase), and GOGAT (glutamine oxoglutarate aminotransferase) (key genes in the nitrogen metabolism pathways) were significantly enhanced in the OFR40 group. This study’s omics-based approach demonstrates that the combined use of chemical and organic fertilizers enhances nitrogen absorption and utilization through an increased expression of key genes and enzymatic activities within the nitrogen metabolic pathways. This synergistic effect not only maintains crop yields but also reduces the reliance on chemical fertilizers, offering a sustainable strategy for agricultural production.

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.