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Plant genomes encode large numbers of nucleotide-binding (NB) leucine-rich repeat (LRR) immune receptors (NLR) that mediate effector triggered immunity (ETI) and play key roles in protecting crops from diseases caused by devastating pathogens. Fitness costs are associated with plant NLR genes and regulation of NLR genes by micro(mi)RNAs and phased small interfering RNAs (phasiRNA) is proposed as a mechanism for reducing these fitness costs. However, whether NLR expression and NLR-mediated immunity are regulated during plant growth is unclear. We conducted genome-wide transcriptome analysis and showed that NLR expression gradually increased while expression of their regulatory small RNAs (sRNA) gradually decreased as plants matured, indicating that sRNAs could play a role in regulating NLR expression during plant growth. We further tested the role of miRNA in the growth regulation of NLRs using the tobacco mosaic virus (TMV) resistance gene N, which was targeted by miR6019 and miR6020. We showed that N-mediated resistance to TMV effectively restricted this virus to the infected leaves of 6-week old plants, whereas TMV infection was lethal in 1- and 3-week old seedlings due to virus-induced systemic necrosis. We further found that N transcript levels gradually increased while miR6019 levels gradually decreased during seedling maturation that occurs in the weeks after germination. Analyses of reporter genes in transgenic plants showed that growth regulation of N expression was post-transcriptionally mediated by MIR6019/6020 whereas MIR6019/6020 was regulated at the transcriptional level during plant growth. TMV infection of MIR6019/6020 transgenic plants indicated a key role for miR6019-triggered phasiRNA production for regulation of N-mediated immunity. Together our results demonstrate a mechanistic role for miRNAs in regulating innate immunity during plant growth.

We developed an easy-traceable TRV vector, TRV2-GFP, by tagging a GFP to the coat protein. TRV2-GFP-infected plants could be identified efficiently by GFP monitoring. TRV2-GFP is useful for functional genomics in many plants, especially for non-Solanaceae plants, like rose

Tomato yellow leaf curl virus (TYLCV) is one of the most well-known tomato-infecting begomoviruses and transmitted by Bemisia tabaci . Seed transmission has previously been reported for some RNA viruses, but TYLCV has not previously been described as a seed-borne virus. In 2013 and 2014, without whitefly-mediated transmission, TYLCV was detected in young tomato plants germinated from fallen fruits produced from TYLCV-infected tomato plants in the previous cultivation season. In addition, TYLCV-Israel (TYLCV-IL) was also detected in seeds and their seedlings of TYLCV-infected tomato plants that were infected by both viruliferous whitefly-mediated transmission and agro-inoculation. The seed infectivity was 20–100%, respectively and the average transmission rate to seedlings was also 84.62% and 80.77%, respectively. TYLCV-tolerant tomatoes also produced TYLCV-infected seeds, but the amount of viral genome was less than seen in TYLCV-susceptible tomato plants. When tomato plants germinated from TYLCV-infected seeds, non-viruliferous whiteflies and healthy tomato plants were placed in an insect cage together, TYLCV was detected from whiteflies as well as receiver tomato plants six weeks later. Taken together, TYLCV-IL can be transmitted via seeds and tomato plants germinated from TYLCV-infected seeds can be an inoculum source of TYLCV. This is the first report about TYLCV seed transmission in tomato.

‘Yu Tai Yi Hao’ ( Chrysanthemum × morifolium Ramat.) is a perennial herbaceous plant from the Asteraceae family and Chrysanthemum genus.As the first officially approved tea chrysanthemum variety in the country, ‘Yu Tai Yi Hao’ has gained significant market demand due to its high tea (medicinal) value and nutritional content.However, ‘Yu Tai Yi Hao’ faces serious issues in propagation and cultivation, such as genetic degeneration and virus contamination in seedlings, which significantly hinder its widespread use and application.This study used new shoots of the ‘Yu Tai Yi Hao’ tea chrysanthemum as plant material to induce callus formation from stem cross-sections and differentiate adventitious buds into seedlings. RT-PCR was employed to detect four viruses: Chrysanthemum B virus (CVB), Chrysanthemum stunt virus (CSVd), Chrysanthemum chlorotic mottle virus (CChMVd), and Tomato spotted wilt virus (TSWV).Plants testing positive for viruses were selected, and their shoot-tip explants were used for further propagation and culture. The study optimized the combinations of hormone types and concentrations at various culture stages to provide a reference for developing a virus-free tissue culture system for ‘Yu Tai Yi Hao’. The results showed that in the induction of callus and differentiation of adventitious buds for ‘Yu Tai Yi Hao’, a medium containing MS, 2.0 mg/L 6-BA, and 0.3 mg/L NAA achieved 100% induction and differentiation rates, with an average differentiation coefficient of 42.83 and a maximum of 90. In the rooting medium (MS + 0.1 mg/L NAA), 100% rooting rate was achieved in 15 days.After 5 days of hardening treatment, the seedlings were transplanted into a growth medium with a 1:1 peat moss: perlite ratio, achieving a survival rate of 100%. Virus testing on regenerated plants revealed that 9 samples were free of CVB and CSVd viruses, with a 100% virus elimination rate, while 2 samples were free of CChMVd and TSWV, resulting in a 22.2% virus elimination rate. This study has preliminarily developed a virus-free tissue culture system for ‘Yu Tai Yi Hao’, providing technical support for the high-quality and efficient industrial propagation of virus-free seedlings for ‘Yu Tai Yi Hao’. It also lays the foundation for exploring targeted virus elimination techniques, virus resistance, as well as for establishing a genetic transformation system for ‘Yu Tai Yi Hao’ and conducting related gene functional verification studies.

Physical mutagens such as low-dose gamma irradiation and cold plasma have recently emerged as eco-friendly tools for enhancing plant vigor, stress tolerance, and disease resistance. However, their impact on genetic stability remains insufficiently characterized. Here, we performed transcriptome-wide single-nucleotide polymorphism (SNP) discovery in Solanum lycopersicum seedlings infected with Tomato brown rugose fruit virus (ToBRFV; Tobamovirus fructirugosum ) and subjected to either 15 Gy gamma irradiation or cold plasma treatment. RNA-Seq analysis revealed distinct mutational footprints: gamma irradiation induced 82 high-confidence SNPs, whereas cold plasma generated 36, with only two SNPs shared between treatments. Chromosomal mapping indicated that gamma-induced SNPs were clustered on chromosomes 7, 12, and 9, while cold plasma-associated mutations were more evenly distributed, predominantly on chromosomes 6 and 11. Most SNPs were localized within protein-coding regions, resulting exclusively in nonsynonymous substitutions; however, the limited SNP dataset and transcriptome-based approach prevent robust inference of selection pressure. Functionally, gamma-induced SNPs were enriched in genes related to terpene biosynthesis, lipid metabolism, and secondary metabolite pathways, while cold plasma targeted genes associated with transcriptional regulation, redox signaling, and chloroplast function, which are closely linked to hormone-mediated signaling networks such as auxin pathways that coordinate plant stress responses and developmental adaptation. Protein modeling further highlighted amino acid substitutions in conserved domains of NB-LRR and regulatory proteins, suggesting possible contributions to plant stress and immune responses. Collectively, our results demonstrate that both treatments induce limited yet functionally relevant transcriptomic mutations within expressed genes, without evidence of widespread mutational disruption at the transcriptome level. However, because the analysis is based on RNA-Seq data, these findings reflect transcriptome-level stability rather than genome-wide genomic safety, and further validation using whole-genome sequencing would be required to assess genome-wide mutational effects.

Two phylogenetically unrelated viruses transmitted by different insect vectors, tomato spotted wilt virus (TSWV) and tomato yellow leaf curl virus (TYLCV), are major threats to tomato and other vegetable production. Although co‐infections of TSWV and TYLCV on the same host plant have been reported on numerous occasions, there is still lack of research attempting to elucidate the mechanisms underlying the relationship between two viruses when they coexist in the same tomato or other plants. After assessing the effect of four TSWV‐coded proteins on suppressing TYLCV in TSWV N transgenic Nicotiana benthamiana seedlings, the TSWV N protein proved to be effective in reducing TYLCV quantity and viral symptoms. Western blot analysis indicated that TSWV N was involved in down‐regulating the expression level of the V1, C3, and C4 proteins of TYLCV, among which V1 was the most significantly suppressed one. Moreover, TSWV N was confirmed to reduce TYLCV V1 within both nucleus and cytoplasm, but a greater suppression was observed in cytoplasm. The co‐immunoprecipitation and mass spectrometry identified 244 differential proteins from the TYLCV‐infected TSWV N transgenic N. benthamiana seedling. These proteins pertaining to energy metabolism pathways were enriched, suggesting that TSWV N could inhibit TYLCV through competing for energy or regulating energy‐related metabolism. The evidence presented here offers a novel perspective that will facilitate a comprehensive understanding of virus–virus and virus–host interactions, as well as a potential strategy for plant virus control through using TSWV N in the near future. N protein of tomato spotted wilt virus reduces the expression of the key protein V1 of tomato yellow leaf curl virus in co‐transfected Nicotiana benthamiana, through affecting host energy metabolism‐related pathways.

The effects of increasing yield and quality of virus-free chewing cane seedlings and their physiological and molecular basis were studied in this study. Results showed that compared with infected seedlings (the control), the yield of chewing cane stems grown from virus-free seedlings increased by 21.81–29.93%, stem length increased by 28.66–34.49 cm, internode length increased by 2.16–2.68 cm, the single stem weight increased by 20.10–27.68%, the reducing sugar increased by 0.91–1.15% (absolute value), and sucrose increased by − 0.06–1.33% (absolute value). The decrease in sucrose content did not reach significant level, but all other parameters were reached significant level. The chlorophyll content, photosynthetic parameters such as stomatal conductance (Gs), net photosynthetic rate (Pn) and transpiration rate (Tr), the activity of photosynthetic key enzymes ribulose-1,5-bisphosphate carboxylase (Rubisco) and phosphoenolpyruvate carboxylase (PEPC), and gene ( pepc , rbcS, and rbcL ) expression levels were all greater in virus-free seedlings than infected seedlings. The content of superoxide anion (O 2 − ) and malondialdehyde (MDA) in virus-free seedlings was lower than infected seedlings at the main growth stage. With increased development, the activities of the antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were gradually higher in virus-free seedlings than infected seedlings. Our results indicate that virus-free seedlings may improve photosynthesis efficiency and promote photosynthesis by increasing chlorophyll content, photosynthetic key enzyme activity, and the gene expression levels in leaves. By increasing the activity of antioxidant enzymes, reducing the degree of membrane lipid peroxidation, and improving the stress resistance of chewing cane, the virus-free chewing cane seedlings increased yield and quality. Our findings provide a scientific and theoretical basis for the promotion and application of virus-free chewing cane seedlings.

Perception of microbe-associated molecular patterns (MAMPs) elicits transcriptional reprogramming in hosts and activates defense to pathogen attacks. The molecular mechanisms underlying plant pattern-triggered immunity remain elusive. A genetic screen identified Arabidopsis poly(ADP-ribose) glycohydrolase 1 (atparg1) mutant with elevated immune gene expression upon multiple MAMP and pathogen treatments. Poly(ADP-ribose) glycohydrolase (PARG) is predicted to remove poly(ADP-ribose) polymers on acceptor proteins modified by poly(ADP-ribose) polymerases (PARPs) with three PARPs and two PARGs in Arabidopsis genome. AtPARP1 and AtPARP2 possess poly(ADP-ribose) polymerase activity, and the activity of AtPARP2 was enhanced by MAMP treatment. AtPARG1, but not AtPARG2, carries glycohydrolase activity in vivo and in vitro. Importantly, mutation (G450R) in atparg1 blocks its activity and the corresponding residue is highly conserved and essential for human HsPARG activity. Consistently, mutant atparp1atparp2 plants exhibited compromised immune gene activation and enhanced susceptibility to pathogen infections. Our study indicates that protein poly(ADP-ribosyl)ation plays critical roles in plant immune gene expression and defense to pathogen attacks.

Even though plant cells are highly plastic, plants only develop hyperplasia under very specific abiotic and biotic stresses, such as when exposed to pathogens like Beet curly top virus (BCTV). The C4 protein of BCTV is sufficient to induce hyperplasia and alter Arabidopsis development. It was previously shown that C4 interacts with two Arabidopsis Shaggy-like protein kinases, AtSK21 and 23, which are negative regulators of brassinosteroid (BR) hormone signaling. Here we show that the C4 protein interacts with five additional AtSK family members. Bikinin, a competitive inhibitor of the seven AtSK family members that interact with C4, induced hyperplasia similar to that induced by the C4 protein. The Ser49 residue of C4 was found to be critical for C4 function, since: 1) mutagenesis of Ser49 to Ala abolished the C4-induced phenotype, abolished C4/AtSK interactions, and resulted in a mutant protein that failed to induce changes in the BR signaling pathway; 2) Ser49 is phosphorylated in planta; and 3) plant-encoded AtSKs must be catalytically active to interact with C4. A C4 N-myristoylation site mutant that does not localize to the plasma membrane and does not induce a phenotype, retained the ability to bind AtSKs. Taken together, these results suggest that plasma membrane associated C4 interacts with and co-opts multiple AtSKs to promote its own phosphorylation and activation to subsequently compromise cell cycle control.

Apple latent spherical virus (ALSV) was successfully used in promoting flowering (virus-induced flowering, VIF) in apple and pear seedlings. In this paper, we report the use of ALSV vectors for VIF in seedlings and in vitro cultures of grapevine. After adjusting experimental conditions for biolistic inoculation of virus RNA, ALSV efficiently infected not only progeny seedlings of Vitis spp. ‘Koshu,’ but also in vitro cultures of V. vinifera ‘Neo Muscat’ without inducing viral symptoms. The grapevine seedlings and in vitro cultures inoculated with an ALSV vector expressing the ‘florigen’ gene (Arabidopsis Flowering locus T, AtFT) started to set floral buds 20–30 days after inoculation. This VIF technology was successfully used to promote flowering and produce grapes with viable seeds in in vitro cultures of F1 hybrids from crosses between V. ficifolia and V. vinifera and made it possible to analyze the quality of fruits within a year after germination. High-temperature (37 °C) treatment of ALSV-infected grapevine disabled virus movement to newly growing tissue to obtain ALSV-free shoots. Thus, the VIF using ALSV vectors can be used to shorten the generation time of grapevine seedlings and accelerate breeding of grapevines with desired traits.