Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genome-wide SSR characterization and marker development across seven Nicotiana genomes. Here, we initially characterized 2,483,032 SSRs (repeat units of 1–10 bp) from seven genomic sequences of Nicotiana and developed SSR markers using the GMATA® software package. Of investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana (NIX) markers were developed, of which 99.98% are novel. An efficient and uniform genotyping protocol for NIX markers was developed and validated. We created a web-based database of NIX marker information including amplicon sizes of alleles in each genome for downloading and online analysis. The present work constitutes the first deep characterization of SSRs in seven genomes of Nicotiana, and the development of NIX markers for these SSRs. Our online marker database and an efficient genotyping protocol facilitate the application of these markers. The NIX markers greatly expand Nicotiana marker resources, thus providing a useful tool for future research and breeding. We demonstrate a novel protocol for SSR marker development and utilization at the whole genome scale that can be applied to any lineage of organisms. The Tobacco Markers & Primers Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html

Sanqi (Panax notoginseng (Burk.) F. H. Chen) is a traditional Chinese medicinal plant with a long planting cycle of 2-3 years that makes it vulnerable to root diseases caused by several pathogens, including Fusarium solani, Alternaria panax, Phytophthoracactorum, and Pseudomonas sp. In April 2019, root soft rot samples of Sanqi were collected from a plantation site in Songming, southwest of China. Typical symptoms included root softening and necrosis, yellow leaf, and stem wilting. Ten diseased roots samples were collected and sterilized with 0.1% HgCl2 for 1 min, 75% ethanol for 2min, and then rinsed thrice with sterile water. Sterilized roots were cut into small pieces of 5 × 5 mm and cultured on the nutrient agar (NA) medium for 48 h at 28°C. From the root cultures, a total of thirteen bacterial strains were obtained. Three strains, SM 2-5, SM 2-13, and SM 2-14 were selected for further study. These three strains were gram-negative, short rod-shaped (1～2×0.5～1μm), non-spore-forming and had polar tufted flagella as observed under a transmission electron microscope (TEM). Also, the strains were positive for oxidase, beta-galactosidase, arginine dihydrolase, and lysine decarboxylase while negative for amylase and urease tested by biochemical methods (Wang 2017). To further determine the pathogenic species, genomic DNA of these three strains was extracted using a Genomic DNA Kit (Tsing Ke, Beijing, China), to PCR amplify 16S rDNA using universal primers 27F/1492R (Wang et al. 2017). Also, S. maltophilia 23S rDNA specific primers SM1/SM4 (Whitby et al. 2000) were used for PCR amplification to confirm the species. 16S rDNA sequence analysis showed that SM 2-5 (GenBank Accession No. MW555227), SM 2-13 (GenBank Accession No. MW555228), and SM 2-14 (GenBank Accession No. MW555229) shared the highest identity (>99.9%) with the S. maltophilia strains (GenBank Accession No. MT323142, MH669295, MN826555). Furthermore, 23S rDNA sequence analysis of SM 2-5 (GenBank Accession No. MZ707732), SM 2-13 (GenBank Accession No. MZ645941) and SM 2-14 (GenBank Accession No. MZ707733) revealed their high identity (>99.8%) with the S. maltophilia species. 16S and 23S rDNA phylogenetic analysis (Mega6.06) using the neighbor-joining (NJ) method with 1,000 bootstrap replicates revealed the three strains clustering with the other S. maltophilia strains. Therefore, based on morphology, metabolic profile, and sequence analysis, the three strains were identified as Stenotrophomonas maltophilia. To test pathogenicity, the strains were grown in the nutrient broth (NB) medium for 48h at 28°C until bacterial suspension reached to OD600≈1.0 (2.0×109CFU/mL). Then, healthy roots of one-year-old Sanqi plants, pre-washed with sterilized water and -poked with a sterilized needle, were soaked in bacterial suspension (2.0×109CFU/mL) of the three strains separately for inoculation 10min. Sterilized water treatment was used as a control. Subsequently, bacteria-inoculated plants were planted in sterile soil pots and cultured in a greenhouse at 28°C with shading rate of 70%. Each treatment group included 3 plants with 3 replicates. Ten days post inoculation, symptoms similar to the ones in natural conditions were observed in the bacteria-inoculated plants. Based on the disease index (Li et al. 2020), we found that among the three strains, SM 2-13 displayed the highest virulence, while no symptoms were observed in the control plants. The same bacterial strains were re-isolated from these inoculated roots and identified by the methods described above. Previous studies showed that some Stenotrophomonas species cause plant diseases such as rice white stripe (Singh et al. 2001), strawberry leaf black spot (Wang et al. 2017), Cyclobalanopsis patelliformis leaf spot (Bian et al. 2020), and Jatropha curcas L. seed borne and stem necrosis (Wang et al. 2018). To our knowledge, this is the first report confirming Stenotrophomonas maltophilia causing root soft rot of Panax notoginseng in China.

In July 2016, more than 60% hydroponic commercially grown spinach (Spinacia oleracea) suddenly wilted in commercial greenhouse production in Songming (25°N, 103°E), Yunnan province. The infected pl...

Panax notoginseng (Burkill) F.H. Chen, known as ‘‘sanqi’’, is widely used for its medicinal and tonic effects in China, such as treatment of cardiovascular diseases and antioxidant effects. However...

Chilli yellow ringspot orthotospovirus (CYRSV) causes colored lesions in tomato fruits. In this study, tomato fruits with different-colored lesions were used as experimental materials to explore the color formation mechanism. After CYSRV infection, the structure of chromoplasts inside the cells of tomato fruits was distorted and the number of plastoglobules per chromoplast significantly decreased, but the plastoglobule areas increased, as determined via ultrathin sectioning and transmission electron microscopy. Transcriptome and metabolome analyses revealed enrichment of secondary metabolites, carotenoids, and flavonoids in tomatoes with colored lesions. Metabolome analysis revealed markedly reduced carotenoid metabolites (lycopene and α-carotene) in both red-yellow and yellow tomatoes. The flavonoid metabolites rutin, catechin, and naringenin chalcone were markedly increased in the yellow group only. RT-qPCR analysis revealed that the expression of genes involved in carotenoid and flavonoid synthesis increased, but the expression of C4H decreased. Transcription regulators such as AP2 and MYB12 play important roles in flavonoid and carotenoid biosynthesis in CYRSV-infected tomato fruits. The results of greenhouse isolation experiments revealed that CYRSV may induce color lesions via decreases in plastoglobule numbers and chromoplast areas, the absence of carotenoid metabolites, and the presence of yellow-colored flavonoid metabolites. These results provide new insights into the interaction between CYRSV and tomato plants.

Because of the scarcity of fresh water and its limited availability for human use, some places have resorted to utilizing alternative water sources, such as saline water, which negatively impacts plant growth and development. Hydrogen peroxide (H₂O₂) signalling molecule, aids in plant defence as a signal in the production of systemic acquired resistance and modulating ROS detoxification and regulating multiple stress-responsive pathways and gene expression. Our study suggests that using H₂O₂ as a stimulating substance to boost the production of antioxidant compounds in plants resulting in enhanced growth. During the 2022 and 2023 seasons, we used H₂O₂ as a foliar application at concentrations (0, 20, 40, 60, and 80 mM) on Taxodium distichum seedlings receiving saline water at concentrations (0, 3000, 5000, and 7000 ppm). The results indicated that applying H₂O₂ at 20 mM enhanced most of growth attributes and lowered the production of proline, lipid peroxidation (MDA), and improved the accumulation of chlorophyll a and b which suggests that plants Irrigated with this concentration were able to handle all of the salt levels. Compared to other treatments, applying a H₂O₂ at 40 mM treatment resulted in the highest plant Salt Resistance Index (SRI%) and root growth parameters. Carotenoids, flavonoids, phenols, and sugars in the plant reached peak production when treated with a 60 mM of H₂O₂, regardless of salinity concentrations. The activity of peroxidase (POD) as an antioxidant isoenzyme increased as the salinity and H₂O₂ concentrations increased. The treatment with salinity at 7000 ppm+ H₂O₂ at 60 or 80 mM showed the maximum number of bands and the greatest intensity of POD.