Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici.

The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.

CRISPR/Cas9-mediated seamless gene replacement in protoplasts expands the resistance spectrum to TMV-U1 strain in regenerated Nicotiana tabacum.

CRISPR/Cas-based genome editing is now extensively used in plant breeding and continues to evolve. Most CRISPR/Cas current applications in plants focus on gene knock-outs; however, there is a pressing need for new methods to achieve more efficient delivery of CRISPR components and gene knock-ins to improve agronomic traits of crop cultivars. We report here a genome editing system that combines the advantages of protoplast technologies with recent CRISPR/Cas advances to achieve seamless large fragment insertions in the model Solanaceae plant Nicotiana tabacum. With this system, two resistance-related regions of the N' gene were replaced with homologous fragments from the N'alata gene to confer TMV-U1 resistance in the T0 generation of GMO-free plants. Our study establishes a reliable genome-editing tool for efficient gene modifications and provides a detailed description of the optimization process to assist other researchers adapt this system for their needs.

Construction of a high-density genetic map with whole genome sequencing in Nicotiana tabacum L.

Tobacco (Nicotiana tabacum L.) is an essential commercial crop and an ideal model plant for biological mechanism studies. As an allopolyploid species, tobacco harbors a massive and complex genome, which makes the application of molecular markers complicated and challenging. In our study, we performed whole-genome sequencing of an intraspecific recombinant inbred line (RIL) population, a F1 generation and their parents. With the Nicotiana tabacum (K326 cultivar) genome as reference, a total of 45,081 markers were characterized to construct the genetic map, which spanned a genetic distance of 3486.78 cM. Evaluation of a two-dimensional heat map proved the high quality of the genetic map. We utilized these markers to anchor scaffolds and analyzed the ancestral genome origin of linkage groups (LGs). Furthermore, such a high-density genetic map will be applied for quantitative trait locus (QTL) detection, gene localization, genome-wide association studies (GWAS), and marker-assisted breeding in tobacco.

Genome-wide association study of leaf chemistry traits in tobacco.

Leaf chemistry traits are some of the key factors influencing tobacco quality, which can be significantly reduced by lower chemical components in cured leaf. To improve tobacco quality through breeding, genetic diversity analysis, population structure analysis, and genome-wide association studies were performed in a panel of 347 tobacco germplasms and the markers associated with five leaf chemistry traits, including total sugar (TS), reducing sugar (RS), total nitrogen (TN), nicotine (NIC), and total potassium (TP) contents were identified. Four groups were classified at a genetic distance of 0.316 by genetic diversity analysis based on coefficient parameter NEI72 using a program NTSYS-pc2.10e, whereas four well-differentiated subpopulations were postulated in the 347 tobacco accessions. A total of 47 target trait-associated SNPs was detected in at least three environments as well as the best linear unbiased predictions (BLUPs) across all environments, among which two, two, four, six, and one highly suggestive associated SNPs were repeatedly detected in all environments and BLUPs for TS, RS, TN, NIC, and TP, respectively. On the basis of the phenotypic effects of the alleles corresponding to suggestive associated SNPs, five tobacco accessions harboring favorable alleles with elite phenotypic performance in leaf chemistry traits were identified. The results could facilitate quality tobacco breeding for higher leaf chemistry trait contents through molecular marker-assisted approaches.

Comprehensive assessment of heavy metals pollution of farmland soil and crops in Jilin Province.

As a major agricultural province in China, it is necessary to study the content of heavy metals in farmland soil and crop in Jilin Province and to evaluate the risks to ecology and human health. This study presented the work completed on 79 soil samples, 10 rice samples, 66 maize samples and 15 soybean samples collected from Jilin Province farmland and evaluated six heavy metals (Zn, Cu, Pb, Cd, Hg and As) concentrations. The results showed that the concentrations of the six heavy metals in farmland soil and crop samples from Jilin Province basically met the soil standards and food health standards of China. The agricultural soil pollution spatial distribution was the most serious in the south of Jilin Province and the lightest in the west. The non-carcinogenic risks faced by children eating crops were higher than those of adults, but the carcinogenic risks were lower than those of adults. Both of the two health risks to adults and children from eating crops were very limited. The results would help determine the heavy metals pollution in farmland soil in Jilin Province efficiently and accurately and helped decision makers to achieve a balance between production and environmental regulation.

Transcriptomic profile of tobacco in response to Tomato zonate spot orthotospovirus infection.

BACKGROUND: Tomato zonate spot virus (TZSV), a dominant species of thrips-transmitted orthotospoviruses in Yunnan and Guangxi provinces in China, causes significant loss of yield in lots of crops and is a major threat to incomes of rural families. However, the detailed molecular mechanism of crop disease caused by TZSV remains obscure. METHODS: Next-generation sequencing (NGS)-based transcriptome analysis (RNA-seq) was performed to investigate and compare the gene expression changes in systemic leaves of tobacco upon infection with TZSV and mock-inoculated plants as a control. RESULTS: De novo assembly and analysis of tobacco transcriptome data by RNA-Seq identified 135,395 unigenes. 2102 differentially expressed genes (DEGs) were obtained in tobacco with TZSV infection, among which 1518 DEGs were induced and 584 were repressed. Gene Ontology enrichment analysis revealed that these DEGs were associated with multiple biological functions, including metabolic process, oxidation-reduction process, photosynthesis process, protein kinase activity. The KEGG pathway analysis of these DEGs indicated that pathogenesis caused by TZSV may affect multiple processes including primary and secondary metabolism, photosynthesis and plant-pathogen interactions. CONCLUSION: Our global survey of transcriptional changes in TZSV infected tobacco provides crucial information into the precise molecular mechanisms underlying pathogenesis and symptom development. This is the first report on the relationships in the TZSV-plant interaction using transcriptome analysis. Findings of present study will significantly help enhance our understanding of the complicated mechanisms of plant responses to orthotospoviral infection.

Effects of particle size on bidirectional reflectance factor measurements from particulate surfaces.

The bidirectional reflectance factor (BRF) is commonly used to study the structure of a particulate surface based on photometric measurements. In this paper, we describe the bidirectional reflectance factor distribution of natural particulate surfaces with particles sizes varying from 0.15 mm to 0.9 mm. Two types of natural particulate surfaces (one with low reflectance and the other with moderate reflectance) were measured at visible and near-infrared wavelengths using the Northeast Normal University Laboratory Goniospectrometer System (NENULGS). Both the BRFs and anisotropic reflectance factors (ARFs) at selected wavelengths were compared with previously published results to verify the accuracy of our measurements, and we also quantitatively analyzed the effects of particle size on the BRF. It was found that the maximum reflectance difference, which was more distinct for the low-reflectance samples, between particulate surfaces with particle sizes of 0.15 mm and 0.9 mm occurred in the forward scattering direction for all samples, and the value of this maximum difference reached 59% for the low-reflectance samples. Then, we conducted a test of a photometric model to determine which parameters could be confidently linked to the surfaces' reflectance behavior. The inverted parameters were compared with the known physical parameters of our samples, such as the particle size. We found that the single-scattering albedo could be empirically used to determine the particle sizes of our samples when measurements of particulate surfaces with different particle sizes were performed under the same incidence conditions and with wide viewing angles. The potential applications of our results appear very promising for empirically resolving the spatial distribution of particle size within a given particulate sample as well as for deepening our understanding of the scattering properties of particulate media.

Large-scale development of SSR markers in tobacco and construction of a linkage map in flue-cured tobacco.

Tobacco (Nicotiana tabacum L.), particularly flue-cured tobacco, is one of the most economically important nonfood crops and is also an important model system in plant biotechnology. Despite its importance, only limited molecular marker resources are available for genome analysis, genetic mapping, and breeding. Simple sequence repeats (SSR) are one of the most widely-used molecular markers, having significant advantages including that they are generally co-dominant, easy to use, abundant in eukaryotic organisms, and produce highly reproducible results. In this study, based on the genome sequence data of flue-cured tobacco (K326), we developed a total of 13,645 mostly novel SSR markers, which were working in a set of eighteen tobacco varieties of four different types. A mapping population of 213 backcross (BC1) individuals, which were derived from an intra-type cross between two flue-cured tobacco varieties, Y3 and K326, was selected for mapping. Based on the newly developed SSR markers as well as published SSR markers, we constructed a genetic map consisting of 626 SSR loci distributed across 24 linkage groups and covering a total length of 1120.45 cM with an average distance of 1.79 cM between adjacent markers, which is the highest density map of flue-cured tobacco till date.

[An Identification Study on Field-Derived Spectra of Grassland Combustibles and Soil Based on Fractal Theory].

Grassland fire disaster is an important influence factor to grassland ecological system in China. Therefore, it is crucial to study on the monitoring, prediction and management of grassland fire. Remote Sensing (RS) provides detailed data and saves a lot of manpower, material resources and financial resources on the research of grassland fire. However, it is difficult to identify the grassland fuel and soil with Remote Sensing. In this paper, we introduced fractal into the spectral analyses of the field-derived spectra (FDS) of grassland fuel and soil to solve the problem above. The study area laid on the Westward of Changling, Jinlin province, China. Study subjects included soil and dominant species: Leymus chinensis, Reed, Chloris virgate, Kalimeris integrifolia and Artemisia mongolica. FDS of study subjects were measured with ASD FS3 and continuums of FDS were calculated by Matlab 2010. Meanwhile, Box-counting values of FDS and continuums were calculated by Matlab 2010. According to the spectral and continuum analysis, it is difficult to identify soil, Leymus chinensis, Reed, Chloris virgate, and Artemisia mongolica because of the similar spectral curves. However, the Artemisia mongolica can be identified for the strong reflection. For typical fractal characteristics of FDS and continuum, clustering analyses of study subjects were done according to box-counting values of FDS and continuum. The results of clustering analyses show that Box-counting values of FDS and continuum are important indexes to identify the study subjects. This study provides a new thought to identity the grassland combustibles and soil with Remote Sensing.

Climate change reduces elevational and latitudinal differences in spring phenology of pine caterpillar (Dendrolimus spectabilis Bulter).

The pine caterpillar (Dendrolimus spectabilis Bulter, Lepidoptera: Lasiocampidae), as an ectotherm, temperature plays a crucial role in its development. With climate change, earlier development of insect pests is expected to pose a more frequent threat to forest communities. Yet the quantitative research about the extent to which global warming affects pine caterpillar populations is rarely understood, particularly across various elevations and latitudes. Spring phenology of pine caterpillars showed an advancing trend with 0.8 d/10a, 2.2 d/10a, 2.2 d/10a, and 3.3 d/10a under the SSP1-2.6, SSP2-4.5, SSP3-7.0 and SSP5-8.5 scenario, respectively. There was a maximum advance of 20 d in spring phenology of pine caterpillars during the 2090s, from mid-March to early March, and even late February. This study highlighted the significant advance in spring phenology at elevations >1000 m and lower latitudes. Consequently, the differences in elevational and latitudinal gradients were relatively small as the increasing temperatures at the end of the 21st century. And the average temperature in February-March was effective in explaining theses variability. These findings are crucial for adapting and mitigating to climate change.

Dynamic evolution characteristics and hazard assessment of compound drought/waterlogging and low temperature events for maize.

Hazard assessment is fundamental in the field of disaster risk management. With the increase in global warming, compound water and temperature events have become more frequent. Current research lacks risk assessments of low temperatures and their compound events, necessitating relevant hazard assessment work to improve the accuracy and diversity of maize disaster prevention and mitigation strategies. This study comparatively analyzed the dynamic evolution characteristics and hazards of compound drought/waterlogging and low temperature events (CDLEs and CWLEs) for maize in the Songliao Plain during different growth periods from 1981 to 2020. First, composite drought/waterlogging and low temperature magnitude indices (CDLMI and CWLMI) were constructed to quantify the intensity of CDLEs and CWLEs by fitting non-exceedance probabilities. Next, static and dynamic hazard assessment models were developed by fitting probability density and cumulative probability density curves to CDLMI and CWLMI. The results showed that the correlations between SPRI and LTI across different decades were mainly negative during the three growth periods. The hazard ratings for both CDLEs and CWLEs were relatively high in the northern part of the study area, consistent with the higher occurrence, duration, and severity of both CDLEs and CWLEs at higher latitudes. Relative to 2001-2010, the center of gravity of hazard shifted southward for CDLEs and northward for CWLEs in 2011-2020. The mean duration, frequency, and hazard were generally higher for CWLEs, but CDLEs were associated with more severe maize yield reductions. This study provides new insights into compound disaster risk assessment, and the research methodology can be generalized to other agricultural growing areas to promote sustainable development of agricultural systems and food security.

Establishment and application of Agrobacterium-delivered CRISPR/Cas9 system for wild tobacco (Nicotiana alata) genome editing.

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system has been widely applied in cultivated crops, but limited in their wild relatives. Nicotiana alata is a typical wild species of genus Nicotiana that is globally distributed as a horticultural plant and well-studied as a self-incompatibility model. It also has valuable genes for disease resistance and ornamental traits. However, it lacks an efficient genetic transformation and genome editing system, which hampers its gene function and breeding research. In this study, we developed an optimized hypocotyl-mediated transformation method for CRISPR-Cas9 delivery. The genetic transformation efficiency was significantly improved from approximately 1% to over 80%. We also applied the CRISPR-Cas9 system to target the phytoene desaturase (NalaPDS) gene in N. alata and obtained edited plants with PDS mutations with over 50% editing efficiency. To generate self-compatible N. alata lines, a polycistronic tRNA-gRNA (PTG) strategy was used to target exonic regions of allelic S-RNase genes and generate targeted knockouts simultaneously. We demonstrated that our system is feasible, stable, and high-efficiency for N. alata genome editing. Our study provides a powerful tool for basic research and genetic improvement of N. alata and an example for other wild tobacco species.

Identification of QTLs associated with yield-related traits and superior genotype prediction using recombinant inbred line population in tobacco.

Tobacco is an economically significant industrial crop and model plant for genetic research, yet little is known about its genetic architecture. Quantitative trait loci (QTL) analysis was performed for six agronomic traits on an F_7 population of 341 genotypes, parents, and F1 plants using 1974 SSR markers across two environments. 31 QTLs contributing single-locus additive effects on 13 linkage groups (LGs) and 6 QTL pairs contributing epistatic effects on 6 LGs, were detected by the QTLNetwork 2.0 which was developed for the mixed-linear-model-based composite interval mapping (MCIM). Notably, 5 QTLs and 1 epistatic QTL pair were found to have pleiotropic effects on some genetically related traits. Moreover, the Broad sense heritability of the detected QTLs ranged from 1.05% to 43.33%, while genotype-by-environment interaction heritability spanned from 27.09% to 56.25%. Based on the results of QTL mapping, the potential superior lines for all or specific environments were designed and evaluated. Five major QTLs were finely dissected based on the tobacco reference genome of K326, and 31 candidate genes were predicted. This study offered new insights into the complicated genetic architecture and QTL resources for efficient breeding design for genetic improvement of agronomic traits in tobacco.

Comparative transcriptome analysis reveals nicotine metabolism is a critical component for enhancing stress response intensity of innate immunity system in tobacco.

The pyridine alkaloid nicotine acts as one of best-studied plant resistant traits in tobacco. Previous research has shown that NtERF199 and NtERF189, acting as master regulators within the NIC1 and NIC2 locus, quantitatively contribute to nicotine accumulation levels in N. tabacum. Genome editing-created Nic1(Nterf199) and Nic2 (Nterf189) double mutant provides an ideal platform for precisely dissecting the defensive role of nicotine and the connection between the nicotine biosynthetic pathway with other putative metabolic networks. Taking this advantage, we performed a comparative transcriptomic analysis to reevaluate the potential physiological and metabolic changes in response to nicotine synthesis defect by comparing the nic1nic2 and NIC1NIC2 plants. Our findings revealed that nicotine reduction could systematically diminishes the expression intensities of genes associated with stimulus perception, signal transduction and regulation, as well as secondary metabolic flux. Consequently, this global expression reduction might compromise tobacco adaptions to environmental fitness, herbivore resistances, and plant growth and development. The up-regulation of a novel set of stress-responsive and metabolic pathway genes might signify a newly established metabolic reprogramming to tradeoff the detrimental effect of nicotine loss. These results offer additional compelling evidence regarding nicotine's critical defensive role in nature and highlights the tight link between nicotine biosynthesis and gene expression levels of quantitative resistance-related genes for better environmental adaptation.

Dissection of genetic architecture of nine hazardous component traits of mainstream smoke in tobacco (Nicotiana tabacum L.).

Tobacco (Nicotiana tabacum L.) use is the leading cause of preventable death, due to deleterious chemical components and smoke from tobacco products, and therefore reducing harmful chemical components in tobacco is one of the crucial tobacco breeding targets. However, due to complexity of tobacco smoke and unavailability of high-density genetic maps, the genetic architecture of representative hazardous smoke has not been fully dissected. The present study aimed to explore the genetic architecture of nine hazardous component traits of mainstream smoke through QTL mapping using 271 recombinant inbred lines (RILs) derived from K326 and Y3 in multiple environments. The analysis of genotype and genotype by environment interaction (GE) revealed substantially greater heritability over 95% contributed mostly by GE interaction effects. We also observed strong genetic correlations among most studied hazardous smoke traits, with the highest correlation coefficient of 0.84 between carbon monoxide and crotonaldehyde. Based on a published high-density genetic map, a total of 19 novel QTLs were detected for eight traits using a full QTL model, of which 17 QTLs showed significant additive effects, six showed significant additive-by-environment interaction effects, and one pair showed significant epistasis-by-environment interaction effect. Bioinformatics analysis of sequence in QTL region predicted six genes as candidates for four traits, of which Nt21g04598.1, Nt21g04600.1, and Nt21g04601.1 had pleiotropic effects on PHE and TAR.

Residues, potential source and ecological risk assessment of polycyclic aromatic hydrocarbons (PAHs) in surface water of the East Liao River, Jilin Province, China.

The environmental risks posed by polycyclic aromatic hydrocarbons (PAHs) and the diversity of their anthropogenic origins make them a global issue. Therefore, it is of utmost significance for protecting the aquatic environment and the growth of neighboring populations to identify their possible origins and ecological risk. Here, we detail the contamination profiles of 15 PAHs found in the East Liao River's surface waters in Jilin Province and use the receptor model Absolute Principal Component Analysis - Multiple Linear Regression (APCS-MLR) and diagnostic ratios method to identify the primary potential sources of pollution. Based on the natural hazard risk formation theory (NHRFT), an ecological risk assessment (ERA) model for PAHs in the East Liao River was developed. The method assesses the ecological risk status of PAHs by integrating the risk quotient (RQ) approach and the DPSIRM (driving force, pressure, state, impact, response, management) conceptual framework. Total concentrations in the surface water body were between 396.42 and 624.06 ng/L, with an average of 436.99 ng/L. The source research revealed that coal, biomass, and traffic emission sources are the most likely PAH contributors to the East Liao River. The ERA found that the majority of the sites' locations of the study were at low risk for PAHs in surface water bodies (30.7 % and 32.2 %, respectively), while only a tiny percentage of sites were at high or very high risk (1.8 % and 13.6 %). The study results provide theoretical support for the East Liao River's ecological, environmental protection, and policy formulation.

Construction of a high-density genetic map and dissection of genetic architecture of six agronomic traits in tobacco (Nicotiana tabacum L.).

Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies on plant biology and genetics. A population of 271 recombinant inbred lines (RIL) derived from K326 and Y3, two elite flue-cured tobacco parents, has been constructed to investigate the genetic basis of agronomic traits in tobacco. Six agronomic traits including natural plant height (nPH), natural leaf number (nLN), stem girth (SG), inter-node length (IL), length of the largest leaf (LL) and width of the largest leaf (LW) were measured in seven environments, spanning the period between 2018 and 2021. We firstly developed an integrated SNP-indel-SSR linkage map with 43,301 SNPs, 2,086 indels and 937 SSRs, which contained 7,107 bin markers mapped on 24 LGs and covered 3334.88 cM with an average genetic distance of 0.469cM. Based on this high-density genetic map, a total of 70 novel QTLs were detected for six agronomic traits by a full QTL model using the software QTLNetwork, of which 32 QTLs showed significant additive effects, 18 QTLs showed significant additive-by-environment interaction effects, 17 pairs showed significant additive-by-additive epistatic effects and 13 pairs showed significant epistasis-by-environment interaction effects. In addition to additive effect as a major contributor to genetic variation, both epistasis effects and genotype-by-environment interaction effects played an important role in explaining phenotypic variation for each trait. In particular, qnLN6-1 was detected with considerably large main effect and high heritability ( h a 2 =34.80%). Finally, four genes including Nt16g00284.1, Nt16g00767.1, Nt16g00853.1, Nt16g00877.1 were predicted as pleiotropic candidate genes for five traits.

[Mapping of Sanming dominant genic male sterility gene in rice].

The mutant of "Sanming Dominant Genic Male Sterile Rice" was found from an F2 population of cross "SE2lS/Basmati370" by Sanming Institute of Agricultural Science in 2001. It has proven that the male sterility of this mutant is controlled by a dominant gene (named as SMS). By multiple backcrosses, this dominant male sterile allele was introduced into the genetic background of an indica rice cultivar Jiafuzhan (which was known as Jiabuyu). In order to map SMS, a mapping population was constructed by crossing Jiabuyu with a japonica cultivar Nipponbare and further crossing the F1 with Jiafuzhan. By bulked segregant analysis and linkage analysis using SSR and INDEL markers, SMS was mapped to a 99 kb interval between INDEL markers ZM30 and ZM9 on chromosome 8. This result will facilitate cloning of SMS.

The complete chloroplast genome of Nicotiana plumbaginifolia.

Nicotiana plumbaginifolia Vivianiis 1802 is an annual herb, native to Mexico and South America. It is one of the most widely distributed tobacco species. As a wild tobacco, N. plumbaginifolia has provided several economically important disease-resistance genes to cultivated tobacco. We assembled the complete chloroplast genome of N. plumbaginifolia. The chloroplast genome is 155,945 bp in length, which includes a large single copy region (86,621 bp), a small single copy region (18,528 bp) and two separated inverted repeat regions (25,398 bp). A total of 117 unique genes were annotated, consisting of 84 protein-coding genes, 29 tRNA genes and 4 rRNA genes. Based on chloroplast genomes of 17 Nicotiana species, phylogenetic analyses indicated that N. plumbaginifolia was closely related to N. suaveolens and N. amplexicaulis.

Transcriptomics and iTRAQ-proteomics analyses provide novel insights into the defense mechanism of black shank disease in tobacco.

Black shank disease caused by Phytophthora nicotianae is one of the most important diseases in tobacco worldwide and can result in a devastating loss in tobacco cultivation. Many efforts have been carried out to identify the chromosome segment from Nicotiana plumbaginifolia containing a resistance locus carrying a gene named Php; however, the Php gene has not been cloned, and knowledge of the potential mechanism of the Php gene in the resistant lines is limited. To further characterize the resistance mechanism of the Php gene, we first used the resistant line "RBST" and the susceptible cultivar "Honghuadajinyuan" (HD) to obtain the near-isogenic line RBS89 containing the Php gene from RBST. RBS89 showed high resistance to black shank disease. Transcriptomic and iTRAQ analyses were applied to explore the potential defense mechanisms in RBS89 plants in comparison with HD plants with or without inoculation. Many differentially expressed genes (DEGs) and proteins were identified, and some pathogenesis-related (PR) proteins were extensively abundant in the RBS89 plants when compared with the HD plants in response to black shank disease. Importantly, overexpression of the PR gene NtPR-1B in HD plants improved the resistance of tobacco plants to black shank disease, indicating that NtPR-1B and Php genes might have similar roles in protecting tobacco from black shank disease. However, the relationship between NtPR-1B and Php genes requires further analysis. Therefore, our study provides valuable information for breeding tobacco cultivars with black shank disease resistance and sheds light on the defense mechanism of black shank disease in tobacco for enhancing Phytophthora resistance in other Solanaceae crops.