Black shank, caused byPhytophthora nicotianae(P. nicotianae), is a serious disease of cultivated tobacco (Nicotiana tabacum) worldwide. The interactions between tobacco andP. nicotianaeare complex and the outcomes of the interactions depend on the tobacco genotype,P. nicotianaestrain, and environmental conditions. In this study, we used RNA-sequencing (RNA-Seq) to investigate and compare transcriptional changes in the stems of tobacco upon inoculation withP. nicotianaestrain race 0. We used two tobacco varieties: RBST (named from resistance to black shank and tobacco mosaic virus), which was resistant to theP. nicotianaestrain race 0, and Honghuadajinyuan (HD), which was susceptible toP. nicotianaerace 0. Samples were collected 12 and 72-hour post inoculation (hpi). Analysis of differentially expressed genes (DEGs) and significantly enriched GO terms indicated that several basic defense mechanisms were suppressed in both varieties, which included response to wounding (GO: 0009611), and defense response to fungus (GO: 0050832). We also found some genes that may especially be related to mechanisms of resistance in RBST, such as the one encoding a chitinase. These results will provide a valuable resource for understanding the interactions betweenP. nicotianaeand tobacco plants.

Introduction: Nicotiana tabacum, widely cultivated for its economic and scientific value, produces a broad range of secondary metabolites that play critical roles in determining leaf quality and flavor. Despite substantial progress, the comprehensive regulatory landscape governing secondary metabolite biosynthesis during N. tabacum leaf development remains largely unclear.Methods: To better understand the molecular regulatory mechanisms underlying the biosynthesis of secondary metabolites, particularly flavonoids, during N. tabacum leaf development, we conducted a transcriptomic and non-targeted metabolomic sequencing and analysis at three critical developmental stages: vigorous growth stage (T1), topping stage (T2), and harvest stage (T3).Results: Based on our transcriptomic and metabolomic data, 25 unigenes exhibiting stage-specific expression patterns that were strongly associated with flavonoid accumulation were identified. We found that during early developmental stages (T1-T2), upregulated expression of chalcone synthase (CHS) and chalcone isomerase (CHI) correlated with enhanced flavonoid backbone biosynthesis. In contrast, during the later stage (T3), increased expression of dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) was consistent with elevated anthocyanin accumulation.Conclusion: This study systematically analyzed the coordinated regulatory network of flavonoid biosynthesis during leaf development in N. tabacum, revealing dynamic metabolic shifts across developmental stages. The findings offer novel molecular insights into the mechanisms underlying leaf quality formation and establish a theoretical framework for functional studies of candidate genes, reinforcing the utility of N. tabacum as a model species for secondary metabolism research and breeding innovation.

Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies of plant biology and genetics. As an allotetraploid plant generated from interspecific hybridization, tobacco has a massive genome (4.5 Gb). Recently, a genetic map with 45,081 single nucleotide polymorphism (SNP) markers was constructed using whole-genome sequencing data for a tobacco population including 274 individuals. This provides a basis for quantitative trait locus (QTL) mapping and genomic selection, which have been widely applied to other crops but have not been feasible in tobacco. Based on this high-density genetic map, we identified QTLs associated with important agronomic traits, chemical compounds in dry leaves, and hazardous substances in processed cigarettes. The LOD values for major QTLs were highest for agronomic traits, followed by chemical compounds and hazardous substances. In addition to the identification of molecular markers, we evaluated genomic selection models and found that BayesB had the highest prediction accuracy for the recombinant inbred line population. Our results offer new insights into the genetic mechanism underlying important traits, such as agronomic traits and quality-related chemical compounds in tobacco, and will be able to support the application of molecular breeding to tobacco.

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 (ha2=34.80%). Finally, four genes including Nt16g00284.1, Nt16g00767.1, Nt16g00853.1, Nt16g00877.1 were predicted as pleiotropic candidate genes for five traits.