Retrospect and prospect of Nicotiana tabacum genome sequencing.

Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technology, several Nicotiana tabacum genomes have been published. In this paper, we reviewed the progress on N. tabacum genome assembly and quality, from the initial draft genomes to the recent high-quality chromosome-level assemblies. The application of long-read sequencing, optical mapping, and Hi-C technologies has significantly improved the contiguity and completeness of N. tabacum genome assemblies, with the latest assemblies having a contig N50 size over 50 Mb. Despite these advancements, further improvements are still required and possible, particularly on the development of pan-genome and telomere-to-telomere (T2T) genomes. These new genomes will capture the genomic diversity and variations among different N. tabacum cultivars and species, and provide a comprehensive view of the N. tabacum genome structure and gene content, so to deepen our understanding of the N. tabacum genome and facilitate precise breeding and functional genomics.

Real-time hazard assessment of maize based on the chilling injury process -- Using a standard curve to establish a daily cumulative assessment method.

Cold damage caused by low temperatures is known as chilling injury (CI), and it has consistently been one of the primary meteorological disasters affecting maize. With ongoing global climate change, the issue of chilling injury is becoming more prominent, exhibiting new characteristics and presenting new challenges. Consequently, understanding the disaster process and conducting a more refined real-time chilling injury identification have become significant challenges. In this study, we divided maize planting areas into seven maturity types based on the accumulated temperature, constructed a standard curve of the daily accumulated temperature from 1991 to 2020, proposed real-time identification indicators based on the CI process, and developed a real-time CI hazard assessment model. The results indicated that the model can capture independent CI events and rapidly determine the location, intensity, duration and scope of CIs, thereby providing a basis for accurately understanding the impact of chilling injury and taking timely countermeasures. The combination of accumulated temperature standard curves for seven maturity types of maize and the CI curve was used to construct the CI daily scale identification indicator, ΔEAT. Judgment thresholds for the CI identification indicators at various maturity levels were obtained by correlating them with historical disaster data. The frequency and intensity of maize CI gradually increased from the extremely late-maturing zone to the extremely early-maturing zone, with the seeding and emergence periods being the peak periods for CI. The spatiotemporal evolution characteristics of the three different degrees of CI events in 1992, 2004, and 2017 were consistent with the historical disaster records. Northeastern Inner Mongolia and most of Heilongjiang were found to be high-hazard areas for maize CIs. The constructed daily CI identification indicators can accurately and rapidly identify maize CIs, providing practical and targeted guidance for combating these injuries.

Single-cell landscape of long and short glandular trichomes in Nicotiana tabacum leaves.

Glandular trichomes (GTs) play a crucial role in plant defenses and the synthesis of secondary metabolites. Understanding the developmental trajectory of GTs is essential for unraveling their functional significance and potential applications. Here we established a comprehensive single-cell atlas of Nicotiana tabacum leaves, a model plant for GT studies. The atlas included a total of 40,433 cells and successfully captured both long GTs (LGTs) and short GTs (SGTs) from Nicotiana leaves. The developmental trajectories of these trichomes were delineated, revealing potential disparities in epidermal development. Comparative analysis of Arabidopsis and Nicotiana trichome development indicated limited similarity between Arabidopsis epidermal non-glandular trichomes and Nicotiana LGTs and SGTs, implying the essentiality of studying the genes directly involved in the development of Nicotiana GTs for a proper and comprehensive understanding of GT biology. Overall, our results provide profound insights into the developmental intricacies of the specialized GTs.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Comprehensive Risk Assessment of High Temperature Disaster to Kiwifruit in Shaanxi Province, China.

In recent years, the main kiwifruit producing region, central-south Shaanxi Province, has often suffered from the threat of extreme high temperatures. Assessing the risk of high-temperature disasters in the region is essential for the rational planning of agricultural production and the development of resilience measures. In this study, a database was established to assess the risk of a high-temperature disaster to kiwifruit. Then, four aspects, hazard, vulnerability, exposure and disaster prevention and mitigation capacity, were taken into account and 19 indexes were selected to make an assessment of the risk of a high-temperature disaster. At the same time, 16 indexes were selected for the assessment of the climatic suitability of kiwifruit in terms of light, heat, water, soil and topography, and were used as one of the indexes for exposure assessment. The analytic hierarchy process and the entropy weighting method were combined to solve the weights for each index. The results reveal that: (1) The Guanzhong Plain has a high climatic suitability for kiwifruit, accounting for 15.14% of the study area. (2) The central part of the study area and southern Shaanxi are at high risk, accounting for 22.7% of the study area. The major kiwifruit producing areas in Shaanxi Province (e.g., Baoji) are at a low risk level, which is conducive to the development of the kiwifruit industry. Our study is the first to provide a comprehensive assessment of the risk of a high-temperature disaster to the economic fruit kiwifruit, providing a reference for disaster resilience and mitigation.

Wan-Nian-Qing, a Herbal Composite Prescription, Suppresses the Progression of Liver Cancer in Mice by Regulating Immune Response.

The Wan-Nian-Qing prescription (WNQP), an herbal composite containing Ornithogalum caudatum, has been used in China for several years for cancer treatment. However, the mechanism of its pharmacological action against liver cancer is not clear. This study aimed to investigate the role of WNQP in inhibiting tumor growth in hepatocellular carcinoma model mice and determine its mechanism of action. We established HepG2- and SMMC-7721-xenografted tumor models in nude mice and BALB/c mice. The mice were administered WNQP for 2 weeks. The bodyweight of each mouse was monitored every day, and the tumor size was measured using vernier caliper before each round of WNQP administration. After the last dose, mice were sacrificed. The tumors were removed, lysed, and subjected to proteome profiling, enzyme-linked immunosorbent assay, and western blotting. The liver, spleen, and kidney were collected for histopathological examination. The effects of WNQP against liver cancer were first systematically confirmed in HepG2- and SMMC-7721-xenografted nude mice and BALB/c mice models. WNQP inhibited tumor growth, but failed to affect bodyweight and organ structures (liver and spleen), confirming that it was safe to use in mice. In BALB/c mice, WNQP regulated immune function, inferred from the modulation of immune-related cytokines such as interleukins, interferon, tumor necrosis factors, and chemokines. Further results confirmed that this regulation occurred via the regulatory effects of WNQP on Nrf2 signaling. WNQP can inhibit the growth of HepG2- and SMMC-7721-xenografted tumors in nude mice and BALB/c mice. This effect manifests at least partially through immunomodulation mediated apoptosis.

GIS- and MCD-based suitability assessment for optimized location of solid waste landfills in Dar es Salaam, Tanzania.

Despite recent advancements in waste management technologies, landfills remain the dominant approach for the final disposal of solid waste (SW) around the world. However, landfills are associated with adverse environmental and health-related impacts. This study is primarily applied to Dar es Salaam, a city in the East African region that has failed to follow appropriate approaches for site selection and that the methods used to select the current sites are manually operated. The study used a geographical information system (GIS) combined with multicriteria decision analysis (MCDA) to objectively determine the optimal landfill sites. A comprehensive list of assessment criteria was examined through a computerized site selection procedure based on GIS to analyze the ground that was surveyed and to remotely obtain data. Analytical hierarchy process (AHP)-one of the best MCDA approaches-was used to assign relative weight and evaluate each criterion. Finally, the study computed site suitability indices (SSIs), which aids in the identification of site suitability levels (SSLs) for the entire region. The final suitability map produced by overlaying the criteria map layers showed that a large part of the study area (60.92%) was completely unsuitable for landfill siting. The remaining areas consisted of land with varying suitability level, which were grouped into four classes: very low (30.92%), low (2.05%), moderate (5.65%), and high (0.46). To this end, only the high suitability class (0.46%) was of acceptable suitability levels (ASLs) (SSI ≥ 2.0). From the numerous identified sites with ASL, only three sites were suggested. Due to concerns regarding the lifespan and environment-related risks associated with these suggested sites, there is a need to further study new environmentally friendly techniques, considering the importance of circular economy agenda of waste to resource/energy for sustainable solid waste management.

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.

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.