Genetic linkage maps are essential for studies of genetics, genomic structure, and genomic evolution, and for mapping quantitative trait loci (QTL). Identification of molecular markers and construction of genetic linkage maps in tobacco (Nicotiana tabacum L.), a classical model plant and important economic crop, have remained limited. In the present study we identified a large number of single nucleotide polymorphism (SNP) markers and constructed a high-density SNP genetic map for tobacco using restriction site-associated DNA sequencing. In 1216.30 Gb of clean sequence obtained using the Illumina HiSeq 2000 sequencing platform, 99,647,735 SNPs were identified that differed between 203 sequenced plant genomes and the tobacco reference genome. Finally, 13,273 SNP markers were mapped on 24 high-density tobacco genetic linkage groups. The entire linkage map spanned 3421.80 cM, with a mean distance of 0.26 cM between adjacent markers. Compared with genetic linkage maps published previously, this version represents a considerable improvement in the number and density of markers. Seven QTL for resistance to cucumber mosaic virus (CMV) in tobacco were mapped to groups 5 and 8. This high-density genetic map is a promising tool for elucidation of the genetic bases of QTL and for molecular breeding in tobacco.

Cucumber mosaic virus (CMV) is one of the most severe viral diseases transmitted by aphids infecting Solanum crops in China, causing great losses of crop yields and income in rural communities. The tobacco cultivars NC82 and Taiyan 8 are closely related but differ in resistance to CMV. NC82 is susceptible to infection and Taiyan 8 is resistant, but the mechanisms underlying this difference in resistance are not clear. In this study, we conducted RNA sequencing to analyze changes in gene expression induced in the leaves of Taiyan 8 and NC82 upon systemic infection with CMV, compared with gene expression in the leaves of mock-inoculated plants. Leaves were sampled at one, three, eight, and 15 days after infection. In total, 3443 and 747 differentially expressed genes were identified in Taiyan 8 and NC82, respectively. Gene ontology and pathway enrichment analyses revealed that the different responses to CMV infection between cultivars were based on microtubule-based processes, pentose and glucuronate interconversions, plant–pathogen interaction, and hormone signal transduction pathways. Genes encoding pathogenesis-related proteins, disease-resistance proteins, lipoxygenase, cellulose synthase, an auxin response factor, and an ethylene receptor showed different expression patterns. The differences in gene expression following CMV infection likely contributed to the different resistance levels of these two tobacco cultivars. The comprehensive transcriptome dataset described here, which includes candidate response genes, will serve as a resource for further studies of the molecular mechanisms associated with tobacco defense responses against CMV.

Cigar line Beinhart 1000-1 has effective durable resistance to black shank (BS) and is considered one of the most resistant sources in tobacco (Nicotiana tabacum L.). To investigate the inheritance and identification of stable quantitative trait loci (QTL) for BS response, F₂, BC₁F₂ individuals and BC₁F_2:3 lines were produced from a cross between Beinhart 1000-1 and Xiaohuangjin 1025. Two major quantitative trait loci (M-QTL) named qBS7 and qBS17 were repeatedly detected under different conditions. QTL qBS7 was mapped to the region between PT30174 and PT60621 and explained 17.40%–25.60% of the phenotypic variance under different conditions. The other QTL qBS17 in interval PT61564–PT61538 of linkage group 17 was detected in a BC₁F₂ population in the field and in BC₁F_2:3 in both the field and at the seedling stage, explaining 6.90% to 11.60% of the phenotypic variance. The results improve our understanding of the inheritance of resistance to BS and provide information that can be used in marker-assisted breeding.