Abstract
Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2–3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene–metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.
Highlights
Tobacco (Nicotiana tabacum) has great social and economic impacts on public health worldwide.[1]
To explore the effects of genetic and environmental factors as well as developmental processes on agronomic and quality traits, we collected 54 tobacco leaf samples (Supplementary Table S1), composed of six developmental stages of three varieties planted in three regions in China
Guizhou lies in the northeast of Yunnan, a subtropical plateau with median temperature and abundant rainfall, but less sun exposure time compared with Yunnan and Henan (Supplementary Fig. S1)
Summary
Tobacco (Nicotiana tabacum) has great social and economic impacts on public health worldwide.[1] One way to mitigate the impacts is to improve the tobacco quality, including both agronomic and quality traits, such as reduction of alkaloid level.[2] Previous studies have revealed that most agronomic and quality traits are primarily influenced by both genetic and environmental factors, as well as developmental processes.[3] molecular networks by which genetic and environmental factors influence these traits remain elusive. Whole-genome and RNA sequencing identified $90,000 genes and over 134,000 transcripts.[4,5,6] Recently, several research groups analysed tobacco transcriptome to understand transcriptional regulation involved in various agronomic and quality traits, such as response to premature senescence[7] and response to topping.[8]
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