In order to have a better understanding of the effects of genotype and environment on the quality of tobacco, three tobacco cultivars were selected as materials and planted at three representative regions of China. Six different developmental stages were sampled for metabolomic analysis.

More than 700 metabolites were identified by metabolomic analysis and target metabolites were around 500. Around 200 metabolites, including sugar, lipid and amino acids, were found to be different among the three regions. Principal component analysis (PCA) results showed that metabolites of tobacco had obvious regional characteristics, especially for Henan. ANOVA analysis revealed the effect of environment is stronger than genotype, and developmental stage is between them. However, interaction among them had little effect. Of the many environmental factors, temperature was the most important one. Different metabolites had different genotype and environment preference. Lipids may be mostly regulated by environment. However, several secondary metabolites may be affected by genotype.

It may be concluded that for different metabolites, different strategies should be used to regulate them, according to the contributions of genotype and environment. Our findings lay a foundation for future genetic studies and provide guidance for breeding high-quality tobacco cultivars.