Recently, the U.S. Food and Drug Administration issued an advance notice of proposed rulemaking to obtain information for consideration in developing a tobacco product standard to set the maximum nicotine level in cigarette filler. Tobacco industry and public institutions have been working on further understanding nicotine biosynthesis and on developing tobacco varieties with reduced nicotine levels. Genetic alteration via traditional breeding, mutation breeding, and genetic engineering has been effective to reduce nicotine to various levels. However, historically, low alkaloid traits are associated with poor leaf quality with characteristics such as delayed maturation, thin body and rigid cured leaf etc. To understand the effect of lowering nicotine on leaf quality, experiments were conducted to obtain transcriptomics and metabolomics expression data using seven Burley and four flue-cured lines at different plant growth stages. An integrative analysis of the “omics” data has provided insightful information towards understanding the complex and tightly regulated tobacco leaf developmental and maturation process. Computational analysis has led to the identification of more than 200 potential candidate genes that include transcription factors, secondary metabolism, cell-wall and senescence-related elements that could be associated with leaf quality. Seventy-four of these genes were validated using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Functional analysis of some of these genes is under way.