Comparative Proteomic Analysis by Isobaric Tags for the Relative and Absolute Quantification Reveals the Responses of Tobacco (Nicotiana tabacum L.) Roots to Different Soil Types

Tobacco (Nicotiana tabacum) root affects the yield and quality of tobacco leaves. To gain insight into the responses of the tobacco root system to different soil types, we integrated morphological characteristics, the physiological index, the metabolic pathways of the root system, and the aboveground biomass of tobacco cultivated in limestone soil (LS), paddy soil (PS), and red soil (RS). Compared with plants growing in LS and PS, the chemical composition of tobacco leaves in RS tended to be coordinated. Red soil facilitated the accumulation of aboveground and belowground biomass of flue-cured tobacco and had the most significant effect on the dry matter quality of the roots. In addition, it promoted an increased root length, root surface area (RSA), root volume, and a higher number of root forks and improved root vigor and nitrate reductase (NR) activity; however, the activities of superoxide dismutase (SOD) and peroxidase (POD) were decreased. We studied differentially the abundant proteins (DAPs) of the flue-cured tobacco roots cultivated in different soil types by isobaric tags for the relative and absolute quantification (iTRAQ) of the proteomic profiles of cultivar. In total, 699, 650, and 569 differentially abundant proteins (DAPs) were identified from limestone soil (LS) vs. PS, LS vs. RS, and PS vs. RS, respectively, including 412/287, 291/359, and 323/246 up-/downregulated proteins, respectively. These DAPs were mainly involved in starch and sucrose metabolism, phenylalanine metabolism, the biosynthesis of secondary metabolites, microbial metabolism in different environments, and ribosomes. The parallel reaction monitoring (PRM) and quantitative reverse transcription PCR (qRT-PCR) analysis showed that the results of the iTRAQ proteomics were reliable. Overall, our study facilitates a new understanding of the responses of tobacco roots to different soil types at the protein level.