Abstract：Tobacco (Nicotiana tabacum) is photophile crop, and its growth can be affected by shading. In order to deeply understand the response mechanism of tobacco under shading stress, explore the effect of shading on photosynthetic physiology of tobacco leaves and the changes of tobacco leaf transcriptome, this study took 'Yunyan 87' as the test material, measured the chlorophyll content and photosynthetic parameters of tobacco leaves under natural light and 40% shading rate, and sequenced the transcriptome of tobacco leaves. The results showed that compared with the control, the contents of photosynthetic pigments chlorophyll a (Chla), Chlb, carotenoids and Chla+Chlb increased (P<0.05) in the upper tobacco leaves of the shading treatment group, and Chla/Chlb did not change significantly. The photosynthetic parameters, net photosynthetic rate (Pn), decreased significantly (P<0.05), and there was no significant change in stomatal conductance (Gs), transpiration rate (Tr) and intercellular CO2 concentration (Ci). Transcriptome data analysis showed that there were a total of 10 110 differentially expressed genes (DEGs) between the control group and the shading group, of which 4 438 DEGs were up-regulated and 5 672 DEGs were down-regulated. GO analysis showed that DEGs were closely related to binding, catalytic activity, cellular fraction, membrane fraction, cellular process, and other items. KEGG analysis found that DEGs were mainly enriched in photosynthesis-antenna protein, plant hormone signal transduction, phagosome, glutathione metabolism, starch and sucrose metabolism, glycerolipid metabolism, porphyrin and chlorophyll metabolism. For photosynthesis-related genes, shading significantly increased the expression of some genes of photosystem Ⅰ (PSA) and photosystemⅡ (PSB), while PsaB, PsbS, PsbR and other genes were down-regulated, and the genes related to photosynthetic electron transport pathway and F-type ATPase were down-regulated. For porphyrin and chlorophyll metabolism-related genes, the genes related to chlorophyll synthesis were up-regulated, and the genes related to chlorophyll degradation were down-regulated. The results of qRT-PCR validation showed that the expression trend of DEGs was highly consistent with that of RNA-seq. This study provides experimental basis for the application of stress-resistant molecules in tobacco planting and new variety breeding.
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