Transcriptome analysis of leaves responses to elevated CO<sub>2</sub> concentration, drought and interaction conditions in soybean [<italic>Glycine max </italic>(Linn.) Merr.]

Global consensus on climate warming and elevated atmospheric CO2 concentrations has increased the frequency and intensity of extreme weather events (droughts) and brought uncertainty about soybean production. In this study, the effects of elevated CO2 concentration, drought and their interaction on gene expression in soybean were elucidated by phenotypic and leaf transcriptome sequencing (RNA-seq) analysis. To provide theoretical reference for soybean breeding under the background of future climate change, we identified the regulatory pathway of CO2 affecting soybean drought tolerance. The phenotypic results showed that elevated CO2 concentration promoted the growth and alleviated the negative effects of drought stress on soybean. The results revealed that a total of 89 CO2-responsive genes were identified by transcriptome sequencing analysis. KEGG classification demonstrated that these genes were mainly involved in antioxidant metabolism (terpenoid, flavonoid, etc.), meanwhile, Functional of the specific differentially expressed gene mainly focused on cell components, growth, and development. Under drought condition, 1006 highly differentially expressed (16-fold) genes were screened out. These genes were mainly involved in various amino acid (proline, tryptophan, etc.) metabolic pathways, and almost all genes involved in protein synthesis and transport were up-regulated, indicating that there were a lot of material exchange processes in soybean leaves under drought stress. A total of 8566 differentially expressed genes, mainly involved in carbohydrate metabolism pathway, were detected under the interaction, and almost all genes related to the photosynthesis-antenna protein pathway were down-regulated, suggesting that the photosynthetic capacity of soybean was decreased under the interaction. 34 genes were found to be differentially expressed under all three conditions. These genes were mainly concentrated in antioxidant metabolism (flavonoids, glutathione, phenylpropanoids, etc.), and most of these genes were involved in the metabolism of various plant hormones and stimulus responses. The qRT-PCR results of six differentially expressed genes related to drought resistance in two soybean varieties with different genetic background showed that the RNA-seq data were accurate. In conclusion, elevated CO2 concentration could increase the relative expression levels of genes related to antioxidant metabolism, growth and development in soybean leaves. Drought stress induced the relative expression levels of genes related to amino acid metabolism and protein synthesis pathway. The photosynthetic capacity of soybean was inhibited under the interactive condition. Elevated CO2 concentration enhanced the tolerance of soybean to drought stress by regulating hormone metabolism, antioxidant (antioxidant enzyme, flavonoid, phenylpropanoid) metabolism and carbohydrate metabolism.