Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress

Integrative Physiological, Transcriptome, and Proteome Analyses Provide Insights into the Photosynthetic Changes in Maize in a Maize-Peanut Intercropping System

Intercropping is a traditional and sustainable planting method that can make rational use of natural resources such as light, temperature, fertilizer, water, and CO2. Due to its efficient resource utilization, intercropping, in particular, maize and legume intercropping, is widespread around the world. However, the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome, and proteome analyses were compared between maize monocropping and maize-peanut intercropping. The results show that an intercropping system enhanced the ability of carbon fixation and carboxylation of maize leaves. Apparent quantum yield (AQY), the light-saturated net photosynthetic rate (LSPn), the light saturation point (LSP), and the light compensation point (LCP) were increased by 11.6%, 9.4%, 8.9%, and 32.1% in the intercropping system, respectively; carboxylation efficiency (CE), the CO2 saturation point (Cisat), the Rubisco maximum carboxylation rate (Vcmax), the maximum electron transfer rate (Jmax), and the triose phosphate utilization rate (TPU) were increased by 28.5%, 7.3%, 18.7%, 29.2%, and 17.0%, respectively; meanwhile, the CO2 compensation point (Γ) decreased by 22.6%. Moreover, the transcriptome analysis confirmed the presence of 588 differentially expressed genes (DEGs), and the numbers of up-regulated and down-regulated genes were 383 and 205, respectively. The DEGs were primarily concerned with ribosomes, plant hormone signal transduction, and photosynthesis. Furthermore, 549 differentially expressed proteins (DEPs) were identified in the maize leaves in both the maize monocropping and maize-peanut intercropping systems. Bioinformatics analysis revealed that 186 DEPs were related to 37 specific KEGG pathways in each of the two treatment groups. Based on the physiological, transcriptome, and proteome analyses, it was demonstrated that the photosynthetic characteristics in maize leaves can be improved by maize-peanut intercropping. This may be related to PS I, PS II, cytochrome b6f complex, ATP synthase, and photosynthetic CO2 fixation, which is caused by the improved CO2 carboxylation efficiency. Our results provide a more in-depth understanding of the high yield and high-efficiency mechanism in maize and peanut intercropping.