Effects of the Herbicide Imazethapyr on Photosynthesis in PGR5- and NDH-Deficient <i>Arabidopsis thaliana</i> at the Biochemical, Transcriptomic, and Proteomic Levels SunChongchong ChenSi JinYujian SongHao RuanSonglin FuZhengwei AsadMuhammad Asad Ullah QianHaifeng 2016 Photosynthesis is a very important metabolic pathway for plant growth and crop yield. This report investigated the effect of the herbicide imazethapyr on photosynthesis in the <i>Arabidopsis thaliana pns</i>B3 mutant (a defect in the NDH pathway) and <i>pgr</i>5 mutant (a defect in the PGR5 pathway) to determine which cyclic electron transport chain (CET) of the NDH and PGR5 pathways is more important for protecting the photosynthetic system under herbicide stress. The results showed that 20 μg/L imazethapyr markedly inhibited the growth of the three ecotypes of <i>A. thaliana</i> and produced more anthocyanins and reactive oxygen species (ROS), particularly in the <i>pgr</i>5 mutant. The chlorophyll fluorescence results showed that PSII was severely damaged in the <i>pgr</i>5 mutant. Additionally, the CET was significantly stimulated to protect the photosynthetic system from light damage in Wt and the <i>pns</i>B3 mutant but not the <i>pgr</i>5 mutant. The real-time PCR analysis indicated that imazethapyr treatment considerably decreased the transcript levels of most photosynthesis-related genes in the three treated groups. Several genes in the PGR5 pathway were significantly induced in the <i>pns</i>B3 mutant, but no genes in the NDH pathway were induced in the <i>pgr</i>5 mutant. The gene transcription analysis showed that the <i>pgr</i>5 mutant cannot compensate for the deficit in the PGR5 pathway by stimulating the NDH pathway, whereas the <i>pns</i>B3 mutant can compensate for the deficit in the CET cycle by regulating the PGR5 pathway. The iTRAQ analyses also showed that the photosynthesis system, glycolysis, and TCA cycle suffered the most severe damage in the <i>pgr</i>5 mutant. All of these results showed that the PGR5 pathway is more critical for electron transfer around PSI than the NDH pathway to resist herbicide stress.