The effects of mepiquat chloride (DPC) on Cry1Ac protein contents in Bacillus thuringiensis (Bt) cotton boll shells under high temperature and drought stress were investigated to provide a theoretical reference for Bt cotton breeding and high-yield and high-efficiency cotton cultivation. This study was undertaken on the Bt cotton cultivar ‘Sikang 3’ during the 2020 and 2021 growing seasons at Yangzhou University Farm, Yangzhou, China. The potted cotton plants were exposed to high temperature and drought stress, and 20 mg L−1 DPC and water (CK) were sprayed on cotton plants. Seven days after treatment, Cry1Ac protein content, α-ketoglutarate content, pyruvic acid content, glutamate synthase activity, glutamic oxaloacetic transaminase activity, soluble protein content, and amino acid content were measured, and transcriptome sequencing was performed. DESeq was used for differential gene analysis. Under the DPC treatment, in contrast with the water treatment (CK), Cry1Ac protein content increased by 4.7-11.9%. α-Ketoglutarate content, pyruvic acid content, glutamate synthase activity, glutamic oxaloacetic transaminase activity, soluble protein content, and amino acid content all increased. Transcriptome analysis revealed that there were 7542 upregulated genes and 10449 downregulated genes for DPC vs. CK. GO and KEGG analyses showed that differentially expressed genes were mainly involved in biological processes, such as amino acid metabolism and carbon metabolism. Genes coding 6-phosphofructokinase, pyruvate kinase, glutamic pyruvate transaminase, pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase, glutamate synthase, 1-pyrroline-5-carboxylate dehydrogenase, glutamic oxaloacetic transaminase, amino-acid N-acetyltransferase, and acetylornithine deacetylase were all significantly upregulated. DPC increased pyruvate, α-ketoglutarate, and oxaloacetate by increasing the operating rate of the glycolytic pathway, the citric acid cycle. It also significantly up-regulated the genes encoding glutamate synthase and pyrrolidine-5-carboxylic acid dehydrogenase, and down-regulated the genes encoding glutamine synthetase as well as up-regulated the genes encoding glutamate oxaloacetate transaminase and N-acetylglutamate synthetase. Therefore, the synthesis ability of aspartic acid, glutamic acid, pyruvate, and arginine was increased by DPC, and then Cry1Ac protein contents were increased by regulating carbon and amino acid metabolism.
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