Transcriptome Analysis Reveals Key Pathways and Genes Involved in Lodging Resistance of Upland Cotton

Lodging resistance is one of the most important traits of machine-picked cotton. Lodging directly affects the cotton yield, quality and mechanical harvesting effect. However, there are only a few reports on the lodging resistance of cotton. In this study, the morphological and physiological characteristics and transcriptome of two upland cotton varieties with different lodging resistance were compared. The results showed that the stem strength; the contents of lignin, soluble sugar and cellulose; and the activities of several lignin biosynthesis-related enzymes of the lodging-resistant variety M153 were significantly higher than those of the lodging-susceptible variety M5330. Transcriptomic analysis showed that the expression level of several genes related to lignin, cellulose, starch and sucrose synthesis, and photosynthesis were significantly up-regulated in the lodging-resistant variety M153, which was consistent with the content determination results of lignin, cellulose and soluble sugar. Silencing two lignin biosynthesis-related genes (<i>GhPAL</i> and <i>Gh4CL</i>) in cotton via VIGS (Virus-Induced Gene Silencing) resulted in reduced lignin content and decreased lodging resistance in cotton. These results suggested that lignin, cellulose and soluble sugar contents were positively correlated with the lodging resistance of cotton, and lignin, cellulose and soluble sugar biosynthesis-related genes can be used as potential targets for improving the lodging resistance of cotton. These findings provide a theoretical basis for the cultivation of cotton varieties with strong lodging resistance in the future.