Hot pepper (Capsicum annuum L.) is one of the most important vegetable crops in China, but floods bring substantial decreases in production over the past several decades. In order to investigate the mechanisms of waterlogging resistance in mutant hot pepper, we measured the agronomic traits of mutant and wild-type, as well as the activities of root antioxidant enzymes and the contents of osmotic regulation substance. At the same time, we did transcriptome sequencing on the plant roots, and screened for differentially expressed genes between mut...