Abstract:To understand the root response mechanism of Capsicum annuum under continuous cropping obstacles, three types of media, namely substrate soil (CSS), rotation soil (CRS) and continuous cropping soil (CCS), were used to pot the peppers. The root systems were collected when they entered the fruiting period for omics research to analyze the specific components of flavonoids and the information of their synthase genes in the root systems of peppers. The results showed that a total of 31 flavonoids were detected in the root systems of peppers in the three types of media. Compared with CSS, the contents of six flavonoids, namely pelargonidin 3-O-caffeoyl-β- d-glucoside, cyanidin 3-O-glucosides (2 types), delphinidin 3-O-β-d-glucoside, neohesperidin, quercetin 3-O-β-d- glucosyl-β-d-glucoside, were significantly increased in the two cultivation conditions of CRS and CCS, while only one flavonoid, malvidin-3-rutinoside-5-glucoside, was significantly decreased (by 82.37% and 91.29%, respectively). The synthesis of flavonoids involves 202 enzyme genes, among which the families with more genes mainly include cytochrome P450 (15) and UDP glycosyltransferase (14). Compared with CSS, the expression of main synthase genes of these flavonoids in CRS and CCS were significantly different, including 23 flavonoid synthase genes, 3 anthocyanin synthase genes, 7 isoflavone synthase genes, and 5 flavone and flavonol synthase genes. Among them, the expression of UDP glycosyltransferase genes in anthocyanin synthesis metabolism (1) and flavone and flavonol synthesis metabolism (3) were significantly increased on CCS cultivation (by 150.00%, 161.45%, 92.77% and 773.50%, respectively). Therefore, continuous cropping and other adverse stress could significantly increase the content of most flavonoids in the root systems of peppers, and the up and down regulation trends of their synthase genes were not obvious.