An MYB transcription factor regulates capsaicinoid biosynthesis during pepper fruit ripening

Pepper is a fruit, vegetable, and spice crop and is widely cultivated around the world. This study analyzed the transcriptomes and metabolomes of pepper fruits at six different developmental stages to analyze the changes in metabolites and genes during fruit development and further explore and elucidate the functions of the key transcription factors regulating capsaicinoid biosynthesis. A total of 1775 differential metabolites were identified between adjacent developmental stages. These metabolites were mainly amino acids and derivatives, flavonoids, alkaloids, and phenolic acids. The transcriptome analysis revealed 15,741 differential genes between adjacent developmental stages. The functional enrichment analysis indicated that the S3–S4 stage was related to capsaicinoid accumulation, while the S5–S6 stage was associated with fruit color change. CcMYB4 was identified and the transient silencing and overexpression analyses showed that CcMYB4 could regulate the expression of capsaicinoid biosynthetic structural genes and capsaicinoid accumulation. The yeast one-hybrid, electrophoretic mobility shift assays, and dual luciferase demonstrated that CcMYB4 could bind to the Cc4CL promoter and inhibit its expression, thereby regulating capsaicinoid accumulation. Our study investigates the entire developmental process of pepper fruits and identifies CcMYB4 as the regulator of capsaicinoid biosynthesis. The results from this study improve understanding about the molecular regulatory mechanisms associated with pepper fruit development and capsaicinoid biosynthesis.