Integration of physiology, transcriptome and metabolome revealed the molecular mechanism of MYB genes involved in coloring of bud sport Zanthoxylum bungeanum

Bud sport is a natural phenomenon that provides valuable germplasm resources for crops. In this study, we report the first discovery of a bud sport material in Chinese pepper ( Zanthoxylum bungeanum ) found in the wild. We compared the physiological indicators of three above-ground tissues (buds, leaves, and stems) of two variants, designated ‘Green branch’ (the typical phenotype, serving as the control) and ‘Red branch’ (the bud-sport mutant). Additionally, we analyzed transcriptome and metabolome data to evaluate the factors influencing bud development, including changes in pigments and crucial pathways in the mutant. The results of the physiological analyses indicated that the red phenotype of the mutant was primarily attributable to anthocyanin accumulation. RNA sequencing revealed that the three organs of the mutant were enriched in flavonoid synthesis and metabolism, with significant enrichment of genes involved in the anthocyanin biosynthetic pathway. Metabolome analysis indicated that cyanidin-like anthocyanins were chiefly responsible for the red phenotype of the mutant. Using weighted gene co-expression network analysis (WGCNA), we identified four MYB transcription factor family genes— ZbDIV1 , ZbMBS1 , ZbMYB116 , and ZbMYB12 —demonstrating significantly elevated expression levels in the mutant compared to the control group. These findings demonstrate that the functions of anthocyanin synthesis-related marker genes in Z. bungeanum are relatively conserved and are regulated by MYB family members. This research contributes significantly to the existing germplasm resources of Chinese pepper, enhancing the diversity and potential for future studies. Furthermore, it establishes a crucial theoretical framework that can be utilized in subsequent investigations focused on pigmentation within this species. • Bud sport Chinese pepper is redder than wild type. • Cyanidin compounds play a significant role in the pigment accumulation of bud sport Chinese pepper. • ZbMYB12 , ZbMBS1 , ZbDIV1 , ZbMYB116 are associated with the regulation of anthocyanin accumulation in Chinese pepper.