Unraveling the Genetic Control of Pigment Accumulation in Physalis Fruits.

and , members of the Physalis genus, are valued for their delicious and medicinal fruits as well as their different ripened fruit colors-golden for and scarlet for . This study aimed to elucidate the pigment composition and genetic mechanisms during fruit maturation in these species. Fruit samples were collected at four development stages, analyzed using spectrophotometry and high-performance liquid chromatography (HPLC), and complemented with transcriptome sequencing to assess gene expression related to pigment biosynthesis. β-carotene was identified as the dominant pigment in , contrasting with , which contained both lycopene and β-carotene. The carotenoid biosynthesis pathway was central to fruit pigmentation in both species. Key genes and in , and , , and in were associated with carotenoid production. Notably, the MYB-related and bHLH transcription factors (TFs) regulated zeta-carotene isomerase and β-hydroxylase activities in with the MYB-related TF showing dual regulatory roles. In , six TF families-bHLH, HSF, WRKY, M-type MADS, AP2, and NAC-were implicated in controlling carotenoid synthesis enzymes. Our findings highlight the intricate regulatory network governing pigmentation and provide insights into Physalis germplasm's genetic improvement and conservation.