Genomic analysis provides insights into the origin and divergence of fruit flavor and flesh color of pummelo

Summary Pummelo ( Citrus maxima ) is one of the most important citrus crops and have genetically contributed sweet orange, lemon and most citrus cultivars. It has been cultivated for c . 4000 years in China and is also distributed in many Southeast Asian countries. Nevertheless, the origin and dispersal of pummelo remain elusive. We conducted whole‐genome sequencing for 290 pummelo accessions from China and Southeast Asia (SEA). Our findings indicated that pummelo was originated in Yunnan province. The divergence of the China‐SEA accessions occurred c . 2000 years ago and the divergence was likely facilitated through the Maritime Silk Road. We detected the divergence of genomic regions associated with fruit flavor and color, indicating different selection by human activities in different regions. A gene encoding lycopene cyclase 2 (LCYB2) exhibited a high degree of divergence in expression and sequence between red‐flesh and white‐flesh pummelos. A SNP in the coding region of LCYB2 resulted in a reduction in lycopene β‐cyclizing enzyme activity, leading to the accumulation of lycopene and the development of the red‐flesh trait. This study reveals the origin and evolutionary history of pummelo and provides insights into the genomic basis for the divergence of fruit flavor and color.