Validation of scar markers for early sex determination in papaya (Carica papaya L.) under Sri Lankan conditions

Papaya (Carica papaya L.) is a commercially important tropical fruit crop exhibiting three sex types: male, female and hermaphrodite. Because sex expression cannot be identified morphologically at the seedling stage, excess plants are often maintained until flowering, resulting in inefficient use of land, labour and inputs. This study evaluated the transferability and diagnostic performance of widely used sequence-characterized amplified region (SCAR) markers for early sex identification in a Sri Lankan papaya population. Fifty randomly selected 40–45-day-old seedlings from a controlled hermaphrodite × hermaphrodite (H×H) population were screened using SCAR-W11 and SCAR-T12 markers, with SCAR-T1 used as a positive amplification control. SCAR-W11 and SCAR-T12 amplified a specific ~800 bp fragment in hermaphrodite plants, whereas no amplification was observed in female plants. Morphological assessment at flowering showed complete agreement between molecular marker-based identification and phenotypic sex classification within the evaluated dataset showing complete agreement between molecular and morphological sex identification. These findings indicate that SCAR-W11 and SCAR-T12 are reliable markers for distinguishing hermaphrodite and female papaya seedlings under Sri Lankan conditions and can facilitate more efficient nursery management and breeding programs.