Molecular marker-assisted papaya sex determination for improved grower efficiency

The Australian market clearly distinguishes between types of papaya according to flesh colour, which may be yellow or red, and consumers have a distinct preference for fruit shape associated with flesh colour. There are two major preferences 1) round fruit, which are females, with yellow flesh and 2) oblong fruit, which are hermaphrodites, with red flesh. DNA-based markers have been developed to clearly identify the sex of papaya and these may be applied for selection at the early growth/seedling stage. In total, 10 primer pairs from the literature that were reported to amplify loci linked to the sex-related alleles of papaya were assessed. These were screened across bulked DNA of a set of 40 trees of defined sex, representative of female, male and hermaphrodite trees of four cultivars of commercial Australian papaya (1B, RB1, RB2 and RB4). Markers were then blind tested on individuals to determine their accuracy for sex selection. Of these, two primer sets, SCARps and SCAR SDSP, clearly discriminated female and male/hermaphrodite trees. These were subsequently validated on an entire breeding population comprising 2,000 seedlings and were demonstrated to be 100% accurate for sex prediction. The same markers were optimised within a high-throughput extraction and PCR screening bioassay to enable the sex determination of a minimum of 96 individuals within two hours. Therefore, these markers have been validated and are now being applied as a strategy to decrease resource wastage and improve on-farm efficiency within the northern Australian papaya industry.