Development of polymorphic simple sequence repeat (SSR) markers from genome re-sequencing of Carica papaya L. 'Sunrise Solo' and 'RB2' for marker-assisted breeding

Carica papaya L. is one of the top five tropical fruit crops grown worldwide and an important fruit crop in Australia. Expansion of the papaya industry in Australia is reliant on improved fruit qualities, together with consistent productivity. Although marker-assisted breeding has resulted in substantial genetic gains in other species, this approach in papaya is hampered not only by the subjective nature of many of the desirable target fruit quality traits but also by the dearth of polymorphic markers available, in part due to the narrow genetic base within the cultivated genome. To identify a range of polymorphic sites for marker development and subsequent mapping, we performed whole-genome re-sequencing on two commercial cultivars of papaya, 'Sunrise Solo' (Hawaiian cultivar) and 'RB2' (Australian cultivar), and developed highly polymorphic SSR markers. In total, 30.2 and 32.4 Gb of genome sequence data were generated using Illumina Hiseq 4000 sequencing technology for 'Sunrise Solo' and 'RB2', respectively. These data represented approximately 80-85× coverage of the papaya genome, which is estimated to be 372 Mb. Subsequently, 236 Mb of 'Sunrise Solo' and 239 Mb of 'RB2' unique sequences were anchored to the papaya reference genome (https://genomevolution.org/). The initially assembled genomes were compared and analysed for putative polymorphic microsatellite motifs. Microsatellite-containing coding sequences (CDS) were assigned to gene ontology (GO) terms for providing a set of polymorphic markers putatively associated with functional genes. Fifty of the selected microsatellites, with a broad range of putative function, revealed polymorphism as SSR markers on 'Sunrise Solo' and 'RB2' genotypes.