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

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

The purpose of this study was to investigate the use of sequencing technology and in silico polymorphism analysis to increase the efficiency of development of polymorphic SSR markers in papaya. We performed whole-genome re-sequencing on two commercial cultivars of papaya, 'Sunrise Solo' (Hawaiian cultivar) and 'RB2' (Australian cultivar), to identify a range of polymorphic sites to facilitate marker-assisted breeding programs for improving fruit quality traits.
In total, 30.2 Gb and 32.4 Gb of genome sequence data were generated using Illumina Hiseq 4000 sequencing technology for 'Sunrise Solo' and 'RB2', respectively. This represented approximately a 80-85x 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 mapped to the papaya reference genome. The initially assembled genomes were compared and analysed for putative polymorphic SSR loci. At the same time, marker-containing coding sequences (CDS) were assigned to gene ontology (GO) terms for providing a set of polymorphic markers putatively associated with functional genes. There were 1,127 polymorphic SSR-containing sequences discovered, of which 478 were associated with GO term. We selected 50 SSRs loci to be assessed for ability to amplify on 'Sunrise Solo' and 'RB2' genotypes. The result showed 100% amplification and 76% yield polymorphic amplicons of predicted sizes.
By combining whole genome sequencing, functional annotation and in silico polymorphism analysis, this study significantly increased the efficiency of polymorphic marker development for the target genotypes. The novel polymorphic SSR loci will be applied to the future mapping of QTL harbouring desirable traits, potential candidate gene identification and subsequent marker-assisted breeding strategies using these genotypes. The data will be useful for future genetic analysis, mapping and functional genomics studies in papaya.

Usana Nantawan won an ISHS student award for the best oral presentation at the I International Symposium on Tropical Plant Genomes in Australia in November 2016.

Usana Nantawan, School of Natural Sciences, Griffith University, Nathan, Australia, and Environmental Futures Research Institute, Griffith University, Gold Coast, Australia, e-mail: mai.nantawan@griffithuni.edu.au

The full article is available in Chronica Horticulturae

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