BackgroundThe identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya.ResultsFor this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding.ConclusionsThis study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.

High sugar content is a valued papaya fruit quality trait that is difficult to select due to a lack of knowledge regarding the major contributing genetic components and the potential for large environmental effects. The initial step towards better understanding this complex trait is to identify the functional genes involved in the sugar synthesis and accumulation pathways. This was achieved in the current study through differential expression analyses of a suit of sweetness-related genes among two phenotypically contrasting papaya cultivars. The major sugar detected in leaf and ripening fruit tissues of two genotypes (120 days after anthesis to colour break 100%) was sucrose, which accounted for 40-60% of the total sugars detected. In general, genotype 'Sunrise Solo' had higher sugar content than genotype 'RB2' in all tissue types assessed. Subsequently, differential expression of 11 genes potentially associated with the main sugar synthesis and accumulation pathways were investigated. Of these, sucrose phosphate synthase (cpSPS1, cpSPS2, cpSPS3 and cpSPS4) and invertase (cpCWINV1and cpAVIN2) gene family members were expressed significantly differently. In all tissue types, cpSPS2 was between 0.5 to 3 times more highly expressed in 'Sunrise Solo' than 'RB2'. The maximum expression of cpSPS2 in 'Sunrise Solo' was observed in mature fruit at 120 days after anthesis, while its expression remained constant in 'RB2'. Similarly, genes cpCWINV1 and cpAVIN2 were significantly more expressed in 'Sunrise Solo' compared to 'RB2' during ripening stages. Further validation and investigation of the expression of these gene sequences for association with the sweetness trait at specific fruit ripening stages and in different environments will aid in their identification as candidate sweetness markers for future selective breeding strategies.

The application of biotechnology to plant breeding includes the development of tools and knowledge to increase accuracy and efficiency for pre-breeding and selection for crop improvement that have multiple advantages over traditional technologies. This chapter provides information on the in vitro culture, genetic transformation, genome project and sequencing technology, gene identification and characterization, genetic linkage maps and identification of quantitative trait loci (QTL), and molecular markers for crop improvement of pawpaws (Carica papaya).

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 varieties of papaya, 'Sunrise Solo' (Hawaiian variety) and 'RB2' (Australian variety), and developed highly polymorphic SSR markers. 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. These data represented approximately a 80-85× coverage of the papaya genome, which is estimated to be 372 Mb. Subsequently, 236 Mb of 'Sunrise Solo' and 239Mb of 'RB2' unique sequences were anchored to the papaya reference genome (https://genomevolution.org/). The initiatlly 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.

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