Background: The 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. Results: For 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. Conclusions: This 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.

A major challenge to the papaya industry is inconsistency in fruit quality and, in particular, flavour, which is a complex trait that comprises taste perception in the mouth (sweetness, acidity, or bitterness) and aroma produced by several volatile compounds. Current commercial varieties vary greatly in their taste, likely due to historical prioritised selection for fruit appearance as well as large environmental effects. Therefore, it is important to better understand the genetic and biochemical mechanisms and biosynthesis pathways underpinning preferable flavour in order to select and breed for better tasting new commercial papaya varieties. As an initial step, objectively measurable standards of the compound profiles that provide papaya’s taste and aroma, together with ‘mouth feel’, are required. This review presents an overview of the approaches to characterise the flavour profiles of papaya through sugar component determination, volatile compound detection, sensory panel testing, as well as genomics-based studies to identify the papaya flavour.

Inconsistency in flavour is one of the major challenges to the Australian papaya industry. However, objectively measurable standards of the compound profiles that provide preferable taste and aroma, together with consumer acceptability, have not been set. In this study, three red-flesh papayas (i.e., ‘RB1’, ‘RB4’, and ‘Skybury’) and two yellow-flesh papayas (i.e., ‘1B’ and ‘H13’) were presented to a trained sensory panel and a consumer panel to assess sensory profiles and liking. The papaya samples were also examined for sugar components, total soluble solids, and 14 selected volatile compounds. Additionally, the expression patterns of 10 genes related to sweetness and volatile metabolism were assessed. In general, red papaya varieties had higher sugar content and tasted sweeter than yellow varieties, while yellow varieties had higher concentrations of citrus floral aroma volatiles and higher aroma intensity. Higher concentrations of glucose, linalool oxide, and terpinolene were significantly associated with decreased consumer liking. Significant differences were observed in the expression profiles of all the genes assessed among the selected papaya varieties. Of these, cpGPT2 and cpBGLU31 were positively correlated to glucose production and were expressed significantly higher in ‘1B’ than in ‘RB1’ or ‘Skybury’. These findings will assist in the strategic selective breeding for papaya to better match consumer and, hence, market demand.

Knowledge of the heritability, genetic advance, and stability of key traits, such as the height to the first fruit, trunk circumference, number of marketable fruit, wasted fruit, fruit weight, fruit width, fruit length, flesh thickness, cavity width, cavity length, and soluble solid contents, is required. These were determined in ten advanced generation red papaya recombinant inbred lines (RIL; F5 generation). The F5 RIL were grown in four field sites, two each within two distinct agroecological climates: the Tablelands and Coastal regions. At each site, biological replicates (trees) of each RIL and the industry-standard red papaya cultivar, RB1, were grown. Agronomic traits and fruit-specific traits were assessed at five and 10 months, respectively, after seedling transplantation to the field. Height to first fruit, trunk circumference, fruit weight, and soluble solid contents were highly heritable and stable at all field sites (h²_b.s, 0.7–0.9) with genetic gains of almost 18% observed for height to first fruit and fruit weight. Across all sites, the trunks of the F5 lines were 37% wider, the trees set fruit 47% closer to the ground and had 20% more marketable fruit with 33% smaller fruit cavity widths, and their fruit was 11% heavier and 12% sweeter than RB1.

Tomato (Solanum lycopersicum L.) production faces major yield loss due to biotic stresses. Developing genetically resistant cultivars presents a sustainable alternative to chemical controls, which are often costly and ineffective. This study utilized 10 molecular markers, including SSR, SCAR, and CAPS markers, to assess resistance to six major diseases, including Fusarium wilt, late blight, bacterial wilt, root-knot nematode, Tomato Mosaic Virus (ToMV), and Tomato Yellow Leaf Curl Virus (TYLCV), across 964 tomato accessions comprising both wild germplasm (371) and cultivars (593). Wild germplasm, especially S. peruvianum, showed the highest frequencies of resistance loci. Markers linked to TYLCV and Fusarium wilt were particularly prevalent, with frequencies of 31.8% (TY-1/3_K), 34.0% (P1-16), and 55.8% (I2(OH)). Several wild accessions carried up to six resistance loci, highlighting the potential for gene pyramiding and the utility of wild species as reservoirs of multi-locus resistance. In contrast, resistance loci were limited in S. lycopersicum. Two S. lycopersicum germplasm collections were screened: a geographically representative collection from four Southeast Asian national genebanks and a genetically representative core collection from global public genebanks. The highest resistance frequencies in S. lycopersicum were observed for bacterial wilt-associated markers SLM12-2 and SLM12-10. However, the overall scarcity of resistance alleles in S. lycopersicum emphasizes the need for further introgression of resistance genes from wild relatives. This study provides valuable genetic insights into tomato germplasm for combating biotic stress, forming a foundation for sustainable breeding strategies to enhance disease resistance and safeguard global tomato production.