title: Developing biochemical and sensory profiles for the major Australian commercial papaya (Carica papaya L.) varieties
Creators: name: Zhou, Ziwei
Publisher: name: Griffith University
Year: 2023
Subjects: subject: papaya breeding
subject: flavour profiling
subject: biosynthesis pathways
subject: gene identification

description: One of the major challenges to expanding the Australian papaya industry is inconsistency in fruit flavour. Commercial papaya varieties grown in Australia vary greatly in taste and aroma. The industry to date has not purposefully incorporated consumer preferences. Meanwhile, through prior profiling, there are several ‘off tastes’ present in current varieties that exclude a proportion of the population as papaya consumers. Therefore, to drive preferred flavour as a key breeding objective, a better understanding of the genetic mechanisms and biosynthetic pathways underpinning preferred flavours was undertaken. In this thesis, the flavour profiles of commercial papaya varieties ‘RB1’, ‘1B’, ‘H13’, ‘RB4’ and ‘Skybury’ were characterized through sensory panel testing and consumer preference surveying. Subsequently, the diversity of type and concentration of volatile compounds among the varieties was assessed along with sugar components, their concentrations and the sweetness levels (total soluble solid measured in ºBrix). In general, red papaya varieties (‘RB1’, ‘RB4’ and ‘Skybury’) had higher sugar content and tasted sweeter than yellow varieties (‘1B’ and ‘H13’), 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. A multiple linear regression model was generated to establish a consumer liking score using data of percentage of total glucose, as well as the concentrations of the discriminant volatiles linalool oxide and terpinolene. In addition, to uncover a suite of genes related to the consumer preferred flavours, whole RNA sequencing was performed from ripe and unripe fruit samples of extreme flavoured papaya varieties ‘RB1’ (red-fleshed with sweet flavour and floral aroma) and ‘1B’ (yellow-fleshed with bitter flavour and musty aroma). This generated 3.67×108 high-quality clean reads with an average length of 87 bp, which were deposited in the GEO database at the National Center for Biotechnology Information (accession number: GSE213436, September 2022). The reads were then used to de novo assemble the papaya fruit transcriptome. In total, 180,368 transcripts were generated, and 118 transcripts related to flavours were differentially expressed between the two varieties at the ripe stage. Five candidate genes associated with sugar metabolism (cpBGLU42, cpBGLU31, cpBGH3B, cpPFP and cpSUS) and three with volatile biosynthesis (cpGES, cpLIS and cpBAO) were validated through reverse transcription quantitative real-time PCR. Five of these were significantly differentially expressed between ‘RB1’ and ‘1B’ at ripe stage. These genes are proposed to be major metabolic switches in sugar transport, sucrose metabolism and aromatic compound production pathways. Furthermore, a novel Nanostring nCounter system was applied to study differential expression of flavour related gene sequences. This cutting-edge technology was used to assess for differential expressions of a panel of flavour-associated papaya genome sequences among multiple commercial and newly developed Australian advanced breeding lines, to identify potential future selective breeding targets. The replicated differential RNA profiling was performed on varieties ‘RB1’, ‘1B’, ‘H13’, ‘Skybury’, ‘Sunshine’ and ‘Holland’ using a custom designed NanoString Elements Tagset of eight flavour-associated sequences identified from the previous RNA-sequencing and qPCR studies. Also included were three reference sequences previously validated as stably expressed among papaya genotypes, growing seasons and tissue types. The expression of two genes, cpSUS and cpLIS, was lower than the detection threshold of Nanostring with the expression of the remaining six candidate genes mostly consistent between Nanostring and qPCR. This illustrated that Nanostring is a potential high-throughput alternative to qPCR for papaya sequence expression studies. Further research should focus on investigating the target genes for use in future selective breeding strategies through assessment in broader germplasm and growth environments.