Fruit Quality in Red Raspberry

Red raspberry (Rubus ideaeus) is a rich source of nutrition and has established health benefits. Greater consumer interest in fruit and promotions for healthier lifestyles and diets, with the increased availability of affordable and appealing fresh fruit, such as raspberry is one route to achieving a healthier diet.  To increase consumption there is a drive to improve consistency in taste, appearance, appropriate firmness and shelf life of fruit. Most high value fruit quality traits however involve complex quantitative loci that require many different genes to control desired qualities. We are interested in the identification of molecular markers linked to fruit quality in red raspberry.

American cv. Latham has sweet, aromatic, late-cropping, small and firm berries which are glossy and of mid- to dark red colour. The Scottish cv. Glen Moy has a slightly sweet, early, large conical fleshy, dull pale-mid red fruit of aromatic character. Over the past few years a ‘Latham’ x ‘Glen Moy’ segregating population has been used extensively to identify quantitative loci linked to essential quality traits in raspberry fruit. Markers linked to fruit ripening, colour, anthocyanin, volatiles, sugars, acids and flavour components have been mapped to genetic linkage groups. In addition, BAC and cDNA cloning have identified, in some cases, strong candidate genes linked to biochemical pathways with roles in fruit development.

We recently utilised next generation 454 & Illumina sequencing to generate the transcribed genomes of white/red and red fruit from the Glen Moy and Latham parental lines. Combined with Sanger EST sequencing, a total of 56,000 unigenes were assembled. Spatial and temporal expression of genes has a large effect on downstream biochemical pathways and ultimately traits. To take advantage of the increase in raspberry sequence information a custom Agilent microarray was developed representing the unigene sequences and microarray analysis was performed through five fruit developmental stages of both parental lines.  Many genes showed temporal- and genotype-specific gene expression patterns. Gene sequence lists and the microarray data were mined to identify known cell wall hydrolases and enzymes potentially involved in fruit softening which were validated by real-time RT-qPCR. Some genes (aquaporin and pectin methyl esterase) show a steady rate of decline during ripening while others (polygalacturonase, xylan hydrolase, SAMDC) significantly show highest transcriptional levels in red fruit. Some significant variation in the pattern of transcription between fruit stages was found for these selected genes, and there was evidence of a coordinated expression between several of the candidate genes during fruit development and ripening.

SNP markers have been identified in the fruit softening candidate genes and we are investigating their link to variation in fruit softening between Glen Moy and Latham in the segregating population. Exploitation of a full raspberry genomic sequence will allow full gene structures to be established for raspberry fruit genes and allow us to move towards technologies that utilise multiple markers to investigate varietal and wild race variation for complex traits.