Transcriptome analysis of blood orange (Citrus sinensis) following fruit bagging treatment by digital gene expression profiling

Abstract

SummaryBagging has been widely used in fruit crops to improve fruit quality. In this study, the internal qualities of blood orange (Citrus sinensis cv. ‘Tarocco’ ) fruit were significantly affected by bagging treatment. Total flavonoid (TFL) and total anthocyanin (TAN) concentrations increased, while total soluble solids (TSS), total phenolics (TPH), and ascorbic acid (AsA) concentrations and titratable acidity (TA) decreased in response to bagging treatment. To elucidate the molecular mode of action of bagging on fruit, high-throughput tag-sequencing (Tag-seq) analysis was used to analyse gene expression profiles in blood orange fruit in response to a bagging treatment. Over 21 × 106 total clean reads were obtained per library. Approx. 53.7 – 71.7% and 3.1 – 6.4% of the clean reads were mapped onto citrus genes or intergenic regions, respectively. However, approx. 25.2 – 39.9% of the clean reads failed to align with the citrus genome. Overall, bagging treatment resulted in an increase in transcripts involved in a range of metabolic pathways such as hormone synthesis and signalling, transcriptional regulation processes, the tricarboxylic acid (TCA) cycle, sucrose and starch metabolism, ascorbate metabolism, and the phenylpropanoid pathway, many of which are related to fruit quality. Analysis of the differentially expressed genes revealed that decreased TSS concentrations, TA, and AsA concentrations could mainly be attributed to the increased expression of genes involved in catabolic pathways, rather than in anabolic pathways. Competition for limited amounts of substrates for the flavonoid, phenolics, and anthocyanin pathways may have led to an increase in TAN and TFL concentrations, and a decrease in TPH concentration. In addition, our results showed that bagging treatment imposed a variety of stresses on fruit, thereby leading to an array of biochemical, physiological, and molecular changes. One gene (bHLH) that may be involved in anthocyanin biosynthesis in blood orange fruit has been identified and is discussed. These results reveal the extensive biochemical and genetic mechanisms operating in citrus fruit in response to a bagging treatment.