RNA-seq based transcriptomic analysis of CPPU treated grape berries and emission of volatile compounds

Abstract

Grapevine (Vitis vinifera L.) is considered to be one of the most popular and widespread fruit crops in the world. Numerous value added products are prepared from grape fruit and investments are being made to establish new viticulture region (Hoff et al., 2017; Imran et al., 2017). CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] is a synthetic cytokine-like plant regulator which promotes grape berry set and development. The influence of CPPU [forchlorfenuron N-(2-chloro-4-pyridyl)-N-phenylurea] on berry development of 'Shine Muscat' (Vitis labruscana Bailey×V vinifera L.) grapes was evaluated under field conditions. A concentration response was observed over a range of 0, 5, and 10 mgL^-1 CPPU that was applied to fruitlets (mean diameter 6mm) at 2 weeks after full bloom. Gas-chromatography mass-spectrometry (GC-MS) revealed that volatile compounds such as terpenoids and aromatics; especially linalool, geraniol and benzyl alcohols, were greatly reduced in CPPU-treated grapes. In contrast, aliphatics, such as hexanol, were increased in CPPU-treated berries. RNA sequencing (RNA-Seq) was conducted to identify differentially expressed genes (DEGs) that were induced by CPPU, especially those related to volatile biosynthesis. A total of 494, 1237, and 1085 DEGs were detected in CPPU0-vs-CPPU5, CPPU0-vs-CPPU10, and CPPU5-vs-CPPU10 treatments, respectively. The results were compared against two databases (Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)) to annotate gene descriptions and assign a pathway to each gene. GO covers three domains: biological processes, molecular functions and cellular components. Pathway enrichment annotation demonstrated that highly ranked genes were associated with the fatty acid degradation and biosynthesis, phenylpropanoid metabolism and biosynthesis, carotenoid biosynthesis, and plant hormone signal transduction. Analysis with qRT-PCR of twelve selected transcripts validated the data obtained by RNA-seq. Additionally, we also found that genes such as CCDs (carotenoid cleavage dioxygenase), LOX (lipoxygenase), GGDP reductase (geranylgeranyl diphosphate reductase), PAL (phenylalanine ammonia-lyase) and some hormones related genes, were closely involved in the formation of volatiles compounds in CPPU treated berries. In summary, our results provide the first sequential transcriptomic atlas of CPPU treated grape berries which significantly increases our understanding of volatile metabolites and biosynthesis pathways in grape affected by CPPU.

Keywords: CPPU; GC–MS; Grape; RNA-seq; Volatile compounds.