Transcriptome sequencing analyses reveals mechanisms of eliminated russet by applying GA3 and CPPU on ‘Shine Muscat’ grape

Abstract Russet on grape peel is a physiological disorder that effects grape quality and can be reduced or eliminated by different concentrations of GA 3 (gibberellic acid) + CPPU (N-(2-chloro-4-pyridyl)-N'-phenylurea). We have performed transcriptome and differential transcript expression analyses in ‘Shine Muscat’ grape at fruiting stage using Illumina RNA-seq to elucidate the mechanisms of russet elimination. ‘Shine Muscat’ clusters were treated with 25 mg/L GA 3 (GA) at full-bloom stage and 15 days after the full-bloom stage had a far less rusted appearance (˜5% of total peel) as compared to control treatment (CK) (> 20% of total peel). Approximately all russeted peel was eliminated after treatment with (25 mg/L GA3 + 10 mg/L CPPU) at full-bloom stage and 15 days after full-bloom stage (GA + CPPU). Measurement of enzyme activity indicated the GA + CPPU treatment had the lowest phenylalanine ammonia-lyase (PAL), 4-coumarate (4CL), and peroxidase (POD) enzyme activity. Analyses of three RNA-seq libraries identified 2385 transcripts (1271 up-regulated transcripts and 1114 down-regulated transcripts) with significant expression changes. RNA-seq and qRT-PCR following GA3 and CPPU application identified two putative mechanisms responsible for reducing or eliminating russet at berry pericarp: PAL activity was positively correlated with russet on peel and up-regulation of condition-specific genes expressed in the endoplasmic reticulum and Golgi non-clathrin-coated vesicles genes are potentially involved in the elimination of russet. GA 3 coupled with CPPU can approximately eliminate russet after application of above mentioned treatments.and PAL activity is shown to positively correlated with the elimination of russet. Furthermore, other factors are likely to be involved in the elimination of russet due to up-regulation of condition-specific coatomer subunit beta'-2 like genes.