Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin

Abstract

Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the ‘Kyoho’ grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the ‘Kyoho’ berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the ‘Kyoho’ berry.

Transcriptome analysis reveals mechanism of early ripening in Kyoho grape with hydrogen peroxide treatment

“…The other four pathways (spliceosome, mRNA surveillance pathway, glycolysis/gluconeogenesis, and flavone and flavonol biosynthesis) were associated with cluster 5. Notably, the GO terms pigment binding and chlorophyll binding and the KEGG pathways photosynthesis-antenna proteins, photosynthesis, and oxidative phosphorylation are consistent with previous results [22]. Therefore, the genes associated with these GO terms and KEGG pathways were the focus of further analysis.…”

“…In this study, the exogenous H 2 O 2 treatment was equivalent to exogenous stress in the Kyoho grape berry and therefore affected the expression of HSP genes, which resulted in the berry ripening. In a previous study, riboflavin treatment affected the expression of HSP genes [22]. On the basis of that study, in this study, five DEGs were selected that were associated with HSPs: ATHSP22 (VIT_18s0089g01270), VIT_208s0058g00210 (VIT_08s0058g00210), HSP23 (VIT_16s0022g00510, VIT_02s0154g00480), and HSP21 (VIT_01s0010g02290).…”

“…By contrast, the overexpression of HSP genes can alleviate damage caused by abiotic stresses in Arabidopsis and rice, thereby delaying senescence [74,75]. Previous results also indicate that exogenous ROS treatment can promote the early ripening of berries by affecting the expression HSP genes [10,22]. However, the relationship between HSPs genes and berries ripening is unclear at present.…”

“…In this study, some hub genes were selected from the highest K ME values of each significantly different module. Based on the results of a previous study [22], the focus was on the hub genes GDSL (GDSL esterase/lipase, VIT_05s0077g00870) and XTH30 (xyloglucan endotransglucosylase/hydrolase protein 30, VIT_ 02s0012g02220). Figure 7 shows that GDSL and XTH30 included 17 and 11 edges, respectively, and all gene annotations are shown Supplemental Table S3.…”

Construction of a High-Density Genetic Map and Mapping of Firmness in Grapes (Vitis vinifera L.) Based on Whole-Genome Resequencing

“…Glucanase is one of the key cell wall hydrolytic enzymes, which can promote the random hydrolysis of β-1,4-glycosidic bonds to cleave cellulose into smaller fragments and loosen the cell wall [83]. Moreover, increased gene expression of glucanase has been associated with fruit ripening in bananas, pears, strawberries, and grapes [84][85][86][87][88]. The plant hormone, abscisic acid (ABA), plays a crucial role in fruit ripening and responses to environmental stresses [89].…”