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

Abstract

Background In a previous study, the early ripening of Kyoho grape following H2O2 treatment was explored at the physiological level, but the mechanism by which H2O2 promotes ripening at the molecular level is unclear. To reveal the molecular mechanism, RNA-sequencing analysis was conducted on the different developmental stages of Kyoho berry treated with H2O2. Results In the comparison of treatment and control groups, 406 genes were up-regulated and 683 were down-regulated. Time course sequencing (TCseq) analysis showed that the expression patterns of most of the genes were similar between the treatment and control, except for some genes related to chlorophyll binding and photosynthesis. Differential expression analysis and the weighted gene co-expression network were used to screen significantly differentially expressed genes and hub genes associated with oxidative stress (heat shock protein, HSP), cell wall deacetylation (GDSL esterase/lipase, GDSL), cell wall degradation (xyloglucan endotransglucosylase/ hydrolase, XTH), and photosynthesis (chlorophyll a-b binding protein, CAB1). Gene expression was verified with RT-qPCR, and the results were largely consistent with those of RNA sequencing. Conclusions The RNA-sequencing analysis indicated that H2O2 treatment promoted the early ripening of Kyoho berry by affecting the expression levels of HSP, GDSL, XTH, and CAB1 and- photosynthesis- pathways.

The application of ozonated water rearranges the Vitis vinifera L. leaf and berry transcriptomes eliciting defence and antioxidant responses

“…In fact, the endogenous ripening related ROS production does not result in the cell wall and growth inhibition, as this production is suspected to occur just before or at the inception of the second fruit growth phase. Indeed, recent physiological and transcriptomic works evidenced that the less harmful hydrogen peroxide (H 2 O 2 ) accelerated ripening in Kyoho variety 31 , 32 . The genes suggested by the authors to induce the early ripening were associated with the oxidative stress, photosynthesis, cell wall deacetylation and degradation.…”

Identification of optimal and novel reference genes for quantitative real‐time polymerase chain reaction analysis in grapevine

“…In this study, six commonly used endogenous reference genes ( Actin , GAPDH , VvEF1‐α , VvEF1‐γ , EF1‐α and Ubiquitin ) were first selected according to previously published reports (Costantini et al 2008, Gamm et al 2011, Szegedi et al 2018). In addition to those genes, three novel genes (named RRM1 , PPR2 and MRE11 ) were screened from our previous RNA‐sequencing data (Guo et al 2016, 2019a,b, 2020, Wang et al 2019c), in which we demonstrated stable expression patterns in grape berry at different developmental stages and under H 2 O 2 , riboflavin and 5‐azaC treatments (Figure 1). Based on the annotations and references, these three genes have unknown functions in grapevine with RRM1 encoding heterogeneous nuclear ribonucleoprotein, PPR2 encoding pentatricopeptide repeat‐containing protein and MRE11 encoding double‐strand break repair protein (Table 1).…”

“…In brief, the nine berry developmental stages followed the modified Eichhorn and Lorenz developmental scale (Coombe 1995) from 19 May to 13 August in 2013. The treatments of H 2 O 2 , riboflavin and 5‐azaC (5‐azacytidine) were conducted on Kyoho berries according to the previous studies (Guo et al 2019a,b, 2020, Wang et al 2019c). A volume of 20 mL H 2 O 2 solution (300 mmol/L) was sprayed evenly on each berry bunch twice (25 and 35 days post‐anthesis).…”

“…The RNA‐sequencing (RNA‐seq) data of Kyoho untreated berries and berries treated with H 2 O 2 , riboflavin and 5‐azaC were adopted from our previously published work (Guo et al 2016, 2019a,b, 2020, Wang et al 2019c). Additionally, eight published RNA‐seq datasets were downloaded from the GEO database in NCBI (https://www.ncbi.nlm.nih.gov/), with the accession numbers GSE62744, GSE62745, GSE98873, GSE121146, GSE129916, GSE150343, GSE157347 and GSE82317.…”

The Application of Ozonated Water Rearranges the Transcriptome of the Vitis Vinifera L. Fruit

“…In fact, the endogenous ripening related ROS production does not result in the cell wall and growth inhibition, as this production is suspected to occur just before or at the inception of the second fruit growth phase. Indeed, recent physiological and transcriptomic works evidenced that the less harmful hydrogen peroxide (H 2 O 2 ) accelerated ripening in Kyoho variety 29,30 . The genes suggested by the authors to induce the early ripening were associated with the oxidative stress, photosynthesis, cell wall deacetylation and degradation.…”