Investigation of the molecular response of grapevine to salt stress through transcriptomics and proteomics approaches

Abstract

Grape (Vitis vinifera L.) is a perennial woody vine cultivated across the world mainly for wine production and for consumption of fresh grapes or processed raisins. Rising soil salinity is a growing concern in irrigated agricultural systems including viticulture industry. The accumulation of salts near the root zone severely hampers plant growth, leading to a decrease in the productive lifespan of grapevine and causing heavy yield losses to the farmer. Thompson Seedless, a commonly grown table grape variety in India, is sensitive to salinity when grown on its own roots. Therefore, it is frequently grafted onto salinity-tolerant wild grapevine rootstocks. In the present study, we investigated the differences in response to salinity between own-rooted Thompson Seedless (TSOR) and 110R-grafted Thompson Seedless (TS110R) grapevines, wherein 110R is reported to be a salt-tolerant rootstock. The grapevines were subjected to salt stress by treating them with a 150 mM NaCl solution. The stress-induced changes in protein and transcript abundance were investigated using label-free shotgun proteomics and RNA Sequencing approaches, respectively across early (6 h), mid (24 h48 h), and late (7 days) stages of salt treatment. A total of 2793 proteins were identified, of which 246 were differentially abundant at various time-points in TSOR and TS110R vines. Similarly, the RNASeq analysis of salt stressed TS110R vines identified differential expression of 509 genes. The proteomic study revealed that several biological processes such as photosynthesis, amino acid metabolism, translation, chlorophyll biosynthesis, and generation of precursor metabolites was significantly affected by salt stress in both the vines but at different stages of stress. While, the transcriptomic study elucidated the temporal differences in the expression of genes involved in hormonal regulation of salt stress in TS110R. The TSOR grapevines displayed diversion of photo assimilates towards oxidative stress tolerance whereas, the TS110R grapevines displayed the upregulation of photo-protection and prevention of oxidative stress. The regulation of salt stress is a systemic process which involves root to shoot and shoot to root signaling of stress. The transporter proteins play a major role in transport of molecules across tissues. The Major Facilitator Superfamily (MFS) is a superfamily of secondary transporters which regulates transport of diverse molecules like sugars, amino-acids, peptides, hormones, vitamins, etc. We identified 213 and 203 MFS Superfamily (MFSS) transporters in Arabidopsis thaliana and V. vinifera genomes, respectively. The phylogenetic study revealed their substrate specific clustering. The reanalyses of expression of these transporter genes in microarray datasets revealed a significant modulation genes encoding sugar porters (SP) and oligopeptide transporters (POT) in response to salt stress. The subcellular localization prediction showed that majority of the SP and POT transporter proteins were plasma membrane localized suggesting the possible transport of sugars and nitrates/peptides from source to sink/ stressed tissues in response to salt stress. Two unknown-MFS-23 (UMF23) family, transporters along with a phosphate and a POT transporter displayed different gene expression patterns in TSOR and TS110R vines indicating the temporal differences in salt stress response of the two vines. Overall, the results revealed that TSOR vines responded fervently to salt stress, while TS110R vines adopted a preventive approach through efficient regulation of carbohydrate and amino-acid metabolism. The MFS Superfamily study further identified the sugar and peptide transporters whose expression was affected by salt stress. The findings of this study add to the knowledge of salinity response in woody and grafted plants and hence open the scope for further studies on salt stress-specific differences induced by grafting. Future prospects • Transcriptomic analysis of salt tolerant 110R rootstock under saline conditions • The salinity tolerance phenotype displayed by upregulation of proteins in TS110R vines needs to be validated through their overexpression in Thompson Seedless grapevines or other plants • Studies on xylem sap of grafted grapevines to identify the molecules responsible for modulation of gene expression in the scion • Prediction of substrates transported by UMF23 transporter