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Transcriptome analysis of grapevine under salinity and identification of key genes responsible for salt tolerance

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Abstract

The negative effects of soil salinity towards grape yield depend upon salt concentration, cultivar type, developmental stage, and rootstock. Thompson Seedless variety of grape plant is considered moderately sensitive to salinity when grown upon its own root stock. In recent epoch, identification of key genes responsive to salinity offers hope to generate salinity-tolerant crop plants by their overexpression through genetic manipulation. In the present report, salt responsive transcriptome analysis of Thompson Seedless grape variety was done to identify vital genes involved in salinity tolerance which could be used further to generate salt liberal grape plant or other crop plants. Transcriptome libraries for control and 150-mM-NaCl-treated grape leaves were sequenced on Illumina platform where 714 genes were found to be differentially expressed. Gene ontology analysis indicated that under salinity conditions, the genes involved in metabolic process were highly enriched. Keto Encyclopedia of Genes and Genomes analysis revealed that, among the top 22 enriched pathways for the salt stress upregulated genes, the carbohydrate metabolism, signal transduction, energy metabolism, amino acid metabolism, biosynthesis of secondary metabolite, and lipid metabolism pathways possessed the largest number of transcripts. Key salinity-induced genes were selected and validated through qRT-PCR analysis which was comparable to RNA-seq results. Real-time PCR analysis also revealed that after 24 days of salinity, the expression of most of the selected key genes was highest. These salinity-induced genes will be characterized further in a model plant and also in Vitis vinifera through transgenic approach to disclose their role towards salt tolerance.

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Acknowledgements

Facilities and co-operation from the laboratory staff at Madhyamgram Experimental Farm of the Institute are acknowledged.

Funding

This work was supported by Science and Engineering Research Board Young Scientist Scheme (SERB Grant No. - YSS/2015/001872) award received by PD.

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Authors and Affiliations

  1. Division of Plant Biology, Bose Institute, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India

    Priyanka Das & Arun Lahiri Majumder

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  1. Priyanka Das
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  2. Arun Lahiri Majumder
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Correspondence to Priyanka Das or Arun Lahiri Majumder.

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Fig. S1

Library profile of Thompson Seedless (TS) grapevine samples on agilent DNA HS Chip. (a) Library profile of TS-C samples. . (b) Library profile of TS-S samples. (PNG 1457 kb)

High Resolution image (TIF 3140 kb)

Fig. S2

GO enrichment analysis of different functional processes. (a) Enriched GO graph for biological process. (b) Enriched GO graph for molecular function. (c) Enriched GO graph for Cellular Component. Each Enriched Graph shows the GO graph of the significant terms with a node-coloring which is proportional to the significance value (p-value). This type of graphical representations helps to understand the biological context of the functional differences and to find pseudo-redundancies in the parent-child relationships of significant GO term. A node filter value of 0.05 for p-value was chosen. GO-Terms with a value higher than the given filter were not shown. The red boxes represent overrepresented and green boxes under-represented GO terms. The shades vary corresponding to the p-value where a lower p-value has a darker shade. (PNG 1091 kb)

High Resolution image (TIF 1764 kb)

Fig. S3

Expression pattern of randomly selected salinity mediated down-regulated genes in WT and salinity treated grapevine by RNA-seq and qRT-PCR. Expression pattern of selected salinity responsive (down regulated) genes through qRT-PCR after 24 h, 7 d and 24 d of salt (150 mM NaCl) treatment. The data are means ±SD from three independent replicates, and ‘*’ indicates statistical significance between WT and salinity treated samples (P < 0.05). (PNG 347 kb)

High Resolution image (TIF 993 kb)

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Das, P., Majumder, A.L. Transcriptome analysis of grapevine under salinity and identification of key genes responsible for salt tolerance. Funct Integr Genomics 19, 61–73 (2019). https://doi.org/10.1007/s10142-018-0628-6

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  • DOI: https://doi.org/10.1007/s10142-018-0628-6

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