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Functional & Integrative Genomics

, Volume 19, Issue 1, pp 61–73 | Cite as

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

  • Priyanka DasEmail author
  • Arun Lahiri MajumderEmail author
Original Article

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.

Keywords

Grape Transcriptome Salinity RNA-seq Salt-inducible gene 

Notes

Acknowledgements

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

Funding information

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

Supplementary material

10142_2018_628_Fig7_ESM.png (1.4 mb)
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)

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High Resolution image (TIF 3140 kb)
10142_2018_628_Fig8_ESM.png (1.1 mb)
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)

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High Resolution image (TIF 1764 kb)
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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)

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Table S1 (DOCX 15 kb)
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Table S6 (XLS 85 kb)

References

  1. Adaodlu YS, Ergul A, Aras S (2004) Molecular characterization of salt stress in grapevine cultivars (Vitis vinifera L.) and rootstocks. Vitis 43:107–110Google Scholar
  2. Cramer GR (2010) Abiotic stress and plant responses from the whole vine to the genes. Aust J Grape Wine Res 16:86–93CrossRefGoogle Scholar
  3. Cramer GR, Ergul A, Grimplet J et al (2007) Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7:111–134CrossRefGoogle Scholar
  4. Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163CrossRefGoogle Scholar
  5. da Silva FG, Iandolino A, Al-Kayal F, Bohlmann MC, Cushman MA, Lim H, Ergul A, Figueroa R, Kabuloglu EK, Osborne C, Rowe J, Tattersall E, Leslie A, Xu J, Baek J, Cramer GR, Cushman JC, Cook DR (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol 139(2):574–597CrossRefGoogle Scholar
  6. Daldoul S, Guillaumie S, Reustle GM, Krczal G, Ghorbel A, Delrot S, Mliki A, Hofer MU (2010) Isolation and expression analysis of salt induced genes from contrasting grapevine (Vitis vinifera L.) cultivars. Plant Sci 179:489–498CrossRefGoogle Scholar
  7. Daldoul S, Hoefer M, Mliki A (2012) Osmotic stress induces the expression of VvMAP kinase gene in grapevine (Vitis vinifera L.). J Bot.  https://doi.org/10.1155/2012/737035
  8. Dapas M, Kandpal M, Bi Y, Davulur RV (2017) Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. Brief Bioinform 18(2):260–269PubMedGoogle Scholar
  9. Das P, Nutan KK, Singla-Pareek SL, Pareek A (2015a) Oxidative environment and redox homeostasis in plants: dissecting out significant contribution of major cellular organelles. Front Environ Sci 2:70CrossRefGoogle Scholar
  10. Das P, Nutan KK, Singla-Pareek SL, Pareek A (2015b) Understanding salinity responses and adopting ‘omics-based’ approaches to generate salinity tolerant cultivars of rice. Front. Plant Sci 2:1–11Google Scholar
  11. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20:45–58CrossRefGoogle Scholar
  12. Fisarakis IK, Stavrakas D (2001) Response of sultana vines (V. vinifera L.) on six rootstocks to NaCl salinity exposure and recovery. Agric Water Manag 51:13–27CrossRefGoogle Scholar
  13. Gambino G, Perrone I, Gribaudo I (2008) A rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal 19:520–525CrossRefGoogle Scholar
  14. Garg R, Bhattacharjee A, Jain M (2015) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Mol Biol Rep 33:388–400.  https://doi.org/10.1007/s11105-014-0753-x CrossRefGoogle Scholar
  15. Giraud E, Ivanova A, Gordon CS, Whelan J, Considine MJ (2012) Sulphur dioxide evokes a large scale reprogramming of the grape berry transcriptome associated with oxidative signalling and biotic defence responses. Plant Cell Environ 35:405–417CrossRefGoogle Scholar
  16. González-Agüero M, García-Rojas M, Genova AD, Correa J, Maass A, Orellana A, Hinrichsen P (2013) Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data. BMC Genomics 14:499–501CrossRefGoogle Scholar
  17. Goyal E, Amit SK, Singh RS, Mahato AK, Chand S, Kanika K (2016) Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia local. Sci Rep 6:27752CrossRefGoogle Scholar
  18. Henderson SW, Wege S, Qiu J, Blackmore DH, Walker AR, Tyerman SD, Walker RR, Gilliham M (2015) Grapevine and Arabidopsis cation-chloride cotransporters localize to the Golgi and trans-Golgi network and indirectly influence long-distance ion transport and plant salt tolerance. Plant Physiol 169:2215–2229PubMedPubMedCentralGoogle Scholar
  19. Hennig L (2012) Plant gene regulation in response to abiotic stress. Biochim Biophys Acta 1819:85–194CrossRefGoogle Scholar
  20. Hepaksoy S, Ben-Asher J, De Malach Y, David I, Sagih M, Bravdo BA (2006) Grapevine irrigation with saline water: effect of rootstocks on quality and yield of Cabernet Sauvignon. J Plant Nutr 29:783–795CrossRefGoogle Scholar
  21. Huang W, Perez-Garcia P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL et al (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336:75–79CrossRefGoogle Scholar
  22. Ismail AAAM (2013) Grapes for the desert: salt stress signaling in Vitis. Doctorate dissertationGoogle Scholar
  23. Jin C, Huang XS, Li KQ, Yin H, Li LT, Yao ZH et al (2016) Overexpression of a bHLH1 transcription factor of Pyrus ussuriensis confers enhanced cold tolerance and increases expression of stress-responsive genes. Front Plant Sci 7:441PubMedPubMedCentralGoogle Scholar
  24. Leng X, Jia H, Sun X, Shangguan L, Mu Q, Wang B, Fang J (2015) Comparative transcriptome analysis of grapevine in response to copper stress. Sci Rep 5:17749CrossRefGoogle Scholar
  25. Li C, Lv J, Zhao X, Ai X, Zhu X, Wang M, Zhao S, Xia G (2010) TaCHP: a wheat zinc finger protein gene down-regulated by abscisic acid and salinity stress plays a positive role in stress tolerance. Plant Physiol 154:211–221CrossRefGoogle Scholar
  26. Li C, Xu Z, Dong R, Chang S, Wang L, Khalil-Ur-Rehman M, Tao J (2017) An RNA-Seq analysis of grape plantlets grown in vitro reveals different responses to blue, green, red LED light, and white fluorescent light. Front Plant Sci 8:78PubMedPubMedCentralGoogle Scholar
  27. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2[−Delta Delta C(t)] method. Methods 25:402–408CrossRefGoogle Scholar
  28. Mendoza-Cózatl DG, Zhai Z, Jobe TO, Akmakjian GZ, Song WY, Limbo O, Russell MR, Kozlovskyy VI, Martinoia E, Vatamaniuk OK et al (2010) Tonoplast-localized Abc2 transporter mediates phytochelatin accumulation in vacuoles and confers cadmium tolerance. J Biol Chem 285:40416–40426CrossRefGoogle Scholar
  29. Mendoza-Cozatl DG, Xie Q, Akmakjian GZ, Jobe TO, Patel A, Stacey MG, Song L, Demoin DW, Jurisson SS, Stacey G et al (2014) OPT3 is a component of the iron-signaling network between leaves and roots and misregulation of OPT3 leads to an over-accumulation of cadmium in seeds. Mol Plant 7:1455–1469CrossRefGoogle Scholar
  30. Miras-Avalos JM, Intrigliolo DS (2017) Grape composition under abiotic constrains: water stress and salinity. Front Plant Sci 8:851CrossRefGoogle Scholar
  31. Munoz-Espinoza C, Di Genova A, Correa J, Silva R, Maass A, Gonzalez-Aguero M, Orellana Aand Hinrichsen P (2016) Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. BMC Plant Biol 16:104CrossRefGoogle Scholar
  32. Nakashima K, Yamaguchi-Shinozaki K (2013) ABA signalling in stress-response and seed development. Plant Cell Rep 32(7):959–970CrossRefGoogle Scholar
  33. Owais SJ (2015) Morphological and physiological responses of six grape genotypes to NaCl salt stress. Pak J Biol Sci 18:240–246CrossRefGoogle Scholar
  34. Prior LD, Grieve AM, Slavich PG, Cullis BR (1992) Sodium chloride and soil texture interactions in irrigated field grown ‘sultana’ grapevines: II. Plant mineral content, growth and physiology. Aust J Agric Res 43:1067–1083CrossRefGoogle Scholar
  35. Rodrigues NF, da Fonseca GC, Kulcheski FR, Margis R (2017) Salt stress affects mRNA editing in soybean chloroplasts. Genet Mol Biol 40(1 suppl):200–208CrossRefGoogle Scholar
  36. Sah SK, Reddy KR, Li J (2016) Abscisic acid and abiotic stress tolerance in crop plants. Front Plant Sci 7:571CrossRefGoogle Scholar
  37. Seyfferth C, Tsuda K (2014) Salicylic acid signal transduction: the initiation of biosynthesis, perception and transcriptional reprogramming. Front Plant Sci 5:697CrossRefGoogle Scholar
  38. Shani U, Ben-Gal A (2005) Long-term response of grapevines to salinity: osmotic effects and ion toxicity. Am J Enol Vitic 56:148–154Google Scholar
  39. Shankar R, Bhattacharjee A, Jain M (2016) Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci Rep 6:23719CrossRefGoogle Scholar
  40. Sharm J, Upadhyay AK (2008) Rootstock effect on Tas-A-Ganesh (Vitis vinifera L.) for sodium and chloride uptake. Acta Hort 785:113–116CrossRefGoogle Scholar
  41. Sharma P, Jha AB, Dubey RS, Pessarakli M (2012) Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. J Bot 2012:1–26.  https://doi.org/10.1155/2012/217037 CrossRefGoogle Scholar
  42. Song YP, Chen QQ, Ci D, Shao XN, Zhang DQ (2014) Effects of high temperature on photosynthesis and related gene expression in poplar. BMC Plant Biol 14:111CrossRefGoogle Scholar
  43. Strohm AK, Baldwin KL, Masson PH (2012) Multiple roles for membrane-associated protein trafficking and signaling in gravitropism. Front Plant Sci 3:274CrossRefGoogle Scholar
  44. Upreti KK, Murti GSR (2010) Response of grape rootstocks to salinity: changes in root growth, polyamines and abscisic acid. Biol Plant 54:730–734CrossRefGoogle Scholar
  45. Upreti KK, Varalakshmi LR, Jayaram HL (2012) Influence rootstocks on salinity tolerance of grapevine: changes in biomass, photosynthesis, abscisic acid and glycine betaine. Indian J Plant Physiol 17:128–136Google Scholar
  46. Walker RR, Blackmore DH, Clingeleffer PR, Correll RL (2002) Rootstock effects on salt tolerance of field-grown grapevines (Vitis vinifera L. cv. Sultana). 1. Yield and vigour inter-relationships. Aust J Grape Wine Res 8:3–14CrossRefGoogle Scholar
  47. Walker RR, Blackmore DH, Clingeleffer PR, Godden P, Francis L, Valente P, Robinson E (2003) Salinity effects on vines and wines. Bulletin de L’O.I.V 76:200–227Google Scholar
  48. Walker RR, Blackmore DH, Clingeleffer PR (2010) Impact of rootstock on yield and ion concentrations in petioles, juice and wine of Shiraz and Chardonnay in different viticultural environments with different irrigation water salinity. Aust J Grape Wine Res 16:243–257CrossRefGoogle Scholar
  49. Wang Y, Lin A, Loake GJ, Chu C (2013) H2O2-induced leaf cell death and the crosstalk of reactive nitric/oxygen species. J Integr Plant Biol 55:202–208CrossRefGoogle Scholar
  50. Wang L, Liu X, Meng Liang M, Fanglin Tan F, Wenyu Liang W, Yiyong Chen Y, Lin Y, Huang L, Xing J, Chen W (2014a) Proteomic analysis of salt-responsive proteins in the leaves of mangrove Kandelia candel during short-term stress. PLoS One 9(1):e83141CrossRefGoogle Scholar
  51. Wang S, Uddin MI, Tanaka K, Yin L, Shi Z, Qi Y, Mano J, Matsui K, Shimomura N et al (2014b) Maintenance of chloroplast structure and function by overexpression of the rice monogalactosyldiacylglycerol synthase gene leads to enhanced salt tolerance in tobacco. Plant Physiol 165:1144–1155CrossRefGoogle Scholar
  52. Wolf JBW (2013) Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial. Mol Ecol Resour 13:559–572CrossRefGoogle Scholar
  53. Xiong L, Lee H, Ishitani M, Zhu JK (2002) Regulation of osmotic stress-responsive gene expression by the LOS6/ABA1 locus in Arabidopsis. J Biol Chem 277:8588–8569CrossRefGoogle Scholar
  54. Xu C, Sibicky T, Huang B (2010) Protein profile analysis of salt-responsive proteins in leaves and roots in two cultivars of creeping bentgrass differing in salinity tolerance. Plant Cell Rep 29:595–615CrossRefGoogle Scholar
  55. Yang Y, Wu S, Lilley RM, Zhang R (2015) The diversity of membrane transporters encoded in bacterial arsenic-resistance operons. PeerJ 3:e943Google Scholar
  56. Yao Y, Xiao X, Ou Y, Wu X, Xu G (2014) Root transcriptome analysis on the grape genotypes with contrast translocation pattern of excess manganese from root to shoot. Plant Soil 386:49–67Google Scholar
  57. Zhang J, Klueva NY, Wang Z, WU R, TD HO, NGUYEN HT (2000) Genetic engineering for abiotic stress resistance in crop plants. In Vitro Cell Dev Biol Plant 36:108–114CrossRefGoogle Scholar
  58. Zhang T, Liu Y, Yang T, Zhang L, Xu S, Xue L et al (2006) Diverse signals converge at MAPK cascades in plant. Plant Physiol Biochem 44:274–283CrossRefGoogle Scholar
  59. Zhu YN, Shi DQ, Ruan MB, Zhang LL, Meng ZH, Liu J et al (2013) Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.). PLoS One 8:e80218.  https://doi.org/10.1371/journal.pone.0080218 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Division of Plant BiologyBose InstituteKolkataIndia

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