Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato

Abstract

Potato (Solanum tubersosum L.) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms to such stress in potato are largely unknown. To gain insight into the transcriptome dynamics that are associated with drought stress, genome-wide gene expression profile was conducted by Solexa sequencing to generate a large dataset and a comprehensive transcriptome profile for potato. Here, we report a reference for the potato transcriptome using leaf tissues under drought-stressed condition from a local potato cultivar ‘Longshu 3’. Analysis of 86,965,482 RNA-Seq reads permitted the detection and quantification of expression levels of 7,284 genes at transcriptional levels, among them, 6,754 genes were enriched in draught-treated leaves while 6,419 in control. We identified 842 drought-responsive up-regulated and 494 down-regulated candidate genes with significantly differentially expression under continued drought stress treatments. Those differently expressed genes were mostly enriched in 89 gene categories and 21 KEGG pathways. Drought-stressed leaves had increased expression of genes involved in stress response compared with control leaves. A subset of differentially expressed genes associated with drought response was examined using quantitative real-time PCR. These results provide a broad spectrum of candidate genes that are essential for understanding the molecular regulation of potato in response to abiotic stresses.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Abbreviations

DEG:

Differentially expressed genes

ESTs:

Expressed sequence tags

FPKM:

Fragments Per Kilobase of exon model per Million mapped reads

qRT-PCR:

Quantitative real-time PCR

References

  1. 1.

    Papademetriou MK (ed) (2008) In: RAP Publication (FAO), no. 2008/07; Workshop to commemorate the international year of potato, Bangkok (Thailand), 6 May 2008/FAO, Bangkok (Thailand). Regional Office for Asia and the Pacific, p 84

  2. 2.

    Barnabas B, Jager K, Feher A (2008) The effect of drought and heat stress on reproductive processes in cereals. Plant Cell Environ 31:11–38

    CAS  PubMed  Google Scholar 

  3. 3.

    Reynolds M, Tuberosa R (2008) Translational research impacting on crop productivity in drought-prone environments. Curr Opin Plant Biol 11:171–179

    PubMed  Article  Google Scholar 

  4. 4.

    Moore JP, Le NT, Brandt WF, Driouich A, Farrant JM (2009) Towards a systems-based understanding of plant desiccation tolerance. Trends Plant Sci 14:110–117

    CAS  PubMed  Article  Google Scholar 

  5. 5.

    Basu PS, Sharma A, Garg ID, Sukumaran NP (1999) Tuber sink modifies photosynthetic response in potato under water stress. Environ Exp Bot 42:25–39

    Article  Google Scholar 

  6. 6.

    Crookshanks M, Emmersen J, Welinder KG, Lehmann Nielsen K (2001) The potato tuber transcriptome: analysis of 6077 expressed sequence tags. FEBS Lett 506:123–126

    CAS  PubMed  Article  Google Scholar 

  7. 7.

    Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, Van Der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 131:419–429

    PubMed Central  PubMed  Article  Google Scholar 

  8. 8.

    Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR (2005) Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48:598–605

    PubMed  Article  Google Scholar 

  9. 9.

    Flinn B, Rothwell C, Griffiths R, Lague M, DeKoeyer D, Sardana R, Audy P, Goyer C, Li XQ, Wang-Pruski G, Regan S (2005) Potato expressed sequence tag generation and analysis using standard and unique cDNA libraries. Plant Mol Biol 59:407–433

    PubMed  Article  Google Scholar 

  10. 10.

    Li XQ, Griffiths R, Lague M, DeKoeyer D, Rothwell C, Haroon M, Stevens B, Xu C, Gustafson V, Bonierbale M, Regan S, Flinn B (2007) EST sequencing and analysis from cold-stored and reconditioned potato tubers. Acta Hortic 745:491–493

    CAS  Google Scholar 

  11. 11.

    The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195

    Article  Google Scholar 

  12. 12.

    Kyndt T, Denil S, Haegeman A, Trooskens G, De Meyer T, Van Criekinge W, Gheysen G (2012) Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot 63:2141–2157

    CAS  PubMed  Article  Google Scholar 

  13. 13.

    Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  14. 14.

    Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613–619

    CAS  PubMed  Article  Google Scholar 

  15. 15.

    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    CAS  PubMed  Article  Google Scholar 

  16. 16.

    Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  17. 17.

    Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O’Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956–960

    CAS  PubMed  Article  Google Scholar 

  18. 18.

    Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239–1243

    CAS  PubMed  Article  Google Scholar 

  19. 19.

    Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, Tao Y, Kristiansen K, Zhang X, Li S, Yang H, Wang J, Wang J (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20:646–654

    CAS  PubMed  Article  Google Scholar 

  20. 20.

    Morin RD, Bainbridge M, Fejes A, Hirst A, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM, Marra MA (2008) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45:81–94

    CAS  PubMed  Article  Google Scholar 

  21. 21.

    Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    CAS  PubMed  Article  Google Scholar 

  22. 22.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    PubMed  Article  Google Scholar 

  23. 23.

    Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    PubMed Central  PubMed  Article  Google Scholar 

  24. 24.

    Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  25. 25.

    Lee S, Seo CH, Lim B, Yang JO, Oh J, Kim M, Lee B, Kang C, Lee S (2011) Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucl Acids Res 39:e9

    PubMed  Article  Google Scholar 

  26. 26.

    Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300

    Google Scholar 

  27. 27.

    Harris MA, Clark J, Ireland A, Lomax J, Ashburner M et al (2004) The gene ontology (GO) database and informatics resource. Nucl Acids Res 32:D258

    CAS  PubMed  Article  Google Scholar 

  28. 28.

    Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucl Acids Res 34:W293–W297

    CAS  PubMed  Article  Google Scholar 

  29. 29.

    Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucl Acids Res 28:27–30

    CAS  PubMed  Article  Google Scholar 

  30. 30.

    Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939

    CAS  PubMed  Article  Google Scholar 

  31. 31.

    Nicot N, Hausman JF, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56:2907–2914

    CAS  PubMed  Article  Google Scholar 

  32. 32.

    Ishitani M, Xiong L, Stevenson B, Zhu JK (1997) Genetic analysis of osmotic and cold stress signal transduction in Arabidopsis: interactions and convergence of abscisic acid-dependent and abscisic acid-independent pathways. Plant Cell 9:1935–1949

    CAS  PubMed Central  PubMed  Google Scholar 

  33. 33.

    Bray EA (2004) Genes commonly regulated by water-deficit stress in Arabidopsis thaliana. J Exp Bot 55:2331–2341

    CAS  PubMed  Article  Google Scholar 

  34. 34.

    Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T (2009) Transcript profiling of an Arabidopsis pseudo response regulator arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 50:447–462

    CAS  PubMed  Article  Google Scholar 

  35. 35.

    Schafleitner R, Gutierrez Rosales RO, Gaudin A, Alvarado Aliaga CA, Martinez GN, Tincopa Marca LR, Bolivar LA, Delgado FM, Simon R, Bonierbale M (2007) Capturing candidate drought tolerance traits in two native Andean potato clones by transcription profiling of field grown plants under water stress. Plant Physiol Biochem 45:673–690

    CAS  PubMed  Article  Google Scholar 

  36. 36.

    Kakumanu A, Ambavaram MM, Klumas CM, Krishnan A, Batlang U, Myers E, Grene R, Pereira A (2012) Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol 160:846–867

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  37. 37.

    Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR (2005) Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics 5:201–207

    CAS  PubMed  Article  Google Scholar 

  38. 38.

    Agarwal P, Agarwal P, Reddy M, Sopory S (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263–1274

    CAS  PubMed  Article  Google Scholar 

  39. 39.

    Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227

    CAS  PubMed  Article  Google Scholar 

  40. 40.

    Evers D, Legay S, Lamoureux D, Hausman JF, Hoffmann L, Renaut J (2012) Towards a synthetic view of potato cold and salt stress response by transcriptomic and proteomic analyses. Plant Mol Biol 78:503–514

    CAS  PubMed  Article  Google Scholar 

  41. 41.

    Payton P, Kottapalli KR, Kebede H, Mahan JR, Wright RJ, Allen RD (2011) Examining the drought stress transcriptome in cotton leaf and root tissue. Biotechnol Lett 33:821–828

    CAS  PubMed  Article  Google Scholar 

  42. 42.

    Wu G, Robertson AJ, Liu X, Zheng P, Wilen RW, Nesbitt NT, Gusta LV (2004) A lipid transfer protein gene BG-14 is differentially regulated by abiotic stress, ABA, anisomycin, and sphingosine in bromegrass (Bromus inermis). J Plant Physiol 161:449–458

    CAS  PubMed  Article  Google Scholar 

  43. 43.

    Colmenero-Flores JM, Campos F, Garciarrubio A, Covarrubias AA (1997) Characterization of Phaseolus vulgaris cDNA clones responsive to water deficit: identification of a novel late embryogenesis abundant-like protein. Plant Mol Biol 35:393–405

    CAS  PubMed  Article  Google Scholar 

  44. 44.

    Lopez CG, Banowetz GM, Peterson CJ, Kronstad WE (2003) Dehydrin expression and drought tolerance in seven wheat cultivars. Crop Sci 43:577–582

    CAS  Article  Google Scholar 

  45. 45.

    Zeeman SC, Thorneycroft D, Schupp N, Chapple A, Weck M, Dunstan H, Haldimann P, Bechtold N, Smith AM, Smith SM (2004) Plastidial a-glucan phosphorylase is not required for starch degradation in Arabidopsis leaves but has a role in the tolerance of abiotic stress. Plant Physiol 135:849–858

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  46. 46.

    Crifò T, Puglisi I, Petrone G, Recupero GR, Lo Piero AR (2011) Expression analysis in response to low temperature stress in blood oranges: implication of the flavonoid biosynthetic pathway. Gene 476:1–9

    PubMed  Article  Google Scholar 

  47. 47.

    Chen C, Dickman MB (2005) Proline suppresses apoptosis in the fungal pathogen Colletotrichum trifolii. Proc Natl Acad Sci USA 102:3459–3464

    CAS  PubMed  Article  Google Scholar 

  48. 48.

    Bansal KC, Nagarajan S (1986) Leaf water content, stomatal conductance and proline accumulation in leaves of potato (Solanum tubersosum L.) in response to water stress. Indian J Plant Physiol 29:397–404

    Google Scholar 

  49. 49.

    Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410

    CAS  PubMed  Article  Google Scholar 

  50. 50.

    Yano H, Wong JH, Lee YM, Cho MJ, Buchanan BB (2001) A strategy for the identification of proteins targeted by thioredoxin. Proc Natl Acad Sci 98:4794–4799

    CAS  PubMed  Article  Google Scholar 

  51. 51.

    Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF (2004) Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J 40:22–34

    CAS  PubMed  Article  Google Scholar 

  52. 52.

    Han Q, Zhang J, Li H, Luo Z, Ziaf K, Ouyang B, Wang T, Ye Z (2012) Identification and expression pattern of one stress-responsive NAC gene from Solanum lycopersicum. Mol Biol Rep 39:1713–1720

    CAS  PubMed  Article  Google Scholar 

  53. 53.

    Vandenabeele S, Van Der Kelen K, Dat J, Gadjev I, Boonefaes T, Morsa S, Rottiers P, Slooten L, Van Montagu M, Zabeau M, Inze D, Van Breusegem F (2003) A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco. Proc Natl Acad Sci 100:16113–16118

    CAS  PubMed  Article  Google Scholar 

  54. 54.

    Knight H, Trewavas AJ, Knight MR (1997) Calcium signaling in Arabidopsis thaliana responding to drought and salinity. Plant J 12:1067–1078

    CAS  PubMed  Article  Google Scholar 

  55. 55.

    Liu J, Ishitani M, Halfter U, Kim CS, Zhu J (2000) The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proc Natl Acad Sci 97:73730–73734

    Google Scholar 

  56. 56.

    Merlot S, Gosti F, Guerrier D, Vavasseur A, Giraudat J (2001) The ABI1 and ABI2 protein phosphatases 2C act in a negative feedback regulatory loop of the abscisic acid signalling pathway. Plant J 25:295–303

    CAS  PubMed  Article  Google Scholar 

  57. 57.

    Martin DN, Proebsting WM, Hedden P (1999) The SLENDER gene of pea encodes a gibberellin 2-oxidase. Plant Physiol 121:775–781

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  58. 58.

    Xu ZS, Chen M, Li LC, Ma YZ (2008) Functions of the ERF transcription factor family in plants. Botany 86:969–977

    CAS  Article  Google Scholar 

Download references

Acknowledgments

This research program is sponsored by Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20126202110007), and in part by Gansu Provincial Key Laboratory of Aridland Crop Science of Gansu Agricultural University (No. GSCS-2012-02).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Huaijun Si or Di Wang.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Zhang, N., Liu, B., Ma, C. et al. Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato. Mol Biol Rep 41, 505–517 (2014). https://doi.org/10.1007/s11033-013-2886-7

Download citation

Keywords

  • Potato
  • mRNA-Seq
  • Transcriptome
  • Drought stress
  • Leaf