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

Molecular Biology Reports

Volumn 41, Issue 1, 2014, Pages 505-517

  Zhang, Ning ^a   Liu, Bailin ^a   Ma, Congyu ^a   Zhang, Guodong ^a   Chang, Jing ^a   Si, Huaijun ^a   Wang, Di ^a  

^a GANSU AGRICULTURAL UNIVERSITY   (China)

Author keywords

Drought stress; Leaf; mRNA Seq; Potato; Transcriptome

Indexed keywords

RNA; TRANSCRIPTOME;

ABIOTIC STRESS; ARTICLE; CONTROLLED STUDY; CULTIVAR; DOWN REGULATION; DROUGHT STRESS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; NONHUMAN; PLANT GENETICS; PLANT LEAF; POTATO; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SOLANUM TUBERSOSUM; UPREGULATION;

SOLANUM; SOLANUM TUBEROSUM;

ADAPTATION, PHYSIOLOGICAL; CHROMOSOME MAPPING; DEHYDRATION; DROUGHTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; PLANT PROTEINS; SEQUENCE ANALYSIS, DNA; SOLANUM TUBEROSUM; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

EID: 84891945792     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-013-2886-7     Document Type: Article

References (58)

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. 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
3. Reynolds M, Tuberosa R (2008) Translational research impacting on crop productivity in drought-prone environments. Curr Opin Plant Biol 11:171-179
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
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
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
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
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
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
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
11. The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189-195
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
13. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
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
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
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
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
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
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
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
21. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111
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
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
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
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
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
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
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
29. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucl Acids Res 28:27-30
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
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
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
33. Bray EA (2004) Genes commonly regulated by water-deficit stress in Arabidopsis thaliana. J Exp Bot 55:2331-2341
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
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
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
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
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
39. Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221-227
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
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
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
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
44. Lopez CG, Banowetz GM, Peterson CJ, Kronstad WE (2003) Dehydrin expression and drought tolerance in seven wheat cultivars. Crop Sci 43:577-582
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
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
47. Chen C, Dickman MB (2005) Proline suppresses apoptosis in the fungal pathogen Colletotrichum trifolii. Proc Natl Acad Sci USA 102:3459-3464
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
49. Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405-410
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
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
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
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
54. Knight H, Trewavas AJ, Knight MR (1997) Calcium signaling in Arabidopsis thaliana responding to drought and salinity. Plant J 12:1067-1078
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
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
57. Martin DN, Proebsting WM, Hedden P (1999) The SLENDER gene of pea encodes a gibberellin 2-oxidase. Plant Physiol 121:775-781
58. Xu ZS, Chen M, Li LC, Ma YZ (2008) Functions of the ERF transcription factor family in plants. Botany 86:969-977