Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice Jumli Marshi

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Chawade, Aakash ^a   Lindlöf, Angelica ^a,b   Olsson, Björn ^b   Olsson, Olof ^a,c  

^a CropTailor AB   (Sweden)

^b UNIVERSITY OF SKÖVDE   (Sweden)

^c LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHLOROPHYLL FLUORESCENCE; CHROMOSOMAL LOCALIZATION; COLD STRESS; COLD TOLERANCE; CONTROLLED STUDY; CULTIVAR; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; JUMLI MARSHI; LOW TEMPERATURE; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; NONHUMAN; PLANT GENE; PLANT GROWTH; PROMOTER REGION; REGULON; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RICE; SIGNAL TRANSDUCTION;

ADAPTATION, PHYSIOLOGICAL; COLD TEMPERATURE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; GENOTYPE; MOLECULAR SEQUENCE ANNOTATION; NEPAL; ORYZA SATIVA; PLANT PROTEINS; PROMOTER REGIONS, GENETIC; QUANTITATIVE TRAIT LOCI; REGULON; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL;

EID: 84892623587     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081729     Document Type: Article

References (71)

1. Fowler DB, Carles RJ (1979) Growth, Development, and Cold Tolerance of Fall-acclimated Cereal Grains. Crop Science 19: 915-922.
2. Thomashow MF (1999) PLANT COLD ACCLIMATION: Freezing Tolerance Genes and Regulatory Mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50: 571-599.
3. Anderson MD, Prasad TK, Martin BA, Stewart CR (1994) Differential Gene Expression in Chilling-Acclimated Maize Seedlings and Evidence for the Involvement of Abscisic Acid in Chilling Tolerance. Plant Physiol 105: 331-339.
4. Gesch RW, Heilman JL (1999) Responses of photosynthesis and phosphorylation of the light-harvesting complex of photosystem II to chilling temperature in ecologically divergent cultivars of rice. Environmental and Experimental Botany 41: 257-266.
5. Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, et al. (2009) Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant physiology 149: 961-980.
6. Morsy MR, Jouve L, Hausman JF, Hoffmann L, Stewart JM (2007) Alteration of oxidative and carbohydrate metabolism under abiotic stress in two rice (Oryza sativa L.) genotypes contrasting in chilling tolerance. Journal of plant physiology 164: 157-167.
7. Chawade A, Linden P, Brautigam M, Jonsson R, Jonsson A, et al. (2012) Development of a model system to identify differences in spring and winter oat. PloS one 7: e29792.
8. Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, et al. (2011) Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.). BMC genomics 12: 299.
9. Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, et al. (2006) Transcriptome analysis of cold acclimation in barley albina and xantha mutants. Plant physiology 141: 257-270.
10. Janska A, Aprile A, Zamecnik J, Cattivelli L, Ovesna J (2011) Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues. Functional & integrative genomics 11: 307-325.
11. Bräutigam M, Lindlöf A, Zakhrabekova S, Gharti-Chhetri G, Olsson B, et al. (2005) Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology 5: 18.
12. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, et al. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50: 347-363.
13. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, et al. (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130: 2129-2141.
14. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell 14: 1675-1690.
15. Benedict C, Geisler M, Trygg J, Huner N, Hurry V (2006) Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis. Plant Physiol 141: 1219-1232.
16. Maruyama K, Sakuma Y, Kasuga M, Ito Y, Seki M, et al. (2004) Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Plant J 38: 982-993.
17. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, et al. (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31: 279-292.
18. Lindlof A, Brautigam M, Chawade A, Olsson O, Olsson B (2009) In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. Bioinformatics 25: 1345-1348.
19. Chawade A, Brautigam M, Lindlof A, Olsson O, Olsson B (2007) Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC genomics 8: 304.
20. Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, et al. (2003) A network of rice genes associated with stress response and seed development. Proceedings of the National Academy of Sciences of the United States of America 100: 4945-4950.
21. Lindlöf A, Bräutigam M, Chawade A, Olsson B, Olsson O (2007) Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets. 4414: 48-65.
22. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, et al. (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant physiology 133: 1755-1767.
23. Cheng C, Yun KY, Ressom HW, Mohanty B, Bajic VB, et al. (2007) An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC genomics 8: 175.
24. Oda S, Kaneko F, Yano K, Fujioka T, Masuko H, et al. (2010) Morphological and gene expression analysis under cool temperature conditions in rice anther development. Genes & genetic systems 85: 107-120.
25. Yun KY, Park MR, Mohanty B, Herath V, Xu F, et al. (2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC plant biology 10: 16.
26. Mittal D, Madhyastha DA, Grover A (2012) Genome-wide transcriptional profiles during temperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in rice. PloS one 7: e40899.
27. Zhang T, Zhao X, Wang W, Pan Y, Huang L, et al. (2012) Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes. PloS one 7: e43274.
28. Sapkota S, Paudel MN, Thakur NS, Nepali MB, Neupane R (2010) Effect of Climate Change on Rice Production: A Case of Six VDCs in Jumla District. Nepal Journal of Science and Technology 11: 57-62.
29. Caldana C, Scheible WR, Mueller-Roeber B, Ruzicic S (2007) A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods 3: 7.
30. Su CF, Wang YC, Hsieh TH, Lu CA, Tseng TH, et al. (2010) A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant physiology 153: 145-158.
31. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic acids research 29: e45.
32. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome biology 5: R80.
33. Bolstad BM (2004) Low Level Analysis of High-density Oligonucleotide Array Data: Background, Normalization and Summarization. Berkeley: University of California.
34. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315.
35. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, editors. Bioinformatics and computational biology solutions using R and Bioconductor. New York: Springer Science+Business Media. pp. 397-420.
36. Ernst J, Bar-Joseph Z (2006) STEM: a tool for the analysis of short time series gene expression data. BMC bioinformatics 7: 191.
37. Gilmour SJ, Fowler SG, Thomashow MF (2004) Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant molecular biology 54: 767-781.
38. Zhang FD, Huang LM, Wang WD, Zhao XD, Zhu LM, et al. (2012) Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. BMC genomics 13: 461.
39. Siddiq EA, Vemireddy LR, Nagaraju J (2012) Basmati Rices: Genetics, Breeding and Trade. Agricultural Research 1: 25-36.
40. Morris RT, O'Connor TR, Wyrick JJ (2008) Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics 24: 2915-2917.
41. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, et al. (2007) The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 72: 353-363.
42. Perez-Rodriguez P, Riano-Pachon DM, Correa LG, Rensing SA, Kersten B, et al. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic acids research 38: D822-827.
43. Huang GT, Ma SL, Bai LP, Zhang L, Ma H, et al. (2012) Signal transduction during cold, salt, and drought stresses in plants. Molecular biology reports 39: 969-987.
44. Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. The Plant cell 14 Suppl: S165-183.
45. Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant physiology and biochemistry : PPB/Societe francaise de physiologie vegetale 48: 909-930.
46. Hossain Z, Nouri MZ, Komatsu S (2012) Plant cell organelle proteomics in response to abiotic stress. J Proteome Res 11: 37-48.
47. Bae MS, Cho EJ, Choi EY, Park OK (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. The Plant journal : for cell and molecular biology 36: 652-663.
48. Goulas E, Schubert M, Kieselbach T, Kleczkowski LA, Gardestrom P, et al. (2006) The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature. The Plant journal : for cell and molecular biology 47: 720-734.
49. Kawamura Y, Uemura M (2003) Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation. The Plant journal : for cell and molecular biology 36: 141-154.
50. Rasmusson AG, Soole KL, Elthon TE (2004) Alternative NAD(P)H dehydrogenases of plant mitochondria. Annual review of plant biology 55: 23-39.
51. Ni J, Pujar A, Youens-Clark K, Yap I, Jaiswal P, et al. (2009) Gramene QTL database: development, content and applications. Database : the journal of biological databases and curation 2009: bap005.
52. Gautam AK, Shrestha NP (2012) Temperate rice in Nepal. In: Jena KK, Hardy B, editors. Advances in temperate rice research. Metro Manila, Philippines: IRRI. 49-58.
53. Raboin LM, Ramanantsoanirina A, Dzido JL, Andriantsimialona D, Tharreau D, et al. Upland (aerobic) rice breeding for the harsh environment of the High Plateau of Madagascar; 2010; Mali.
54. Joshi BK (2005) Rice Gene Pool for Tarai and Inner Tarai Areas of Nepal. Nepal Agric Res J 6: 10-22.
55. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, et al. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J 33: 751-763.
56. Zhou QY, Tian AG, Zou HF, Xie ZM, Lei G, et al. (2008) Soybean WRKYtype transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant biotechnology journal 6: 486-503.
57. Badawi M, Danyluk J, Boucho B, Houde M, Sarhan F (2007) The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBFs. Molecular genetics and genomics 277: 533-554.
58. Fowler SG, Cook D, Thomashow MF (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137: 961-968.
59. Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, et al. (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant & cell physiology 47: 141-153.
60. Skinner JS, von Zitzewitz J, Szucs P, Marquez-Cedillo L, Filichkin T, et al. (2005) Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol Biol 59: 533-551.
61. Wang X, Liu S, Liu X, Chen Z, Liu X, et al. (2004) Molecular cloning and characterization of a CBF gene from Capsella bursa-pastoris. DNA Seq 15: 180-187.
62. Zhang X, Fowler SG, Cheng H, Lou Y, Rhee SY, et al. (2004) Freezing-sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing-tolerant Arabidopsis. Plant J 39: 905-919.
63. Lee BH, Henderson DA, Zhu JK (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. The Plant cell 17: 3155-3175.
64. del Rio LA, Sandalio LM, Corpas FJ, Palma JM, Barroso JB (2006) Reactive oxygen species and reactive nitrogen species in peroxisomes. Production, scavenging, and role in cell signaling. Plant physiology 141: 330-335.
65. Navrot N, Rouhier N, Gelhaye E, Jacquot J-P (2007) Reactive oxygen species generation and antioxidant systems in plant mitochondria. Physiologia Plantarum 129: 185-195.
66. Matsumura T, Tabayashi N, Kamagata Y, Souma C, Saruyama H (2002) Wheat catalase expressed in transgenic rice can improve tolerance against low temperature stress. Physiologia Plantarum 116: 317-327.
67. Wang Y, Wisniewski M, Meilan R, Cui M, Webb R, et al. (2005) Overexpression of cytosolic ascorbate peroxidase in tomato confers tolerance to chilling and salt stress. J Am Soc Hortic Sci 130: 167-173.
68. Kornyeyev D, Logan BA, Payton PR, Allen RD, Holaday AS (2003) Elevated chloroplastic glutathione reductase activities decrease chilling-induced photoinhibition by increasing rates of photochemistry, but not thermal energy dissipation, in transgenic cotton. Functional Plant Biology 30: 101.
69. Yoshimura K, Miyao K, Gaber A, Takeda T, Kanaboshi H, et al. (2004) Enhancement of stress tolerance in transgenic tobacco plants overexpressing Chlamydomonas glutathione peroxidase in chloroplasts or cytosol. The Plant journal : for cell and molecular biology 37: 21-33.
70. Dowgert MF, Steponkus PL (1984) Behavior of the Plasma Membrane of Isolated Protoplasts during a Freeze-Thaw Cycle. Plant physiology 75: 1139-1151.
71. Oliveros JC (2007) VENNY. An interactive tool for comparing lists with Venn Diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html.