Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]

Journal of Experimental Botany

Volumn 62, Issue 10, 2011, Pages 3387-3401

  Lata, Charu ^a   Bhutty, Sarita ^a   Bahadur, Ranjit Prasad ^b   Majee, Manoj ^a   Prasad, Manoj ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

^b INDIAN INSTITUTE OF TECHNOLOGY   (India)

Author keywords

Allele specific marker; dehydration stress; dehydration responsive element binding protein 2; gene expression; Setaria italica; single nucleotide polymorphism

Indexed keywords

ARABIDOPSIS PROTEIN; DREB2A PROTEIN, ARABIDOPSIS; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; DEHYDRATION; GENE EXPRESSION REGULATION; GENETICS; MILLET; PHYSIOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ARABIDOPSIS PROTEINS; DEHYDRATION; GENE EXPRESSION REGULATION, PLANT; PLANT PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SETARIA PLANT; TRANSCRIPTION FACTORS;

SETARIA ITALICA;

EID: 79960247967     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/err016     Document Type: Article

References (60)

1. Agarwal PK, Agarwal P, Reddy MK, Sopory SK. 2006. Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Reports 25, 1263-1274. (Pubitemid 44786606)
2. Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M. 1998. A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO Journal 17, 5484-5496. (Pubitemid 28427062)
3. Andersen JR, Lübberstedt T. 2003. Functional markers in plants. Trends in Plant Science 8, 554-560. (Pubitemid 37481534)
4. Barrs HD, Weatherley PE. 1962. A re-examination of the relative turgidity technique for estimating water deficit in leaves. Australian Journal of Biological Sciences 15, 413-428.
5. Bhushan D, Pandey A, Choudhary MK, Datta A, Chakraborty S, Chakraborty N. 2007. Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Molecular and Cellular Proteomics 6, 1868-1884. (Pubitemid 350201865)
6. Blum A. 1996. Developing drought and low N-tolerant maize. In: Edmeades GO, Banziger M, Mickelson HR, Pena-Valdivia CB, eds. Proceedings of a Symposium at the International Maize and Wheat Improvement Cente (CIMMYT), El-Batan, March 25-29, 1996. El-Batan, Mexico: CIMMYT, 131-135.
7. Chandra A, Dubey A. 2010. Effect of ploidy levels on the activities of D-pyrroline-5-carboxylate synthetase, superoxide dismutase and peroxidase in Cenchrus species grown under water stress. Plant Physiology and Biochemistry 48, 27-34.
8. Chen M, Wang QY, Cheng XG, Xu ZS, Li LC, Ye XG, Xia LQ, Ma YZ. 2007. GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochemical and Biophysical Research Communications 353, 299-305. (Pubitemid 46019916)
9. Collard BC, Mackill DJ. 2008. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 363, 557-572. (Pubitemid 351437353)
10. Devos KM, Wang Z, Beales CJ, Sasaki T, Gale MD. 1998. Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theoretical and Applied Genetics 96, 63-68. (Pubitemid 28139589)
11. Doust AN, Kellogg EA, Devos KM, Bennetzen JL. 2009. Foxtail millet: a sequence-driven grass model system. Plant Physiology 149, 137-141.
12. Drenkard E, Richter BG, Rozen S, et al. 2000. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiology 124, 1483-1492. (Pubitemid 32053484)
13. Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt-and cold-responsive gene expression. The Plant Journal 33, 751-763. (Pubitemid 36325917)
14. Egawa C, Kobayashi F, Ishibashi M, Nakamura T, Nakamura C, Shiego T. 2006. Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat. Genes and Genetic Systems 81, 77-91. (Pubitemid 43854496)
15. El Hafid R, Smith DH, Karrou M, Samir K. 1998. Physiological attributes associated with early-season drought resistance in spring durum wheat cultivars. Canadian Journal of Plant Science 78, 227-237. (Pubitemid 28338577)
16. Fan C, Yu S, Wang C, Xing Y. 2009. A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theoretical and Applied Genetics 118, 465-472.
17. Fazeli F, Ghorbanli M, Niknam V. 2007. Effect of drought on biomass, protein content, lipid peroxidation and antioxidant enzymes in two sesame cultivars. Biologia Plantarum 51, 98-107.
18. Garcés-Claver A, Fellman SM, Gil-Ortega R, Jahn M, Arnedo-André s MS. 2007. Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theoretical and Applied Genetics 115, 907-916. (Pubitemid 47561698)
19. Gu SL, Liu J, Ren HR, et al. 1987. The relationship between foxtail millet and its environment. In: Shanxi Academy of Agricultural Sciences, ed. Foxtail millet cultivation in China. (In Chinese). Bejing: China Agricultural Press, 64-65.
20. Guo Z, Ou W, Lu S, Zhong Q. 2006. Differential responses of antioxidative system to chilling and drought in four rice cultivars differing in sensitivity. Plant Physiology and Biochemistry 44, 828-836. (Pubitemid 44918353)
21. Hodgson RAJ, Raison JK. 1991. Lipid peroxidation and superoxide dismutase activity in relation to photoinhibition induced by chilling in moderate light. Planta 185, 215-219.
22. Jayaraman A, Puranik S, Rai NK, Vidapu S, Sahu PP, Lata C, Prasad M. 2008. cDNA-AFLP analysis reveals differential gene expression in response to salt stress in foxtail millet (Setaria italica L.). Molecular Biotechnology 40, 241-251.
23. Jin Q, Waters D, Cordeiro GM, Henry RJ, Reinke RF. 2003. A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Science 165, 359-364. (Pubitemid 36872324)
24. Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292, 195-202. (Pubitemid 29435759)
25. Kim MY, Van K, Lestari P, Moon JK, Lee SH. 2005. SNP identification and SNAP marker development for a GmNARK gene controlling supernodulation in soybean. Theoretical and Applied Genetics 110, 1003-1010. (Pubitemid 40607565)
26. Kumutha D, Ezhilmathi K, Sairam RK, Srivastava GC, Deshmukh PS, Meena RC. 2009. Waterlogging induced oxidative stress and antioxidant activity in pigeonpea genotypes. Biologia Plantarum 53, 75-84.
27. Lata C, Sahu PP, Prasad M. 2010. Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochemical and Biophysical Research Communications 393, 720-727.
28. Lenka SK, Katiyar A, Chinnusamy V, Bansal KC. 2010. Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnology Journal (in press).
29. Li YM. 1987. Drought-resistant mechanism and genetic expression of foxtail millet. In: Li YM, ed. Foxtail millet breeding. Beijing: China Agricultural Press, 433-434.
30. Liu J, Van Eck J, Cong B, Tanksley SD. 2002. A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proceedings of the National Academy of Sciences, USA 99, 13302-13306.
31. Liu L, Zhu K, Yang Y, Wu J, Chen F, Yu D. 2008. Molecular cloning, expression profiling and trans-activation property studies of a DREB2-like gene from chrysanthemum (Dendranthema vestitum). Journal of Plant Research 121, 215-226.
32. Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki, Shinozaki K. 1998. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. The Plant Cell 10, 1391-1406. (Pubitemid 28542172)
33. Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCt method. Methods 25, 402-408. (Pubitemid 34164012)
34. Longeman J, Schell J, Willmitzer L. 1987. Improved method for the isolation of RNA from plant tissues. Analytical Biochemistry 163, 16-20.
35. Madhusudan KV, Giridarakumar S, Ranganayakulu GS, Reddy PC, Sudhakar C. 2002. Effect of water stress on some physiological responses in two groundnut (Arachis hypogea L.) cultivars with contrasting drought tolerance. Journal of Plant Biology 29, 199-202.
36. McDonald IK, Thornton JM. 1994. Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology 238, 777-793. (Pubitemid 24168633)
37. Mizuno S, Hirasawa Y, Sonoda M, Nakagawa H, Sato T. 2006. Isolation and characterization of three DREB/ERF-type transcription factors from melon (Cucumis melo). Plant Science 170, 1156-1163.
38. Nagy Z, Tuba Z, Zsoldos F, Erdei L. 1995. CO2 exchange and water relation responses of sorghum and maize during water stress. Journal of Plant Physiology 145, 539-544.
39. Peng J, Richards DE, Hartley NM, et al. 1999. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400, 256-261. (Pubitemid 29334139)
40. Qin F, Kakimoto M, Sakuma Y, et al. 2007. Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. The Plant Journal 50, 54-69. (Pubitemid 46493397)
41. Riechmann JL, Heard J, Martin G, et al. 2000. Arabidopsis transcription factor: genome wide comparative analysis among eukaryotes. Science 290, 2105-2110. (Pubitemid 32001583)
42. Saghai-Maroof MA, Biyaschev RM, Yang GP, Zhang Q, Allard RW. 1984. Extraordinary polymorphism microsatellite DNA in barley: species diversity, chromosomal location and population dynamics. Proceedings of the National Academy of Sciences, USA 91, 5466-5470.
43. Sakuma Y, Liu Q, Dubouzet JG, Abe H, Shinozaki K, Yamaguchi-Shinozaki K. 2002. DNA-binding-specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration-and cold-inducible gene expression. Biochemical and Biophysical Research Communications 290, 998-1009. (Pubitemid 34687462)
44. Sakuma Y, Maruyama K, Osakabe Y, et al. 2006a. Functional analysis of an Arabidopsis transcription factor, DREB2A involved in drought-responsive gene expression. The Plant Cell 18, 1292-1309. (Pubitemid 43956132)
45. Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K. 2006b. Dual function of an Arabidopsis transcription factor DREB2A in water-stress responsive and heat-stress-responsive gene expression. Proceedings of the National Academy of Sciences, USA 103, 18822-18827. (Pubitemid 44913494)
46. Sali A, Blundell T. 1993. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 234, 779-815. (Pubitemid 24007801)
47. Shigeoka S, Ishikawa T, Tamoi M, et al. 2002. Regulation and function of ascorbate peroxidase isoenzymes. Journal of Experimental Botany 53, 1305-1319. (Pubitemid 34544051)
48. Smirnoff N. 1995. Antioxidant systems and plant response to the environment. In: Smirnoff N, ed. Environment and plant metabolism. Oxford: BIOS Scientific Publishers, 217-243.
49. Sreenivasulu N, Ramanjulu S, Ramachandra-Kini K, et al. 1999. Total peroxidase activity and peroxidase isoforms as modified by salt stress in two cultivars of foxtail millet with differential salt tolerance. Plant Science 141, 1-9. (Pubitemid 29161646)
50. Stockinger EJ, Gilmour SJ, Thomashow MF. 1997. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proceedings of the National Academy of Sciences, USA 94, 1035-1040.
51. Takahashi Y, Shomura A, Sasaki T, Yano M. 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the subunit of protein kinase CK2. Proceedings of the National Academy of Sciences, USA 98, 7922-7927. (Pubitemid 32642663)
52. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680. (Pubitemid 24354800)
53. Toshiyuki K, Shizo O, Nobuhiko M, et al. 2003. Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). The Plant Journal 37, 315-325.
54. Wei B, Jing RL, Wang CS, Chang XP. 2006. Assaying single nucleotide polymorphism in wheat (Triticum aestivum L.) with allele-specific PCR. Scientia Agricola Sinica 39, 1313-1320.
55. Wiederstein M, Sippl MJ. 2007. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research 35, 407-410.
56. Wu DY, Ugozzoli L, Pal BK, Wallace RB. 1989. Allele-specific enzymatic amplification of b-globin genomic DNA for diagnosis of sickle cell anemia. Proceedings of the National Academy of Sciences, USA 86, 2757-2760. (Pubitemid 19112620)
57. Yamaguchi-Shinozaki K, Shinozaki K. 2005. Organization of cis-acting regulatory elements in osmotic-and cold-stress-responsive promoters. Trends in Plant Science 10, 88-94. (Pubitemid 40234484)
58. Zhang J, Liu T, Fu J, Zhu Y, et al. 2007. Construction and application of EST library from Setaria italica in response to dehydration stress. Genomics 90, 121-131. (Pubitemid 46891741)
59. Zhang Y. 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 23, 9-40.
60. Zhao L, Hu Y, Chong K, Wang T. 2010. ARAG1, an ABA-responsive DREB gene, plays a role in seed germination and drought tolerance of rice. Annals of Botany 105, 401-409.