Identification of soybean genes involved in circadian clock mechanism and photoperiodic control of flowering time by In silico analyses

Journal of Integrative Plant Biology

Volumn 49, Issue 11, 2007, Pages 1640-1653

  Quecini, Vera ^a   Zucchi, Maria I ^a   Baldin, José ^b   Vello, Natal A ^b  

^a CPqD Telecom and IT Solutions   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Circadian clock; Cryptochrome; Datamining; Flowering; Photoperiod; Phytochrome

Indexed keywords

CIRCADIAN RHYTHM; FLOWERING; GENETIC ANALYSIS; PHOTOPERIOD; SOYBEAN;

ARABIDOPSIS; ARABIDOPSIS THALIANA; GLYCINE MAX; ORYZA SATIVA;

EID: 35448950550     PISSN: 16729072     EISSN: 17447909     Source Type: Journal    
DOI: 10.1111/j.1774-7909.2007.00567.x     Document Type: Article

References (74)

1. Abe J, Xu D, Miyano A, Komatsu K, Kanazawa A, Shimamoto Y (2003). Photoperiod-insensitive Japanese soybean landraces differ at two maturity loci. Crop Sci. 43, 1300-1304.
2. AlabadíD, Oyama T, Yanovsky MJ, Harmon FG, Más P, Kay SA (2001). Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293, 880-883.
3. AlabadíD, Yanovsky MJ, Más P, Harmer SL, Kay SA (2002). Critical role for CCA1 and LHY in maintaining circadian rhythmicity in Arabidopsis. Curr. Biol. 12, 757-761.
4. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
5. Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, Thomas TL et al. (2005). Circadian rhythms from multiple oscillators: Lessons from diverse organisms. Nat. Rev. Genet. 6, 544-556.
6. Bernard RL (1971). Two genes for time of flowering and maturity in soybeans. Crop Sci. 11, 242-244.
7. Blázquez M, Ahn JH, Weigel D (2003). A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nat. Genet. 33, 168-171.
8. Bonato ER, Vello NA (1999). E6, a dominant gene conditioning early flowering and maturity in soybeans. Genet. Mol. Biol. 22, 229-232.
9. Boss PK, Bastow RM, Mylne JS, Dean C (2004). Multiple pathways in the decision to flower: Enabling, promoting, and resetting. Plant Cell 16 (suppl.), S18-S31.
10. Boylan M, Douglas N, Quail PH (1994). Dominant negative suppression of Arabidopsis photoresponses by mutant phytochrome A sequences identifies spatially discrete regulatory domains in the photoreceptor. Plant Cell 6, 449-460.
11. Buzzell RI, Voldeng HD (1980). Inheritance of insensitivity to long daylength. Soybean Genet. Newslett. 7, 26-29.
12. Buzzell RI (1971). Inheritance of a soybean flowering response to fluorescent-daylength conditions. Can. J. Genet. Cytol. 13, 703-707.
13. Cashmore AR, Jarillo JA, Wu YJ, Liu D (1999). Cryptochromes: Blue light receptors for plants and animals. Science 284, 760-765.
14. Cerdán PD, Chory J (2003). Regulation of flowering time by light quality. Nature 423, 881-885.
15. Cober ER, Tanner JW, Voldeng HD (1996). Genetic control of photoperiod response in early-maturing near-isogenic soybean lines. Crop Sci. 36, 601-605.
16. Cober ER, Voldeng HD (2001). A new soybean maturity and photoperiod-sensitivity locus linked to E1 and T. Crop Sci. 41, 698-701.
17. Covington MF, Panda S, Liu XL, Strayer C, Wagner DR, Kay SA (2001). ELF3 modulates resetting of the circadian clock in Arabidopsis. Plant Cell 13, 1305-1315.
18. Curtis DF, Tanner JW, Luzzi BM, Hume DJ (2000). Agronomic and phenological differences of soybean isolines differing in maturity and growth habit. Crop Sci. 40, 1624-1629.
19. Destro D, Carpentieri-Pípolo V, Kiihl RAS, Almeida LA (2001). Photoperiodism and genetic control of the long juvenile period in soybean: A review. Crop Breeding Appl. Biotechnol. 1, 72-92.
20. Doyle MR, Davis SJ, Bastow RM, McWatters HG, Kozma-Bognár L, Nagy F et al. (2002). The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature 419, 74-77.
21. Eriksson ME, Hanano S, Southern MM, Hall A, Millar AJ (2003). Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta 218, 159-162.
22. Fujimori T, Yamashino T, Kato T, Mizuno T (2004). Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana. Plant Cell Physiol. 45, 1078-86.
23. Garner WW, Allard HA (1933). Comparative responses of long-day and short-day plants to relative length of day and night. Plant Physiol. 8, 347-356.
24. Griffiths S, Dunford RP, Coupland G, Laurie DA (2003). The evolution of CONSTANS -like gene families in barley, rice, and Arabidopsis. Plant Physiol. 131, 1855-1867.
25. Guo H, Duong H, Ma N, Lin C (1999). The Arabidopsis blue light receptor cryptochrome 2 is a nuclear protein regulated by a blue ligh-dependent post-transcriptional mechanism. Plant J. 19, 279-87.
26. Halliday KJ, Salter MG, Thingnaes E, Whitelam GC (2003). Phytochrome control of flowering is temperature sensitive and correlates with expression of the floral integrator FT. Plant J. 33, 875-885.
27. Hartmann U, Hohmann S, Nettesheim K, Wisman E, Saedler H, Huijser P (2000). Molecular cloning of SVP: A negative regulator of the floral transition in Arabidopsis. Plant J. 21, 351-360.
28. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T et al. (2000). Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110-2113.
29. Hayama R, Coupland G (2004). The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. Plant Physiol. 135, 677-684.
30. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005). LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc. Natl. Acad. Sci. USA 102, 10387-10392.
31. He Y, Doyle MR, Amasino RM (2004). PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev. 18, 2774-2784.
32. Hecht V, Foucher F, Ferrándiz C, Macknight R, Navarro C, Vardy ME et al. (2005). Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol. 137, 1420-1434.
33. Hicks KA, Millar AJ, CarréIA, Somers DE, Straume M, Meeks-Wagner DR et al. (1996). Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant. Science 274, 790-792.
34. Imaizumi T, Tran HG, Swartz TE, Briggs WR, Kay SA (2003). FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature 426, 302-306.
35. Imaizumi T, Schultz TF, Harmon FG, Ho LA, Kay SA (2005). FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309, 293-297.
36. Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K (2002). Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev. 16, 2006-2020.
37. Kikis EA, Khanna R, Quail PH (2005). ELF4 is a phytochrome-regulated component of a negative-feedback loop involving the central oscillator components CCA1 and LHY. Plant J. 44, 300-313.
38. Koornneef M, Hanhart CJ, van der Veen JH (1991). A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol. Gen. Genet. 229, 57-66.
39. Liu XL, Covington MF, Fankhauser C, Chory J, Wanger DR (2001). ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway. Plant Cell 13, 1293-1304.
40. Makino S, Kiba T, Imamura A, Hanaki N, Nakamura A, Suzuki T et al. (2000). Genes encoding pseudo-response regulators: Insight into His-to-Asp phosphorelay and circadian rhythm in Arabidopsis thaliana. Plant Cell Physiol. 41, 791-803.
41. Makino S, Matsushika A, Kojima M, Oda Y, Mizuno T (2001). Light response of the circadian waves of the APRR1/TOC1 quintet: When does the quintet start singing rhythmically in Arabidopsis ?Plant Cell Physiol. 42, 334-339.
42. Matsushika A, Makino S, Kojima M, Mizuno T (2000). Circadian waves of expression of the APRR1/TOC1 family of pseudoresponse regulators in Arabidopsis thaliana: Insight into the plant circadian clock. Plant Cell Physiol. 41, 1002-1012.
43. McBlain B, Bernard RL (1987). A new gene affecting the time of flowering and maturity in soybean. J. Hered. 78, 160-162.
44. McWatters HG, Bastow RM, Hall A, Millar AJ (2000). The ELF3 zeitnehmer regulates light signaling to the circadian clock. Nature 408, 716-720.
45. Michaels SD, Amasino RM (1999). FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949-956.
46. Millar AJ (2004). Input signals to the plant circadian clock. J. Exp. Bot. 55, 277-283.
47. Mizoguchi T, Wright L, Fujiwara S, Cremer F, Lee K, Onouchi H et al. (2005). Distinct roles of GIGANTEA in promoting flowering and regulating circadian rhythms in Arabidopsis. Plant Cell 17, 2255-2270.
48. Mockler T, Yang H, Yu X, Parikh D, Cheng YC, Dolan S et al. (2003). Regulation of photoperiodic flowering by Arabidopsis photoreceptors. Proc. Natl. Acad. Sci. USA 100, 2140-2145.
49. Mueller CL, Porter SE, Hoffman MG, Jaehning JA (2004). The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol. Cell 14, 447-456.
50. Nakamichi N, Kita M, Ito S, Sato E, Yamashino T, Mizuno T (2005). PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Plant Cell Physiol. 46, 686-698.
51. Nelson DC, Lasswell J, Rogg LE, Cohen MA, Bartel B (2000). FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis. Cell 101, 331-340.
52. Noh B, Lee S-H, Kim H-J, Yi G, Shin EA, Lee M et al. (2004). Divergent roles of a pair of homologous Jumonji/Zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16, 2601-2613.
53. Noh YS, Bizzell CM, Noh B, Schomburg FM, Amasino RM (2004). EARLY FLOWERING 5 acts as a floral repressor in Arabidopsis. Plant J. 38, 664-672.
54. Onouchi H, Igeno MI, Perilleux C, Graves K, Coupland G (2000). Mutagenesis of plants overexpressing CONSTANS demonstrates novel interactions among Arabidopsis flowering-time genes. Plant Cell 12, 885-900.
55. Parker MW, Borthwick HA (1950). Influence of light on plant growth. Annu. Rev. Plant Physiol. 1, 43-58.
56. Putterill J, Robson F, Lee K, Simon R, Coupland G (1995). The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80, 847-857.
57. Quecini V, Zucchi MI, Baldin J, Vello NA (2007). In silico analysis of candidate genes involved in light sensing and signal transduction pathways in soybean. Brazil. J. Plant Physiol. (submitted).
58. Ray JD, Hinson K, Manjono JEB, Malo MF (1995). Genetic control of a long-juvenile trait in soybean. Crop Sci. 35, 1001-1006.
59. Saindon G, Voldeng HD, Beversdorf WD, Buzzell RI (1989). Genetic control of long daylength response in soybean. Crop Sci. 29, 1436-1439.
60. SaloméPA, McClung CR (2005). PSEUDO-RESPONSE REGULATOR 7 and 9 are partially redundant genes essential for the temperature responsiveness of the Arabidopsis circadian clock. Plant Cell 17, 791-803.
61. Schultz TF, Kiyosue T, Yanovsky M, Wada M, Kay SA (2001). A role for LKP2 in the circadian clock of Arabidopsis. Plant Cell 13, 2659-2670.
62. Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, CarréIA et al. (1998). The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93, 1219-1229.
63. Sharrock RA, Quail PH (1989). Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 3, 1745-1757.
64. Strayer CA, Oyama T, Schultz TF, Raman R, Somers DE, Más P et al. (2000). Cloning of the Arabidopsis clock gene TOC1, an auto-regulatory response regulator homolog. Science 289, 768-771.
65. Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410, 1116-1120.
66. Summerfield RJ, Roberts EH (1985). Glycine max. In: Halevy AH, ed. CRC Handbook of Flowering. Vol. I. CRC Press, Boca Raton. pp. 100-117.
67. Tasma IM, Shoemaker RC (2003). Mapping flowering time gene homologs in soybean and their association with maturity (E) loci. Crop Sci. 43, 319-328.
68. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The CLUSTALX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25, 4876-4882.
69. Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G (2004). Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 303, 1003-1006.
70. Wang ZY, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EM (1997) A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9, 491-507.
71. Wang ZY, Tobin EM (1998). Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93, 1207-1217.
72. Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU et al. (2005). Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309, 1056-1059.
73. Yanovsky MJ, Kay SA (2002). Molecular basis of seasonal time measurement in Arabidopsis. Nature 419, 308-312.
74. Yanovsky MJ, Kay SA (2003). Living by the calendar: How plants know when to flower. Mol. Cell Biol. 4, 265-275.