Expression analysis of epigenetic and abscisic acid-related genes during maturation of Quercus suber somatic embryos

Plant Cell, Tissue and Organ Culture

Volumn 121, Issue 2, 2015, Pages 353-366

  Pérez, Marta ^a,b   Cañal, Maria Jesús ^a,b   Toorop, Peter E ^c  

^a UNIVERSITY OF OVIEDO   (Spain)

^b CSIC   (Spain)

^c ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

ABA; Epigenetic regulation; Gene expression; Maturation; Somatic embryogenesis

Indexed keywords

ANIMAL CELL CULTURE; GENE EXPRESSION; GENES;

ABA; CHROMATIN REMODELING; EPIGENETIC REGULATION; EXPRESSED SEQUENCE TAGS; EXPRESSION PATTERNS; HISTONE DEACETYLASES; MATURATION; SOMATIC EMBRYOGENESIS;

GENE EXPRESSION REGULATION;

EID: 84940006947     PISSN: 01676857     EISSN: 15735044     Source Type: Journal    
DOI: 10.1007/s11240-014-0706-y     Document Type: Article

References (53)

1. Aichinger E, Villar CBR, Di Mambro R, Sabatini S, Köhler C (2011) The CHD3 chromatin remodeler PICKLE and polycomb group proteins antagonistically regulate meristem activity in the Arabidopsis root. Plant Cell 23:1047–1060
2. Bassel GW, Fung P, Freeman Chow TF, Foong JA, Provart NJ, Cutler SR (2008) Elucidating the germination transcriptional program using small molecules. Plant Physiol 1476(1):143–155
3. Bueno MA, Gómez A, Manzanera JA (2000) Somatic and gametic embryogenesis in Quercus suber L. In: Jain SM, Gupta PK, Newton RJ (eds) Somatic embryogenesis in woody plants, forestry sciences, vol 6. Kluwer Academic Publishers, Dordrecht, pp 470–508
4. Chaves I, Passarinho JAP, Capitão C, Chaves MM, Fevereiro P, Ricardo CPP (2011) Temperature stress effects in Quercus suber leaf metabolism. J Plant Physiol 168:1729–1734
5. Chernys JT, Zeevaart JAD (2000) Characterization of the 9-cis-epoxycarotenoid dioxygenase gene family and the regulation of abscisic acid biosynthesis in avocado. Plant Physiol 124:343–353
6. Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12(2):133–139
7. Chinnusamy V, Gong Z, Zhu JK (2008) Abscisic acid-mediated epigenetic processes in plant development and stress responses. J Integr Plant Biol 50(10):1187–1195
8. Demidov D, Van Damme D, Geelen D, Blattner FR, Houben A (2005) Identification and dynamics of two classes of aurora-like kinases in Arabidopsis and other plants. Plant Cell 17:836–848
9. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797
10. Fleury D, Himanen K, Cnops G, Nelissen H, Boccardi TM, Maere S, Beemster GTS, Neyt P, Anami S, Robles P, Micol JL, Inzé D, van Lijsebettens M (2007) The Arabidopsis thaliana homolog of yeast BRE1 has a function in cell cycle regulation during early leaf and root growth. Plant Cell 19:417–432
11. Gao MJ, Gropp G, Wei S, Hegedus DD, Lydiate DJ (2012) Combinatorial networks regulating seed development and seed filling. In: Sato KI (ed) Embryogenesis. InTech, Rijeka. doi:10.5772/35960
12. Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C (2007) Combined networks regulating seed maturation. Trends Plant Sci 12(7):294–300
13. Kawabe A, Matsunaga S, Nakagawa K, Kurihara D, Yoneda A, Hasezawa S, Uchiyama S, Fukui K (2005) Characterization of plant aurora kinases during mitosis. Plant Mol Biol 58:1–13
14. Kermode AR (2005) Role of abscisic acid in seed dormancy. J Plant Growth Regul 24:319–344. doi:10.1007/s00344-005-0110-2
15. Kim JM, To TK, Seki M (2012) An epigenetic integrator: new insights into genome regulation, environmental stress responses and developmental controls by HISTONE DEACETYLASE 6. Plant Cell Physiol 53(5):794–800
16. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693–705
17. Lauria M, Rossi V (2011) Epigenetic control of gene regulation in plants. Biochim Biophys Acta 1809:369–378
18. Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB (2010) Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc Natl Acad Sci USA 107:8063–8070
19. Liu Y, Koornneef M, Soppe WJJ (2007) The abscense of Histone H2B Monoubiquitination in the Arabidopsishub1 (rdo4) mutant reveals a role for chromatin remodeling in seed dormancy. Plant Cell 19:433–444
20. −∆∆CT method. Methods 25:402–408
21. Long JA, Ohno C, Smith ZR, Meyerowitz EM (2006) TOPLESS regulates apical embryonic fate in Arabidopsis. Science 312:1520–1523
22. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczyzki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Dong JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acid Res 39:D225–D229
23. Marum L, Miguel A, Ricardo CP, Miguel C (2012) Reference gene selection for quantitative real-time PCR normalization in Quercus suber. PLoS ONE 7(4):e35113. doi:10.1371/journal.pone.0035113
24. Neelakandan AK, Wang K (2012) Recent progress in the understanding of tissue culture-induced genome level changes in plants and potential applications. Plant Cell Rep 31:597–620. doi:10.1007/s00299-011-1202-z
25. Pérez M, Viejo M, Lacuesta M, Toorop P, Cañal MJ (2015) Epigenetic and hormonal profile during maturation of Quercus suber L. somatic embryos. J Plant Physiol 173:51–61. doi:10.1016/j.jplph.2014.07.028
26. Puigderrajols P, Jofré A, Mir G, Pla M, Verdaguer D, Huguet G, Molinas M (2002) Developmentally and stress-induced small heat shock proteins in cork oak somatic embryos. J Exp Bot 53(373):1445–1452
27. Rai MK, Shehawat NS, Harish Gupta AK, Phulwaria M, Ram K, Jaiswal U (2011) The role of abscisic acid in plant tissue culture: a review of recent progress. Plant Cell, Tissue Organ Cult 106:179–190. doi:10.1007/s11240-011-9923-9
28. Ramakers C, Ruitjer JM, Lekanne Deprez RH, Moorman AFM (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 13:62–66
29. Rodríguez-Gacio MC, Matilla-Vázquez MA, Matilla AJ (2009) Seed dormancy and ABA signaling. Plant Signal Behav 4(11):1035–1048
30. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386
31. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37(6):e45. doi:10.1093/nar/gkp045
32. Santamaría ME, Rodríguez R, Cañal MJ, Toorop PE (2011) Transcriptome analysis of chesnut (Castanea sativa) tree buds suggests a putative role for epigenetic control of bud dormancy. Ann Bot 108:485–498
33. Seo M, Koshiba T (2002) Complex regulation of ABA biosynthesis in plants. Trends Plant Sci 7(1):41–48
34. Soler M, Serra O, Molinas M, García-Berthou E, Caritat A, Figueras M (2008) Seasonal variation in transcript abundance in cork tissue analyzed by real time RT-PCR. Tree Physiol 28:743–751
35. Šunderlíková V, Wilhem E (2002) High accumulation of legumin and Lea-like mRNAs during maturation is associated with increased conversion frequency of somatic embryos from pedunculate oak (Quercus robur L.). Protoplasma 220:97–103. doi:10.1007/s00709-002-0025-8
36. Šunderlíková V, Salaj J, Kopecky D, Salaj T, Wilhem E, Matušiková I (2009a) Dehydrin genes and their expression in recalcitrant oak (Quercus robur) embryos. Plant Cell Rep 28:1011–1021
37. Šunderlíková V, Salaj J, Matušiková I, Wilhem E (2009b) Isolation and characterization of an embryo-specific Em-like gene of pedunculate oak (Quercus robur L.) and its temporal and spatial expression patterns during somatic and zygotic embryo development. Trees 23:135–144
38. Suzuki M, McCarty DR (2008) Functional symmetry of the B3 network controlling seed development. Curr Opin Plant Biol 11:548–553
39. Suzuki M, Wang H, McCarty DR (2007) Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol 143:902–911
40. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
41. Tan BC, Joseph LM, Deng WT, Liu L, Li QB, Cline K, McCarty DR (2003) Molecular characterization of the Arabidopsis 9-cis-epoxycarotenoid dioxygenase gene family. Plant J 35:44–56
42. Tanaka M, Kikuchi A, Kamada H (2008) The Arabidopsis histone deacetylases HDA6 and HDA19 contribute to the repression of embryonic properties after germination. Plant Physiol 146:149–161
43. Tsukagoshi H, Morikami A, Nakamura K (2007) Two B3 domain transcriptional repressors prevent sugar-inducible expression of seed maturation genes in Arabidopsis seedlings. Proc Natl Acad Sci USA 104(7):2543–2547
44. Van Damme D, De Rybel B, Gudesblat G, Demidov D, Grunewald W, De Smet I, Houben A, Beeckman T, Russinova E (2011) Arabidopsis α Aurora Kinases function in formative cell división plane orientiation. Plant Cell 23(11):4013–4024
45. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:RESEARCH0034
46. Verdier J, Thompson RD (2008) Transcriptional regulation of storage protein synthesis during dicotyledon seed filing. Plant Cell Physiol 49(9):1263–1271
47. Vieitez AM, Corredoira E, Martínez MT, San-José MC, Sánchez C, Valladares S, Vidal N, Ballester A (2012) Application of biotechnological tools to Quercus improvement. Eur J Forest Res 131:519–539. doi:10.1007/s10342-011-0526-0
48. Viejo M, Santamaría ME, Rodríguez JL, Valledor L, Meijón M, Pérez M et al (2012) Epigenetics, the role of DNA methylation in tree development. In: Loyola-Vargas VM, Ochoa-Alejo N (eds) Plant cell culture methods, methods in molecular biology, vol 877. Springer, Netherlands, pp 277–301
49. Wilhem E (2000) Somatic embryogenesis in oak (Quercus spp.). In Vitro Cell Dev Biol Plant 36:349–357
50. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2:e718
51. Yadav RK, Girke T, Pasala S, Xie M, Reddy GV (2009) Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc Natl Acad Sci USA 106:4941–4946
52. Zhang H, Ogas J (2009) An epigenetic perspective on developmental regulation of seed genes. Mol Plant 2(4):610–627
53. Zhou Y, Tan B, Luo M, Li Y, Liu C, Chen C, Yu CW, Yang S, Dong S, Ruan J, Yuan L, Zhang X, Zhao L, Li C, Chen H, Cui Y, Wu K, Huang S (2013) HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings. Plant Cell 25:134–148