Skip to main content
SpringerLink
Log in

Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

The aim of this study has been to identify important processes that regulate early stages of embryo development in conifers. Somatic embryogenesis in Picea abies has become a model system for studying embryology in conifers, providing a well-characterized sequence of developmental stages, resembling zygotic embryogeny, which can be synchronized by specific treatments, making it possible to collect a large number of somatic embryos at specific developmental stages. We have used this model to analyze global changes in gene expression during early stages of embryo development by generating an expression profile of 12,536 complementary DNA clones. This has allowed us to identify molecular events regulating putative processes associated with pattern formation during the earliest stages of embryogenesis which have not been identified on the molecular level in conifers before. We recognize notable changes in the expression of genes involved in regulating auxin biosynthesis and auxin response, gibberellin-mediated signaling, signaling between the embryo and the female gametophyte, tissue specification including the formation of boundary regions, and the switch from embryonic to vegetative development. In addition, our results confirm the involvement of previously described processes, including stress, differentiation of a protoderm, and programmed cell death.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J (2006) The LCB data warehouse. Bioinformatics 22:1024–1026

    Article  PubMed  CAS  Google Scholar 

  • Azevedo H, Lino-Neto T, Tavares R (2003) An improved method for high-quality RNA isolation from needles of adult maritime pine trees. Plant Mol Biol Report 21:333–338. doi:10.1007/BF02772582

    Article  CAS  Google Scholar 

  • Becerra C, Puigdomenech P, Vicient CM (2006) Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development. BMC Genomics 7:38. doi:1471-2164-7-38

    Article  PubMed  Google Scholar 

  • Berardini TZ, Mundodi S, Reiser L et al (2004) Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol 135:745–755

    Article  PubMed  CAS  Google Scholar 

  • Bozhkov PV, Arnold SV (1998) Polyethylene glycol promotes maturation but inhibits further development of Picea abies somatic embryos. Physiol Plant 104:211–224. doi:10.1034/j.1399-3054.1998.1040209.x

    Article  CAS  Google Scholar 

  • Bozhkov PV, Filonova LH, Suarez MF, Helmersson A, Smertenko AP, Zhivotovsky B, von Arnold S (2004) VEIDase is a principal caspase-like activity involved in plant programmed cell death and essential for embryonic pattern formation. Cell Death Differ 11:175–182

    Article  PubMed  CAS  Google Scholar 

  • Bozhkov PV, Suarez MF, Filonova LH, Daniel G, Zamyatnin AA, Rodriguez-Nieto S, Zhivotovsky B, Smertenko A (2005) Cysteine protease mcII-Pa executes programmed cell death during plant embryogenesis. Proc Natl Acad Sci USA 102:14463–14468. doi:10.1073/pnas.0506948102

    Article  PubMed  CAS  Google Scholar 

  • Busov V, Meilan R, Pearce DW, Rood SB, Ma C, Tschaplinski TJ, Strauss SH (2006) Transgenic modification of gai or rgl1 causes dwarfing and alters gibberellins, root growth, and metabolite profiles in Populus. Planta 224:288–299. doi:10.1007/s00425-005-0213-9

    Article  PubMed  CAS  Google Scholar 

  • Cairney J, Pullman GS (2007) The cellular and molecular biology of conifer embryogenesis. New Phytol 176:511–536. doi:NPH2239

    Article  PubMed  CAS  Google Scholar 

  • Cairney J, Zheng L, Cowels A et al (2006) Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. Plant Mol Biol 62:485–501

    Article  PubMed  Google Scholar 

  • Ciavatta VT, Egertsdotter U, Clapham D, von Arnold S, Cairney J (2002) A promoter from the loblolly pine PtNIP1;1 gene directs expression in an early-embryogenesis and suspensor-specific fashion. Planta 215:694–698. doi:12172854

    Article  PubMed  CAS  Google Scholar 

  • Doebley J, Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10:1075–1082

    Article  PubMed  CAS  Google Scholar 

  • Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321. doi:10.1016/j.cell.2006.12.006

    Article  PubMed  CAS  Google Scholar 

  • Filonova LH, Bozhkov PV, von Arnold S (2000a) Developmental pathway of somatic embryogenesis in Picea abies as revealed by time-lapse tracking. J Exp Bot 51:249–264

    Article  PubMed  CAS  Google Scholar 

  • Filonova LH, Bozhkov PV, Brukhin VB, Daniel G, Zhivotovsky B, von Arnold S (2000b) Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm, Norway spruce. J Cell Sci 113(Pt 24):4399–4411

    PubMed  CAS  Google Scholar 

  • Footitt S, Ingouff M, Clapham D, von Arnold S (2003) Expression of the viviparous 1 (Pavp1) and p34cdc2 protein kinase (cdc2Pa) genes during somatic embryogenesis in Norway spruce (Picea abies [L.] Karst). J Exp Bot 54:1711–1719. doi:12754264

    Article  PubMed  CAS  Google Scholar 

  • Franks L, Fischer (2006) SEUSS and LEUNIG regulate cell proliferation, vascular development and organ polarity in Arabidopsis petals. Planta 224:801–811. doi:10.1007/s00425-006-0264-6

    Article  PubMed  CAS  Google Scholar 

  • Gaj MD, Zhang S, Harada JJ, Lemaux PG (2005) Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis. Planta 222:977–988. doi:10.1007/s00425-005-0041-y

    Article  PubMed  CAS  Google Scholar 

  • Giraudat J, Hauge BM, Valon C, Smalle J, Parcy F, Goodman HM (1992) Isolation of the Arabidopsis ABI3 gene by positional cloning. Plant Cell 4:1251–1261. doi:10.1105/tpc.4.10.1251

    Article  PubMed  CAS  Google Scholar 

  • Goldberg RB, Paiva GD, Yadegari R (1994) Plant embryogenesis: zygote to seed. Science 266:605–614

    Article  PubMed  CAS  Google Scholar 

  • Gong Z, Koiwa H, Cushman MA et al (2001) Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiol 126:363–375. doi:10.1104/pp.126.1.363

    Article  PubMed  CAS  Google Scholar 

  • Gyllenstrand N, Clapham D, Källman T, Lagercrantz U (2007) A Norway spruce FLOWERING LOCUS T homolog is implicated in control of growth rhythm in conifers. Plant Physiol 144:248–257. doi:pp.107.095802

    Article  PubMed  CAS  Google Scholar 

  • Haecker A, Gross-Hardt R, Geiges B, Sarkar A, Breuninger H, Herrmann M, Laux T (2004) Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131:657–668. doi:10.1242/dev.00963

    Article  PubMed  CAS  Google Scholar 

  • Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J (2000) A concise guide to cDNA microarray analysis. Biotechniques 29:548–550, 552–4, 556 passim

    PubMed  CAS  Google Scholar 

  • Hirano H, Harashima H, Shinmyo A, Sekine M (2008) Arabidopsis RETINOBLASTOMA-RELATED PROTEIN 1 is involved in G1 phase cell cycle arrest caused by sucrose starvation. Plant Mol Biol 66:259–275. doi:10.1007/s11103-007-9268-2

    Article  PubMed  CAS  Google Scholar 

  • Ikeda-Iwai M, Umehara M, Satoh S, Kamada H (2003) Stress-induced somatic embryogenesis in vegetative tissues of Arabidopsis thaliana. Plant J 34:107–114. doi:10.1046/j.1365-313X.2003.01702.x

    Article  PubMed  CAS  Google Scholar 

  • Indrianto A, Barinova I, Touraev A, Heberle-Bors E (2001) Tracking individual wheat microspores in vitro: identification of embryogenic microspores and body axis formation in the embryo. Planta 212:163–174

    Article  PubMed  CAS  Google Scholar 

  • Ingouff M, Farbos I, Lagercrantz U, von Arnold S (2001) PaHB1 is an evolutionary conserved HD-GL2 homeobox gene expressed in the protoderm during Norway spruce embryo development. Genesis 30:220–230

    Article  PubMed  CAS  Google Scholar 

  • Jang JC, Fujioka S, Tasaka M, Seto H, Takatsuto S, Ishii A, Aida M, Yoshida S, Sheen J (2000) A critical role of sterols in embryonic patterning and meristem programming revealed by the fackel mutants of Arabidopsis thaliana. Genes Dev 14:1485–1497

    PubMed  CAS  Google Scholar 

  • Jenik PD, Gillmor CS, Lukowitz W (2007) Embryonic patterning in Arabidopsis thaliana. Annu Rev Cell Dev Biol 23:207–236. doi:10.1146/annurev.cellbio.22.011105.102609

    Article  PubMed  CAS  Google Scholar 

  • Koyama T, Furutani M, Tasaka M, Ohme-Takagi M (2007) TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis. Plant Cell 19:473–484

    Article  PubMed  CAS  Google Scholar 

  • Kragh KM, Jacobsen S, Mikkelsen JD, Nielsen KA (1993) Tissue specificity and induction of class I, II and III chitinases in barley (Hordeum vulgare). Physiol Plant 89:490–498. doi:10.1111/j.1399-3054.1993.tb05203.x

    Article  CAS  Google Scholar 

  • Kunieda T, Mitsuda N, Ohme-Takagi M, Takeda S, Aida M, Tasaka M, Kondo M, Nishimura M, Hara-Nishimura I (2008) NAC family proteins NARS1/NAC2 and NARS2/NAM in the outer integument regulate embryogenesis in Arabidopsis. Plant Cell 20:2631–2642. doi:10.1105/tpc.108.060160

    Article  PubMed  CAS  Google Scholar 

  • Larsson E, Sitbon F, Ljung K, von Arnold S (2008) Inhibited polar auxin transport results in aberrant embryo development in Norway spruce. New Phytol 177:356–366. doi:10.1111/j.1469-8137.2007.02289.x

    PubMed  CAS  Google Scholar 

  • Laux T, Würschum T, Breuninger H (2004) Genetic regulation of embryonic pattern formation. Plant Cell 16(Suppl):S190–S202. doi:10.1105/tpc.016014

    Article  PubMed  CAS  Google Scholar 

  • Lindsey K, Topping JF (1993) Embryogenesis: a question of pattern. J Exp Bot 44:359–374. doi:10.1093/jxb/44.2.359

    Article  Google Scholar 

  • Lotan T, Ohto M, Yee KM, West MA, Lo R, Kwong RW, Yamagishi K, Fischer RL, Goldberg RB, Harada JJ (1998) Arabidopsis LEAFY COTYLEDON1 is sufficient to induce embryo development in vegetative cells. Cell 93:1195–1205

    Article  PubMed  CAS  Google Scholar 

  • Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, Masson P, Barton MK (1999) The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126:469–481

    PubMed  CAS  Google Scholar 

  • Mikkelsen MD, Naur P, Halkier BA (2004) Arabidopsis mutants in the C-S lyase of glucosinolate biosynthesis establish a critical role for indole-3-acetaldoxime in auxin homeostasis. Plant J 37:770–777

    Article  PubMed  CAS  Google Scholar 

  • Navarro C, Efremova N, Golz JF, Rubiera R, Kuckenberg M, Castillo R, Tietz O, Saedler H, Schwarz-Sommer Z (2004) Molecular and genetic interactions between STYLOSA and GRAMINIFOLIA in the control of Antirrhinum vegetative and reproductive development. Development 131:3649–3659

    Article  PubMed  CAS  Google Scholar 

  • Nolan KE, Kurdyukov S, Rose RJ (2009) Expression of the SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1 (SERK1) gene is associated with developmental change in the life cycle of the model legume Medicago truncatula. J Exp Bot 60:1759–1771. doi:10.1093/jxb/erp046

    Article  PubMed  CAS  Google Scholar 

  • Pagnussat GC, Yu H, Ngo QA, Rajani S, Mayalagu S, Johnson CS, Capron A, Xie L, Ye D, Sundaresan V (2005) Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 132:603–614. doi:dev.01595

    Article  PubMed  CAS  Google Scholar 

  • Palovaara J, Hakman I (2008) Conifer WOX-related homeodomain transcription factors, developmental consideration and expression dynamic of WOX2 during Picea abies somatic embryogenesis. Plant Mol Biol 66:533–549. doi:10.1007/s11103-008-9289-5

    Article  PubMed  CAS  Google Scholar 

  • Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10:603–609. doi:10.1016/j.tplants.2005.10.003

    Article  PubMed  CAS  Google Scholar 

  • Rieu I, Eriksson S, Powers SJ et al (2008) Genetic analysis reveals that C19-GA 2-oxidation is a major gibberellin inactivation pathway in Arabidopsis. Plant Cell 20:2420–2436. doi:10.1105/tpc.108.058818

    Article  PubMed  CAS  Google Scholar 

  • Sahlén K (1992) Anatomical and physiological ripening of Pinus sylvestris L. seeds in northern Fennoscandia. Sveriges lantbruksuniversitet, Uppsala

  • Schmidt ED, Guzzo F, Toonen MA, de Vries SC (1997) A leucine-rich repeat containing receptor-like kinase marks somatic plant cells competent to form embryos. Development 124:2049–2062

    PubMed  CAS  Google Scholar 

  • Shin R, Burch AY, Huppert KA, Tiwari SB, Murphy AS, Guilfoyle TJ, Schachtman DP (2007) The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell 19:2440–2453. doi:10.1105/tpc.107.050963

    Article  PubMed  CAS  Google Scholar 

  • Shuai B, Reynaga-Peña CG, Springer PS (2002) The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol 129:747–761. doi:10.1104/pp.010926

    Article  PubMed  CAS  Google Scholar 

  • Silverstone AL, Tseng T, Swain SM, Dill A, Jeong SY, Olszewski NE, Sun T (2007) Functional analysis of SPINDLY in gibberellin signaling in Arabidopsis. Plant Physiol 143:987–1000. doi:pp.106.091025

    Article  PubMed  CAS  Google Scholar 

  • Singh H (1978) Embryology of conifers. In: Zimmermann O, Carlquist S, Ozenda P, Wulff HD (eds) Handbuch der Pflanzenanatomie. Gerbruder Borntraeger, Berlin, pp 187–241

    Google Scholar 

  • Smith SA, Beaulieu JM, Donoghue MJ (2010) An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci USA 107:5897–5902. doi:10.1073/pnas.1001225107

    Article  PubMed  CAS  Google Scholar 

  • Stasolla C, van Zyl L, Egertsdotter U, Craig D, Liu W, Sederoff RR (2003) The effects of polyethylene glycol on gene expression of developing white spruce somatic embryos. Plant Physiol 131:49–60. doi:12529514

    Article  PubMed  CAS  Google Scholar 

  • Stasolla C, Bozhkov PV, Chu T, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR (2004) Variation in transcript abundance during somatic embryogenesis in gymnosperms. Tree Physiol 24:1073–1085

    PubMed  CAS  Google Scholar 

  • Suarez MF, Filonova LH, Smertenko A, Savenkov EI, Clapham DH, von Arnold S, Zhivotovsky B, Bozhkov PV (2004) Metacaspase-dependent programmed cell death is essential for plant embryogenesis. Curr Biol 14:R339–R340

    Article  PubMed  CAS  Google Scholar 

  • Swidzinski JA, Sweetlove LJ, Leaver CJ (2002) A custom microarray analysis of gene expression during programmed cell death in Arabidopsis thaliana. Plant J 30:431–446

    Article  PubMed  CAS  Google Scholar 

  • Tahir M, Law DA, Stasolla C (2006) Molecular characterization of PgAGO, a novel conifer gene of the Argonaute family expressed in apical cells and required for somatic embryo development in spruce. Tree Physiol 26:1257–1270

    PubMed  CAS  Google Scholar 

  • Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121

    Article  PubMed  CAS  Google Scholar 

  • Tzafrir I, Pena-Muralla R, Dickerman A et al (2004) Identification of genes required for embryo development in Arabidopsis. Plant Physiol 135:1206–1220. doi:15266054

    Article  PubMed  CAS  Google Scholar 

  • van Zyl L, von Arnold S, Bozhkov P, Chen Y, Egertsdotter U, Mackay J, Sederoff RR, Shen J, Zelena L, Clapham DH (2002) Heterologous array analysis in pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. taeda, P. sylvestris or Picea abies. Comp Funct Genomics 3:306–318. doi:10.1002/cfg.199

    Article  PubMed  Google Scholar 

  • van Zyl L, Bozhkov PV, Clapham DH, Sederoff RR, von Arnold S (2003) Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis. Gene Expr Patterns 3:83–91

    Article  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • von Arnold S, Clapham D (2008) Spruce embryogenesis. In: Suárez MF, Bozhkov PV (eds) Plant embryogenesis methods in molecular biology. Humana, Totowa, pp 31–47

    Chapter  Google Scholar 

  • von Arnold S, Sabala I, Bozhkov P, Dyachok J, Filonova L (2002) Developmental pathways of somatic embryogenesis. Plant Cell Tissue Organ Cult 69:233–249. doi:10.1023/A:1015673200621

    Article  Google Scholar 

  • Wadenbäck J, von Arnold S, Egertsdotter U, Walter MH, Grima-Pettenati J, Goffner D, Gellerstedt G, Gullion T, Clapham D (2008) Lignin biosynthesis in transgenic Norway spruce plants harboring an antisense construct for cinnamoyl CoA reductase (CCR). Transgenic Res 17:379–392. doi:10.1007/s11248-007-9113-z

    Article  PubMed  Google Scholar 

  • Wang T, Li H, Zhang J, Ouyang B, Lu Y, Ye Z (2009) Initiation and development of microspore embryogenesis in recalcitrant purple flowering stalk (Brassica campestris ssp. chinensis var. purpurea Hort.) genotypes. Sci Hortic 121:419–424. doi:10.1016/j.scienta.2009.03.012

    Article  Google Scholar 

  • Wiweger M, Farbos I, Ingouff M, Lagercrantz U, Von Arnold S (2003) Expression of Chia4-Pa chitinase genes during somatic and zygotic embryo development in Norway spruce (Picea abies): similarities and differences between gymnosperm and angiosperm class IV chitinases. J Exp Bot 54:2691–2699. doi:10.1093/jxb/erg299

    Article  PubMed  CAS  Google Scholar 

  • Xing S, Rosso MG, Zachgo S (2005) ROXY1, a member of the plant glutaredoxin family, is required for petal development in Arabidopsis thaliana. Development 132:1555–1565. doi:10.1242/dev.01725

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to Robin Buell at TIGR for conducting microarray assays and to Adam Ameur for helping with the microarray analysis. The work was supported by grants from the Swedish Research Council, the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (SvA), and National Science Foundation (No 0543503, JC).

Author information

Authors and Affiliations

  1. Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07, Uppsala, Sweden

    Daniel Vestman, Emma Larsson, Daniel Uddenberg, David Clapham, Eva Sundberg & Sara von Arnold

  2. NanoBiotechnologies, 2910 North Druid Hills Road, Suite D, Atlanta, GA, 30329, USA

    John Cairney

Authors
  1. Daniel Vestman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Emma Larsson
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Daniel Uddenberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. John Cairney
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. David Clapham
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Eva Sundberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Sara von Arnold
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel Vestman.

Additional information

Communicated by J. Dean

Electronic supplementary materials

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

Microarray experimental design (GIF 13 kb)

High-Resolution (TIFF 223 kb)

Supplemental Fig. 2

Evaluation of reference genes. Ten potential reference genes were evaluated using the GeNorm software (Vandesompele et al. 2002). The most suitable pair of genes share the top ranking while the remaining genes are ordered according to their potential as additional reference genes. Three genes (EF1-α, PHOSPHOGLUCOMUTASE, and CDC2) were selected for further use as qRT-PCR internal controls. (PDF 91 kb)

Supplementary Table 1

Primer sequences used for qRT-PCR (5′ to 3′ orientation) (PDF 61 kb)

Supplementary Table 2

Differentially expressed genes in Norway spruce. (XLS 351 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vestman, D., Larsson, E., Uddenberg, D. et al. Important processes during differentiation and early development of somatic embryos of Norway spruce as revealed by changes in global gene expression. Tree Genetics & Genomes 7, 347–362 (2011). https://doi.org/10.1007/s11295-010-0336-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-010-0336-4

Keywords

Search

Navigation