Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis
- 72 Downloads
Suitability of wood biomass for pulp production is dependent on the cellular architecture and composition of secondary cell wall. Presently, systems genetics approach is being employed to understand the molecular basis of trait variation and co-expression network analysis has enabled holistic understanding of complex trait such as secondary development. Transcription factors (TFs) are reported as key regulators of meristematic growth and wood formation. The hierarchical TF network is a multi-layered system which interacts with downstream structural genes involved in biosynthesis of cellulose, hemicelluloses and lignin. Several TFs have been associated with wood formation in tree species such as Populus, Eucalyptus, Picea and Pinus. However, TF-specific co-expression networks to understand the interaction between these regulators are not reported. In the present study, co-expression network was developed for TFs expressed during wood formation in Eucalyptus tereticornis and ethylene-responsive element-binding factor, EtERF2, was identified as the major hub transcript which co-expressed with other secondary cell wall biogenesis-specific TFs such as EtSND2, EtVND1, EtVND4, EtVND6, EtMYB70, EtGRAS and EtSCL8. This study reveals a probable role of ethylene in determining natural variation in wood properties in Eucalyptus species. Understanding this transcriptional regulation underpinning the complex bio-processing trait of wood biomass will complement the Eucalyptus breeding program through selection of industrially suitable phenotypes by marker-assisted selection.
KeywordsCo-expression network Ethylene Regulation Transcription factor Wood formation
We acknowledge the guidance given by Dr. Jennifer Dewoody, National Forest Genetics Laboratory, USDA Forest Service, Placerville, CA; Dr. Sucheta Tripathy, Structural Biology and Bio-informatics Division, Indian Institute of Chemical Biology, Kolkata, India; Dr. Saravanakumar Selvaraj, Centre for Pharmacology and Toxicology, Hannover Medical School, Hannover, Germany, and Dr. Gayatri Ramakrishnan, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India, for developing gene regulatory networks. The funding for the research work was provided to Dr. Modhumita Ghosh Dasgupta by Department of Biotechnology, Government of India, under the research project with grant number BT/PR10055/PBD/16/772/2007. The funding support as research fellowship was provided to Dr. Veeramuthu Dharanishanthi by Department of Biotechnology, Government of India.
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
- Andersson-Gunnerås S, Mellerowicz EJ, Love J, Segerman B, Ohmiya Y, Coutinho PM, Nilsson P, Henrissat B, Moritz T, Sundberg B (2006) Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis. Plant J 45:144–165CrossRefPubMedGoogle Scholar
- Barros E, Staden CA, Lezar S (2009) A microarray-based method for the parallel analysis of genotypes and expression profiles of wood-forming tissues in Eucalyptus grandis. BMC Biotechnol 9(51):1472–6750Google Scholar
- Goicoechea M, Lacombe E, Legay S, Mihaljevic S, Rech P, Jauneau A, Lapierre C, Pollet B, Verhaegen D, Chaubet-Gigot N, Grima-Pettenati J (2005) EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis. Plant J 43:553–567CrossRefPubMedGoogle Scholar
- Hussey SG, Mizrachi E, Spokevicius AV, Bossinger G, Berger DK, Myburg AA (2011) SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus. BMC Plant Biol 11:173CrossRefPubMedPubMedCentralGoogle Scholar
- Li E, Bhargava A, Qiang W, Friedmann MC, Forneris N, Savidge RA, Johnson LA, Mansfield SD, Ellis BE, Douglas CJ (2012) The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus. New Phytol 194:102–115CrossRefPubMedGoogle Scholar
- Mizrachi E, Verbeke L, Christie N, Fierro AC, Mansfield SD, Davis MF, Gjersing E, Tuskan GA, Montagu MV, de Peer YV, Marchal K, Myburg AA (2017) Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. Proc Natl Acad Sci 114:1195–1200CrossRefPubMedGoogle Scholar
- Porth I, Klápště J, Skyba O, Friedmann MC, Hannemann J, Ehlting J, El-Kassaby YA, Mansfield SD, Douglas CJ (2013) Network analysis reveals the relationship among wood properties, gene expression levels and genotypes of natural Populus trichocarpa accessions. New Phytol 200:727–742CrossRefPubMedGoogle Scholar
- Salazar MM, Nascimento LC, Camargo EL, Gonçalves DC, Lepikson Neto J, Marques WL, Teixeira PJ, Mieczkowski P, Mondego JM, Carazzolle MF, Deckmann AC, Pereira GA (2013) Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. BMC Genom 14:201CrossRefGoogle Scholar
- Shinya T, Iwata E, Nakahama K, Fukuda Y, Hayashi K, Nanto K, Rosa AC, Kawaoka A (2016) Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition. Front Plant Sci 7:443CrossRefPubMedPubMedCentralGoogle Scholar
- Soler M, Plasencia A, Larbat R, Pouzet C, Jauneau A, Rivas S, Pesquet E, Lapierre C, Truchet I, Grima-Pettenati J (2017) The Eucalyptus linker histone variant EgH1.3 cooperates with the transcription factor EgMYB1 to control lignin biosynthesis during wood formation. New Phytol 213:287–299CrossRefPubMedGoogle Scholar
- Vahala J, Felten J, Love J, Gorzsas A, Gerber L, Lamminmaki A, Kangasjarvi J, Sundberg B (2013) A genome-wide screen for ethylene-induced ethylene response factors (ERFs) in hybrid aspen stem identifies ERF genes that modify stem growth and wood properties. New Phytol 200:511–522CrossRefPubMedPubMedCentralGoogle Scholar
- Zhong R, Ye ZH (2014) Transcriptional regulation of biosynthesis of cell wall components during Xylem differentiation. In: Fukuda H (ed) Plant cell wall patterning and cell shape. Wiley, Hoboken, pp 351–377Google Scholar