title: Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions.
abstract: Seed germination is a complex trait of key ecological and agronomic significance. Few genetic factors regulating germination have been identified, and the means by which their concerted action controls this developmental process remains largely unknown. Using publicly available gene expression data from Arabidopsis thaliana, we generated a condition-dependent network model of global transcriptional interactions (SeedNet) that shows evidence of evolutionary conservation in flowering plants. The topology of the SeedNet graph reflects the biological process, including two state-dependent sets of interactions associated with dormancy or germination. SeedNet highlights interactions between known regulators of this process and predicts the germination-associated function of uncharacterized hub nodes connected to them with 50% accuracy. An intermediate transition region between the dormancy and germination subdomains is enriched with genes involved in cellular phase transitions. The phase transition regulators SERRATE and EARLY FLOWERING IN SHORT DAYS from this region affect seed germination, indicating that conserved mechanisms control transitions in cell identity in plants. The SeedNet dormancy region is strongly associated with vegetative abiotic stress response genes. These data suggest that seed dormancy, an adaptive trait that arose evolutionarily late, evolved by coopting existing genetic pathways regulating cellular phase transition and abiotic stress. SeedNet is available as a community resource (http://vseed.nottingham.ac.uk) to aid dissection of this complex trait and gene function in diverse processes.
authors: Division of Plant and Crop Sciences, School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, United Kingdom. george.bassel@nottingham.ac.uk
authors: George W
authors: GW
authors: Bassel
authors: Hui
authors: H
authors: Lan
authors: Enrico
authors: E
authors: Glaab
authors: Daniel J
authors: DJ
authors: Gibbs
authors: Tanja
authors: T
authors: Gerjets
authors: Natalio
authors: N
authors: Krasnogor
authors: Anthony J
authors: AJ
authors: Bonner
authors: Michael J
authors: MJ
authors: Holdsworth
authors: Nicholas J
authors: NJ
authors: Provart
references: Plant Cell. 2001 May;13(5):1011-24
references: 11340178
references: Plant J. 2006 Sep;47(6):841-50
references: 16889646
references: Plant J. 2006 Jun;46(5):805-22
references: 16709196
references: Plant Cell. 2003 Mar;15(3):681-93
references: 12615941
references: Plant Cell Physiol. 2007 Mar;48(3):381-90
references: 17251202
references: Dev Biol. 2000 Apr 15;220(2):412-23
references: 10753527
references: Development. 1999 Nov;126(21):4763-70
references: 10518493
references: Plant Cell Physiol. 2000 Mar;41(3):251-7
references: 10805587
references: New Phytol. 2010 Jun;186(4):817-831
references: 20406407
references: Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18843-8
references: 19843695
references: BMC Genomics. 2007 Jul 24;8:246
references: 17645808
references: Plant J. 2007 Jul;51(1):60-78
references: 17461781
references: Plant J. 2005 Mar;41(5):697-709
references: 15703057
references: Mamm Genome. 2007 Jul;18(6-7):463-72
references: 17668265
references: BMC Bioinformatics. 2009 Oct 28;10:358
references: 19863798
references: Plant Cell. 1997 Jul;9(7):1055-1066
references: 12237375
references: Plant Cell. 2004 Feb;16(2):367-78
references: 14729916
references: Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4776-81
references: 20176939
references: Plant Cell. 2003 Jul;15(7):1591-604
references: 12837949
references: Science. 2010 Jan 29;327(5965):546
references: 20110497
references: Plant Cell Environ. 2009 Dec;32(12):1633-51
references: 19712066
references: Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11661-6
references: 19564609
references: Plant J. 2007 Apr;50(2):347-63
references: 17376166
references: Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4264-9
references: 20145108
references: Plant J. 2008 Jan;53(2):214-24
references: 18028281
references: Science. 1999 Oct 15;286(5439):509-12
references: 10521342
references: Plant Cell. 2006 Dec;18(12):3415-28
references: 17194765
references: Nat Biotechnol. 2010 Feb;28(2):149-56
references: 20118918
references: Plant J. 2005 Jul;43(1):153-63
references: 15960624
references: Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4549-54
references: 19255443
references: Stat Appl Genet Mol Biol. 2005;4:Article17
references: 16646834
references: New Phytol. 2008;179(1):33-54
references: 18422904
references: Plant Cell. 2006 Aug;18(8):1887-99
references: 16844907
references: Plant Physiol. 2008 May;147(1):143-55
references: 18359847
references: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
references: 11309499
references: Cell. 2000 Jul 7;102(1):109-26
references: 10929718
references: BMC Bioinformatics. 2003 Jan 13;4:2
references: 12525261
references: Plant Physiol. 2007 Jul;144(3):1391-406
references: 17478635
references: Plant J. 2000 Jan;21(2):143-55
references: 10743655
references: Trends Plant Sci. 2008 Jan;13(1):36-43
references: 18160330
references: Plant J. 2001 Jun;26(6):627-35
references: 11489176