Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways

The identification of a gene regulatory network related to seed longevity in both Medicago truncatula and Arabidopsis reveals a role for biotic defense-related genes in acquisition of longevity. Seed longevity, the maintenance of viability during storage, is a crucial factor for preservation of genetic resources and ensuring proper seedling establishment and high crop yield. We used a systems biology approach to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes from seed developmental time courses obtained in five growth environments, we generated a robust, stable coexpression network (MatNet), thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a coexpression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis of the maturation processes in M. truncatula and Arabidopsis thaliana seeds and mining Arabidopsis interaction databases revealed conserved connectivity for 87% of longevity module nodes between both species. Arabidopsis mutant screening for longevity and maturation phenotypes demonstrated high predictive power of the longevity cross-species network. Overrepresentation analysis of the network nodes indicated biological functions related to defense, light, and auxin. Characterization of defense-related wrky3 and nf-x1-like1 (nfxl1) transcription factor mutants demonstrated that these genes regulate some of the network nodes and exhibit impaired acquisition of longevity during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating the activation of defense against pathogens.

[1]  G. Leubner‐Metzger.  Functions and regulation of β-1,3-glucanases during seed germination, dormancy release and after-ripening , 2003, Seed Science Research.

[2]  V. Lionetti,et al.  Pectin methylesterase is induced in Arabidopsis upon infection and is necessary for a successful colonization by necrotrophic pathogens. , 2011, Molecular plant-microbe interactions : MPMI.

[3]  C. Almoguera,et al.  Improved Resistance to Controlled Deterioration in Transgenic Seeds1[W][OA] , 2006, Plant Physiology.

[4]  Siobhan M Brady,et al.  Systems approaches to identifying gene regulatory networks in plants. , 2008, Annual review of cell and developmental biology.

[5]  H. Rogniaux,et al.  The regulatory gamma subunit SNF4b of the sucrose non-fermenting-related kinase complex is involved in longevity and stachyose accumulation during maturation of Medicago truncatula seeds. , 2007, The Plant journal : for cell and molecular biology.

[6]  Mingyi Wang,et al.  BMC Bioinformatics BioMed Central Database The Medicago truncatula gene expression atlas web server , 2009 .

[7]  Klaas Vandepoele,et al.  Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks1[C][W] , 2009, Plant Physiology.

[8]  Sandra Pelletier,et al.  A Regulatory Network-Based Approach Dissects Late Maturation Processes Related to the Acquisition of Desiccation Tolerance and Longevity of Medicago truncatula Seeds1[C][W][OPEN] , 2013, Plant Physiology.

[9]  J. Keilwagen,et al.  Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. , 2012, The Plant journal : for cell and molecular biology.

[10]  R. Dixon.  Engineering of plant natural product pathways. , 2005, Current opinion in plant biology.

[11]  I. Baldwin,et al.  HSPRO acts via SnRK1-mediated signaling in the regulation of Nicotiana attenuata seedling growth promoted by Piriformospora indica , 2013, Plant signaling & behavior.

[12]  R. Carranco,et al.  The HaDREB2 transcription factor enhances basal thermotolerance and longevity of seeds through functional interaction with HaHSFA9 , 2009, BMC Plant Biology.

[13]  Jonathan M. Garibaldi,et al.  ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization , 2009, BMC Bioinformatics.

[14]  Joost T. van Dongen,et al.  SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots , 2006, Proceedings of the National Academy of Sciences.

[15]  Staffan Persson,et al.  Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. , 2009, Plant, cell & environment.

[16]  M. Jacques,et al.  Identification of a molecular dialogue between developing seeds of Medicago truncatula and seedborne xanthomonads. , 2015, Journal of experimental botany.

[17]  A. Loraine,et al.  Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm1[W] , 2009, Plant Physiology.

[18]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[19]  H. Rogniaux,et al.  LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance , 2013, Journal of experimental botany.

[20]  F. V. van Eeuwijk,et al.  Natural Variation for Seed Longevity and Seed Dormancy Are Negatively Correlated in Arabidopsis1[W][OA] , 2012, Plant Physiology.

[21]  J. Buitink,et al.  The MtSNF4b subunit of the sucrose non-fermenting-related kinase complex connects after-ripening and constitutive defense responses in seeds of Medicago truncatula. , 2010, The Plant journal : for cell and molecular biology.

[22]  F Alex Feltus,et al.  The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks1[C][W][OA] , 2010, Plant Physiology.

[23]  S. Horvath,et al.  Statistical Applications in Genetics and Molecular Biology , 2011 .

[24]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[25]  K. Denby,et al.  Basal resistance against Pseudomonas syringae in Arabidopsis involves WRKY53 and a protein with homology to a nematode resistance protein. , 2007, Molecular plant-microbe interactions : MPMI.

[26]  H. Pritchard,et al.  Glutathione half-cell reduction potential: a universal stress marker and modulator of programmed cell death? , 2006, Free radical biology & medicine.

[27]  C. Morcia,et al.  From Single Genes to Co-Expression Networks: Extracting Knowledge from Barley Functional Genomics , 2005, Plant Molecular Biology.

[28]  M. A. Hemminga,et al.  Is there a role for oligosaccharides in seed longevity? An assessment of intracellular glass stability. , 2000, Plant physiology.

[29]  H. Rogniaux,et al.  Temporal profiling of the heat-stable proteome during late maturation of Medicago truncatula seeds identifies a restricted subset of late embryogenesis abundant proteins associated with longevity. , 2012, Plant, cell & environment.

[30]  M. Daws,et al.  Ecological correlates of ex situ seed longevity: a comparative study on 195 species. , 2009, Annals of botany.

[31]  Richard D. Thompson,et al.  A Combined Proteome and Transcriptome Analysis of Developing Medicago truncatula Seeds , 2007, Molecular & Cellular Proteomics.

[32]  Filip Rolland,et al.  A central integrator of transcription networks in plant stress and energy signalling , 2007, Nature.

[33]  M. Koornneef,et al.  Influence of the testa on seed dormancy, germination, and longevity in Arabidopsis. , 2000, Plant physiology.

[34]  D. Galbraith,et al.  CYP83B1, a Cytochrome P450 at the Metabolic Branch Point in Auxin and Indole Glucosinolate Biosynthesis in Arabidopsis , 2001, Plant Cell.

[35]  T. Mengiste,et al.  Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. , 2006, The Plant journal : for cell and molecular biology.

[36]  D. Walters.  Plant Defense: Warding off attack by pathogens, herbivores and parasitic plants , 2010 .

[37]  M. Kreis,et al.  AKINβγ Contributes to SnRK1 Heterotrimeric Complexes and Interacts with Two Proteins Implicated in Plant Pathogen Resistance through Its KIS/GBD Sequence1 , 2006, Plant Physiology.

[38]  Robert B Goldberg,et al.  Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[39]  François Parcy,et al.  Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. , 2008, The Plant journal : for cell and molecular biology.

[40]  T. Pham,et al.  RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice1[C][W][OA] , 2009, Plant Physiology.

[41]  B. Fan,et al.  Roles of Arabidopsis WRKY3 and WRKY4 Transcription Factors in Plant Responses to Pathogens , 2008, BMC Plant Biology.

[42]  M. Koornneef,et al.  Genetic analysis of seed-soluble oligosaccharides in relation to seed storability of Arabidopsis. , 2000, Plant physiology.

[43]  Jun Dong,et al.  Geometric Interpretation of Gene Coexpression Network Analysis , 2008, PLoS Comput. Biol..

[44]  M. Koornneef,et al.  Genetic differences in seed longevity of various Arabidopsis mutants , 2004 .

[45]  Katherine C. H. Amrine,et al.  Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis , 2015, PloS one.

[46]  Sébastien Baud,et al.  An integrated overview of seed development in Arabidopsis thaliana ecotype WS , 2002 .

[47]  Nathan M. Springer,et al.  Discovering Functional Modules across Diverse Maize Transcriptomes Using COB, the Co-Expression Browser , 2014, PloS one.

[48]  N. Provart,et al.  BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. , 2012, The Plant journal : for cell and molecular biology.

[49]  R. Carranco,et al.  Repression by an auxin/indole acetic acid protein connects auxin signaling with heat shock factor-mediated seed longevity , 2010, Proceedings of the National Academy of Sciences.

[50]  Chuanyou Li,et al.  The Arabidopsis P450 protein CYP82C2 modulates jasmonate-induced root growth inhibition, defense gene expression and indole glucosinolate biosynthesis , 2010, Cell Research.

[51]  R. Seckler,et al.  The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding. , 2011, Biochimica et biophysica acta.

[52]  J. Buitink,et al.  Desiccation tolerance: From genomics to the field , 2010 .

[53]  H. Rolletschek,et al.  Genome-wide association mapping and biochemical markers reveal that seed ageing and longevity are intricately affected by genetic background and developmental and environmental conditions in barley. , 2015, Plant, cell & environment.

[54]  C. M. Karssen,et al.  Acquisition of Desiccation Tolerance and Longevity in Seeds of Arabidopsis thaliana (A Comparative Study Using Abscisic Acid-Insensitive abi3 Mutants) , 1993, Plant physiology.

[55]  M. Pollard,et al.  Vitamin E Is Essential for Seed Longevity and for Preventing Lipid Peroxidation during Germination , 2004, The Plant Cell Online.

[56]  C. Chapple,et al.  Indole Glucosinolate Biosynthesis Limits Phenylpropanoid Accumulation in Arabidopsis thaliana , 2015, Plant Cell.

[57]  Hua Li,et al.  Co-expression analysis reveals a group of genes potentially involved in regulation of plant response to iron-deficiency. , 2015, Gene.

[58]  A. Bonner,et al.  Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions , 2011, Proceedings of the National Academy of Sciences.

[59]  J. Keilwagen,et al.  Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon , 2012, Nucleic acids research.

[60]  Santa Jeremy Ono,et al.  A novel cysteine-rich sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex class II genes via a repeated Cys-His domain and functions as a transcriptional repressor , 1994, The Journal of experimental medicine.

[61]  Maarten Koornneef,et al.  Natural modifiers of seed longevity in the Arabidopsis mutants abscisic acid insensitive3-5 (abi3-5) and leafy cotyledon1-3 (lec1-3). , 2009, The New phytologist.

[62]  T. Altmann,et al.  The AtNFXL1 gene encodes a NF‐X1 type zinc finger protein required for growth under salt stress , 2006, FEBS letters.