title: Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways.
abstract: 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.
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique, SFR 4207 QUASAV, Angers, France.
authors.forename: Karima
authors.initials: K
authors.lastname: Righetti
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique, SFR 4207 QUASAV, Angers, France.
authors.forename: Joseph Ly
authors.initials: JL
authors.lastname: Vu
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique, SFR 4207 QUASAV, Angers, France.
authors.forename: Sandra
authors.initials: S
authors.lastname: Pelletier
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, 49071 Beaucouzé, France.
authors.forename: Benoit Ly
authors.initials: BL
authors.lastname: Vu
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg.
authors.forename: Enrico
authors.initials: E
authors.lastname: Glaab
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique, SFR 4207 QUASAV, Angers, France.
authors.forename: David
authors.initials: D
authors.lastname: Lalanne
authors.affiliation: Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
authors.forename: Asher
authors.initials: A
authors.lastname: Pasha
authors.affiliation: Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
authors.forename: Rohan V
authors.initials: RV
authors.lastname: Patel
authors.affiliation: Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
authors.affiliation: Shanghai Center for Plant Stress Biology, SIBS, Chinese Academy of Sciences, Shanghai 201602, P.R. China.
authors.forename: Jerome
authors.initials: J
authors.lastname: Verdier
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, 49071 Beaucouzé, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Leprince
authors.affiliation: UMR 1345, Institut de Recherche en Horticulture et Semences, Institut National de la Recherche Agronomique, SFR 4207 QUASAV, Angers, France julia.buitink@angers.inra.fr.
authors.forename: Julia
authors.identifier: http://orcid.org/0000-0002-1457-764X
authors.initials: J
authors.lastname: Buitink
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D005075:Biological Evolution; D004777:Environment; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018525:Germination; D046913:Medicago truncatula / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D009154:Mutation; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012639:Seeds / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors