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See detailInference of longevity-related genes from a robust co-expression network of seed maturation identifies new regulators linking seed storability to biotic defense-related pathways
Righetti, Karima; Vu, Joseph Ly; Pelletier, Sandra et al

in Plant Cell (2015), 27(10), 2692-2708

Seed longevity, the maintenance of viability during storage is a crucial factor to preserve genetic resources and to ensure proper seedling establishment and high crop yield. A systems biology approach ... [more ▼]

Seed longevity, the maintenance of viability during storage is a crucial factor to preserve genetic resources and to ensure proper seedling establishment and high crop yield. A systems biology approach was used to identify key genes regulating the acquisition of longevity during seed maturation of Medicago truncatula. Using 104 transcriptomes of seed developmental time courses obtained under five growth environments, a robust, stable co-expression network (MatNet) was generated, thereby capturing the conserved backbone of maturation. Using a trait-based gene significance measure, a co-expression module related to the acquisition of longevity was inferred from MatNet. Comparative analysis between maturation processes in Medicago and A. 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 nfxl1 mutants demonstrated that these genes regulate part of the network nodes and exhibit impaired longevity acquisition during maturation. These data suggest that seed longevity evolved by co-opting existing genetic pathways regulating activation of defense against pathogens. [less ▲]

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See detailEARLY FLOWERING4 Recruitment of EARLY FLOWERING3 in the Nucleus Sustains the Arabidopsis Circadian Clock
Herrero, Eva; Kolmos, Elsebeth; Bujdoso, Nora et al

in Plant Cell (2012), 24(2), 428-443

The plant circadian clock is proposed to be a network of several interconnected feedback loops, and loss of any component leads to changes in oscillator speed. We previously reported that Arabidopsis ... [more ▼]

The plant circadian clock is proposed to be a network of several interconnected feedback loops, and loss of any component leads to changes in oscillator speed. We previously reported that Arabidopsis thaliana EARLY FLOWERING4 (ELF4) is required to sustain this oscillator and that the elf4 mutant is arrhythmic. This phenotype is shared with both elf3 and lux. Here, we show that overexpression of either ELF3 or LUX ARRHYTHMO (LUX) complements the elf4 mutant phenotype. Furthermore, ELF4 causes ELF3 to form foci in the nucleus. We used expression data to direct a mathematical position of ELF3 in the clock network. This revealed direct effects on the morning clock gene PRR9, and we determined association of ELF3 to a conserved region of the PRR9 promoter. A cis-element in this region was suggestive of ELF3 recruitment by the transcription factor LUX, consistent with both ELF3 and LUX acting genetically downstream of ELF4. Taken together, using integrated approaches, we identified ELF4/ELF3 together with LUX to be pivotal for sustenance of plant circadian rhythms. [less ▲]

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See detailFunctional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets
Bassel, George W.; Glaab, Enrico UL; Marquez, Julietta et al

in Plant Cell (2011)

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