ArticlePLoS genetics2012
Genome-wide patterns of Arabidopsis gene expression in nature.
Article in PLoS genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Locally adapted Arabidopsis thaliana accessions show transcriptomic plasticity in a multi-timescale analysis of whole-genome gene expression in a natural environment.Plant biology (Stuttgart, Germany) · 2026Article
- Advancing ecological and evolutionary research in Arabidopsis: Extending insights into model and nonmodel plants.The Plant cell · 2025Review
- Simulation study of factors affecting the accuracy of transcriptome models under complex environments.Plant molecular biology · 2025Article
- Multilayered defense responses in sugarcane againstFrontiers in plant science · 2025Article
- Exploring the Relationship Between Gene Expression and Low-Frequency Somatic Mutations in Arabidopsis with Duplex Sequencing.Genome biology and evolution · 2024Article
- Investigating low frequency somatic mutations inbioRxiv : the preprint server for biology · 2024Article
- Transcriptome-based strategies for identifying aluminum tolerance genes in popcorn (Zea mays L. var. everta).Scientific reports · 2023Article
- A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat.NAR genomics and bioinformatics · 2023Article
- Response and inversion of skewness parameters to meteorological factors based on RGB model of leaf color digital image.PloS one · 2023Article
- Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster.Evolution; international journal of organic evolution · 2022Article
- Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.The Plant cell · 2022Article
- Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species.The New phytologist · 2021Article
- Growth Patterns in Seedling Roots of the Pincushion CactusFrontiers in plant science · 2021Article
- Using single-plant-omics in the field to link maize genes to functions and phenotypes.Molecular systems biology · 2020Article
- Plants are intelligent, here's how.Annals of botany · 2020Article
- Review
- Using a transcriptome sequencing approach to explore candidate resistance genes against stemphylium blight in the wild lentil species Lens ervoides.BMC plant biology · 2019Article
- Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane.Frontiers in plant science · 2019Article
- The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Frontiers in plant science · 2019Article
- Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius.Plant molecular biology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PC(veg)) correlate to temperature and precipitation occurrence in the field. The largest PC(veg) axes included thermoregulatory genes while the second major PC(veg) was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild.
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