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Expression data of 20 Arabidopsis thaliana accessions at dusk, dawn and after an extension of the night

ABSTRACT: Large-scale identification of transcripts with large cross-genotype differences in abundance provides a genome-wide approach to identify natural variation in gene function. Transcript profiling was performed in 20 Arabidopsis accessions at dusk, dawn and after a 6h extension of the night. Individual genes with a high variance in transcript abundances across accessions were identified by inspection at each individual time point and by ANOVA across all three time points. Up to 40% of genes show significant changes in transcript abundance between accessions, with over-enrichment for biotic resistance, including pathogenesis resistance proteins and glucosinolate metabolism, cell wall modification, minor carbohydrate metabolism, amino acid degradation, brassinosteroid metabolism, redox and abiotic stress and underrepresentation of photosynthesis, DNA synthesis, RNA processing, regulation of transcription, protein synthesis and protein targeting. Some functional classes were enriched at all three time points. Genes related to carbon starvation-responses were enriched specifically at dawn, when their transcript abundance varied independently of carbohydrate levels, pointing to genetic variation in the sensitivity with which low carbon is sensed. Cross-accession correlation networks were generated at each time point to identify sets of genes whose transcripts show coordinated change in abundance between accessions. A cluster that was highly enriched for cold-response genes was found at dusk and after an extension of the night. Another cluster found at all three time points was highly enriched for glucosinolate biosynthesis, and correlated with glucosinolate content. We conclude that genes involved in stress and defense related processes show especially large and coordinated natural variation in transcript abundance.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE71188 | GEO | 2023/12/31

SECONDARY ACCESSION(S): PRJNA290514

REPOSITORIES: GEO

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Project description:The goal of the experiment was to perform a large scale study of circadian regulation of gene expression in maize. To identify maize genes with expression regulated by the circadian clock, transcript levels in the aerial tissues of young maize seedlings were determined by transcriptional profiling with the Affymetrix GeneChip Maize Genome Array. Maize inbred B73 seedlings were grown inside Conviron growth chamber. B73 seedlings were grown for 7 days under 12 h light:12 h dark (LD) photocycles, 26° C temperature and 70% humidity. At the 8th day, seedlings were transferred to continuous light (LL) and were allowed to entrain completely for 24 h prior to tissue harvest following which tissue was harvested every 4 hours under LL conditions for a period of 48h. Therefore, for the circadian LL time course 12 time points were collected as follows (also defined as factors in the treatment section): ZT0 - 8:00 am/ subjective dawn/ Day1 ZT4 - 12:00 pm/ subjective mid-day/ Day1 ZT8 - 4:00 pm/ subjective late-day/ Day1 ZT12 - 8:00 pm/ subjective dusk/ Day1 ZT16 - 12:00 am/ subjective mid-night/ Day1 ZT20 - 4:00 am/ subjective pre-dawn/ Day1 ZT24- 8:00 am/ subjective dawn/ Day2 ZT28 - 12:00 pm/ subjective mid-day/ Day2 ZT32 - 4:00 pm/ subjective late-day/ Day2 ZT36 - 8:00 pm/ subjective dusk/ Day2 ZT40 - 12:00 am/ subjective mid-night/ Day2 ZT44 - 4:00 am/ subjective pre-dawn/ Day2 Tissue comprised of aerial portion of the seedlings (corresponding to tissue from the prop roots and up) for RNA isolation. Total RNA was isolated from the entire aerial portion of 7 day-old seedlings (corresponding to tissue from the prop roots and up) by Trizol extraction followed by Qiagen RNeasy columns and treatment with RNase-free DNase I (Qiagen; qiagen.com). RNA was isolated from 3 independent biological replicates was pooled. cRNA was generated from pooled total RNA from 3 biological replicates with the GeneChip One-Cycle Target Labeling kit according to the manufacturer’s recommendations (Affymetrix, affymetrix.com). The University of California, Berkeley Functional Genomics Laboratory hybridized samples to Affymetrix GeneChip Maize Genome Arrays and scanned the washed arrays as suggested by manufacturer. Probe sets called “Not Present” or “Marginal” on one or more microarrays were removed from the downstream analysis, as is common practice with circadian studies. Raw hybridization intensities were normalized across all twelve arrays using RMA express in Perfect Match mode. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Frank G. Harmon. The equivalent experiment is ZM28 at PLEXdb.]

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Expression data of 20 Arabidopsis thaliana accessions at dusk, dawn and after an extension of the night

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