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Series GSE203310 Query DataSets for GSE203310
Status Public on Oct 16, 2023
Title Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
Overall design 1) Single seed RNA-seq: three libraries, each consisting of 32 seeds were prepared for two time points of secondary dormancy induction (3d, 7d+24h) and two seed sizes (small and large). 2) 3'RNA-seq: comparison of transcriptomes of Col-0 small, medium and large dry seeds (four biological replicas).
Contributor(s) Krzyszton M, Swiezewski S
Citation(s) 37828740
Submission date May 18, 2022
Last update date Oct 17, 2023
Contact name Michal Krzyszton
Organization name Institute of Biochemistry and Biophysics, Polish Academy of Sciences
Lab Laboratory of Seeds Molecular Biology
Street address Pawinskiego 5a
City Warsaw
ZIP/Postal code 02-106
Country Poland
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (13)
GSM6166328 SD_S_3d_01
GSM6166329 SD_S_3d_02
GSM6166330 SD_S_3d_03
BioProject PRJNA839397

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GSE203310_RAW.tar 5.8 Mb (http)(custom) TAR (of TSV, TXT)
GSE203310_barcodes.xlsx 8.9 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data provided as supplementary file

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