Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Karrikin responses in Arabidopsis thaliana seed

ABSTRACT: Karrikins promote seed germination in Arabidopsis thaliana. Completion of germination (protrusion of the radicle) is not observed until ~72 h in dormant wildtype seed under these conditions. We used microarrays to examine karrikin-induced transcriptional changes after 24 h of imbibition. Transcriptional changes may indicate events leading to karrikin-induced germination or karrikin-specific markers. Primary dormant seed of wildtype (which can germinate and is promoted by KAR1) and ga1-3 (which cannot germinate, and is not promoted by KAR1) were imbibed on water-agar or 1 uM KAR1 in the light at 20 C and assayed for gene expression after 24 h. Three or four biological replicates per genotype/treatment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Steven Smith

PROVIDER: E-GEOD-20556 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana.

Nelson David C DC Flematti Gavin R GR Riseborough Julie-Anne JA Ghisalberti Emilio L EL Dixon Kingsley W KW Smith Steven M SM

Proceedings of the National Academy of Sciences of the United States of America 20100329 15

Karrikins are a class of seed germination stimulants identified in smoke from wildfires. Microarray analysis of imbibed Arabidopsis thaliana seeds was performed to identify transcriptional responses to KAR(1) before germination. A small set of genes that are regulated by KAR(1), even when germination is prevented by the absence of gibberellin biosynthesis or light, were identified. Light-induced genes, putative HY5-binding targets, and ABRE-like promoter motifs were overrepresented among KAR(1)- ...[more]

PMID: 20351290

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Project description:Plant embryos can survive years in a desiccated, quiescent state within seeds. In many species, seeds are dormant and unable to germinate at maturity. They acquire the capacity to germinate through a period of dry storage called after-ripening (AR), a biological process that occurs at 5-15% moisture when most metabolic processes cease. Because stored transcripts will be among the first proteins translated upon water uptake, they likely impact germination potential. Transcriptome changes associated with the increased seed dormancy of the GA-insensitive sly1-2 mutant, and with dormancy loss through sly1-2 after-ripening or constitutive overexpression of the GA receptor (GID1b) were characterized in dry seeds. This experiment used the same seed batches as a previous experiment (E-MTAB-4782) to characterize transcriptional changes associated with the increased seed dormancy and dormancy loss in imbibing seeds. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. In the sly1-2 mutant, GA-directed DELLA proteolysis cannot occur leading to DELLA protein accumulation and increased dormancy. sly1-2 mutant seeds are fully dormant at 2 weeks of dry storage (0% germination), but germinate well with very long after-ripening (51% germination after 19 months). sly1-2 seed germination can also be rescued by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE), which resulted in 74% germination at 2 weeks of dry storage. In this experiment, we sampled dry seeds of wild-type Ler at 2 weeks of dry storage (non-dormant), dormant sly1-2 (2 weeks of dry storage; sly1-2(D)), long after-ripened sly1-2 (non-dormant, 19 months of dry storage; sly1-2(AR)), and sly1-2 GID1b-OE (non-dormant, 2 weeks of dry storage). This experimental design allowed comparison between these transcriptomes in dry seeds to determine if dry seed stored mRNA differences contribute to the dormancy phenotypes observed once seeds are imbibed. Seeds for Ler wt, sly1-2(D), and sly1-2 GID1b-OE were grown alongside each other under the same conditions and after-ripened for 2 weeks. Seeds from sly1-2(AR) were grown under the same conditions in advance of the other lines to allow for the long after-ripening requirement. RNA was extracted using a phenol-chloroform-based extraction from three biological replicates per treatment.

Project description:Seed dormancy is the inability for seeds to germinate even under favorable conditions. In the Arabidopsis Landsberg erecta (Ler) ecotype, 2 weeks of dry storage, called after-ripening, is sufficient to relieve seed dormancy. Such seed is referred to as after-ripened (AR) and has a high rate of germination when imbibed. While widespread transcriptome changes have been previously observed with seed dormancy loss, this experiment was designed to characterize transcriptional changes associated with the increased seed dormancy and dormancy loss of the gibberellin (GA) hormone-insensitive sleepy1-2 (sly1-2) mutant. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. In the sly1-2 mutant, GA-directed DELLA proteolysis cannot occur leading to DELLA protein accumulation and increased dormancy. sly1-2 mutant seeds are fully dormant at 2 weeks of dry storage (0% germination), but germinate well with very long after-ripening (51% germination after 19 months). sly1-2 seed germination can also be rescued by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE), which resulted in 74% germination at 2 weeks of dry storage. In this experiment, we compared seeds of wild-type Ler at 2 weeks of dry storage (non-dormant), dormant sly1-2 (2 weeks of dry storage; sly1-2(D)), long after-ripened sly1-2 (non-dormant, 19 months of dry storage; sly1-2(AR)), and sly1-2 GID1b-OE (non-dormant, 2 weeks of dry storage). Samples were collected at two imbibition timepoints: 1) a 0h timepoint after 4 days at 4°C, and 2) a 12h timepoint after 4 days at 4°C followed by 12 hours in the light at 22°C. These timepoints were selected to capture the transcriptomes at an early and late time in Phase II of imbibition. Using this experimental design we were able to determine transcriptome differences associated with seed dormancy in the sly1-2 mutation (Ler wt vs sly1-2(D)), and changes associated with sly1-2 dormancy loss through dry after-ripening (sly1-2(AR) vs sly1-2(D)) or through GID1b-overexpression (sly1-2 GID1b-OE vs sly1-2(D)). Seeds for Ler wt, sly1-2(D), and sly1-2 GID1b-OE were grown alongside each other under the same conditions and after-ripened for 2 weeks. Seeds from sly1-2(AR) were grown under the same conditions in advance of the other lines to allow for the long after-ripening requirement. RNA was extracted using a phenol-chloroform-based extraction from three biological replicates per treatment.

Dataset Information

Karrikin responses in Arabidopsis thaliana seed

Publications

Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana.

Similar Datasets

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