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DELAY OF GERMINATION 1 plays a role in Arabidopsis seed maturation

ABSTRACT: We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background. The aim was to obtain a global overview of the effect of different levels of DOG1 expression during seed maturation on the dry seed transcriptome.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE65471 | GEO | 2016/01/14

SECONDARY ACCESSION(S): PRJNA274129

REPOSITORIES: GEO

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DELAY OF GERMINATION 1 plays a role in Arabidopsis seed maturation

Project description:We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background. The aim was to obtain a global overview of the effect of different levels of DOG1 expression during seed maturation on the dry seed transcriptome. Gene expression in dry seeds of three genotypes was compared: Ler, NILDOG1 and the dog1-1 mutant. For each genotype, three replicates were used.

2016-01-14 | E-GEOD-65471 | biostudies-arrayexpress

Combined transcriptome and translatome analyses reveal a role for tryptophan dependent auxin biosynthesis in the control of DOG1 dependent seed dormancy

Project description:Transcriptome and translatome analyses of 6 and 24 hours imbibed seeds dormant and non-dormant seeds of NILDOG1-Cvi with and without addition of the transcription inhibitor Cordycepin. NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006).

2017-10-23 | GSE75368 | GEO

Penfield: Understanding the affect of maternal environment on seed dormancy

Project description:Maternal environment is an important regultor of seed dormancy, but the mechanisms underlying the process are poorly understood. We have found that genes in the circadian clock control dormancy, in part through their regulation of the canonical photoperiod pathway known from research into flowering time control. In this experiment we compare the affects of altering seed maturation temperature or maternal photoperiod on dry seed transcriptomes, and the photoperiod-insenstive ft-1 mutant to wt type Ler. In this way we are identifying gene expression programmes which result from the seed's response to maternal environmental experience. Keywords: Expression profilling by array

2011-04-21 | GSE28747 | GEO

Arabidopsis thaliana DOG1 pull-downs from seed tissues

Project description:Functionally complemented dog1-1 mutant with a YFP-DOG1 fusion protein under the control of its native promoter were used as starting material for in vivo pull-down of YFP: DOG1 and its interacting proteins from seed tissues in native conditions. DOG1 interacting proteins were identified by mass spectrometry. Pull-downs were performed in biological triplicates using dry or 24 h water imbibed seeds, directly after harvest (dormant condition) and after 7 months of dry storage (non-dormant condition).

2017-07-07 | PXD006347 | Pride

Penfield: Understanding the affect of maternal environment on seed dormancy

2011-04-21 | E-GEOD-28747 | biostudies-arrayexpress

Bulk segregant sequencing (Bulk-Seq) analysis to identify paternal suppressors of medea in Arabidopsis thaliana

Project description:Arabidopsis thaliana seeds that maternally inherit a medea (mea) mutant allele abort before completing embryogenesis. However, mea seeds can be rescued by pollen from several natural ecotypes of A. thaliana, including the Cape Verdian accession Cvi-0. We developed a method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks. The strategy is to create an F2 population that contains one set of chromosomes from the maternal parent (mea, in a Ler background) but inherits two segregating sets (Ler and Cvi-0) from the other parent. The two paternally segregating sets have opposite effects in mea penetrance: Ler fathers allow full mea seed abortion, while Cvi fathers rescue 90% of medea seeds. Therefore, the two segregating paternal sets are not equally transmitted to the next generation. DNA extracted from pools of viable F2 seedlings was sequenced on an Illumina HiSeq 2000 platform, mapped to the reference TAIR10 A. thaliana genome and the ratio between Ler and Cvi-0 SNPs used to identify chromosomal regions enriched in Cvi-0 sequences. As a control, DNA pools extracted from crosses between a wild-type Ler mother and a hybrid Cvi-0:Ler father were also sequenced. Three biological replicates were made for each pool. Ler-1 x Ler-1:Cvi-0 hybrid viable seedlings pools (each is a biological replicate): WT_pool_1, WT_pool_2, WT_pool_3 mea-1/mea-1; MEA-GR x Ler-1:Cvi-0 hybrid viable seedlings pool (each is a biological replicate): mea_pool_1, mea_pool_2, mea_pool_3

2016-11-18 | E-MTAB-5196 | biostudies-arrayexpress

Parental Effects on Seed Transcriptome-Metabolome

Project description:Transcriptome analyses on seeds developed in different parental conditions investigating the effect of the parental environment on the transcriptome of dry seeds of three different genotypes RNA isolated from freshly harvested dry seed of three genotypes, the near isogenic line of DELAY OF GEMRMINATION 1 (DOG1), DOG3 and DOG6, grown in 15Â°C, 20Â°, low nitrate (N0), low light (LL) and SL (standard light). Please note that SL (standard light) is the control for the LL (low light), and 20C is the control for both 15C and low nitrate (N0).

2016-07-03 | E-GEOD-75837 | biostudies-arrayexpress

Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean

Project description:To understand the molecular events underlying seed maturation, quiescence and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at four seed developmental stages (cotyledon, early, mid and late maturation), mature dry seeds, and seedlings, eight days after seed sowing.

2017-07-12 | GSE99571 | GEO

Promoter-pervasive transcription causes RNA polymerase II pausing to boost DOG1 expression in response to salt

Project description:Eukaryotic genomes are pervasively transcribed by RNA polymerase II. Yet, the molecular and biological implications of such a phenomenon are still largely puzzling. Here, we describe noncoding RNA transcription upstream of the Arabidopsis thaliana DOG1 gene, which governs salt stress responses and is a key regulator of seed dormancy. We find that expression of the DOG1 gene is induced by salt stress, thereby causing a delay in seed germination. We uncover extensive transcriptional activity on the promoter of the DOG1 gene, which produces a variety of lncRNAs. These lncRNAs, named PUPPIES, are co-directionally transcribed and extend into the DOG1 coding region. We show that PUPPIES RNAs respond to salt stress and boost DOG1 expression, resulting in delayed germination. This positive role of pervasive PUPPIES transcription on DOG1 gene expression is associated with augmented pausing of RNA polymerase II, slower transcription and higher transcriptional burst size. These findings highlight the positive role of upstream co-directional transcription in controlling transcriptional dynamics of downstream genes.

2023-02-01 | GSE208755 | GEO

Methylation Changes in Arabidopsis seed development

Project description:There are four major seed developmental phases in Arabidopsis seed development: morphogenesis, maturation, dormancy and germination. What methylation changes occurring in the different phases, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of four major seed developmental phases of Arabidopsis using Illumina sequencing: global stage (glob) and linear cotyledon stage (lcot) for morphogenesis phase; mature green stage (mg) and post mature green stage (pmg) for maturation phase; dry seed (dry) for dormancy phase; leaves (leaf) from 4 week plant for vegetative tissues.

2015-04-22 | GSE68132 | GEO

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