Tissue-specific RNA-seq of Atsdr4l-5 dig2 mutant seeds
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE282564 | GEO | 2025/12/04
REPOSITORIES: GEO
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Project description:Polycomb Group proteins belonging to the Polycomb Repressive Complex 2 (PRC2) repress seed coat development before fertilization. Removal of PRC2 function in the integuments initiates autonomous seed coat development. We used microarrays to identify those genes that are under PRC2 control and become derepressed in mutants deficient for the PRC2 genes VRN2 and EMF2. Since vrn2 emf2 double mutants have strong developmental aberrations, we used the mutant combination vrn2/- emf2/+ .
2016-11-15 | GSE85751 | GEO
Project description:Arabidopsis seed germination is coordinated with the strong induction of metabolic pathways required for the mobilisation and utilization of seed storage reserves. These are essential to support the seedling before the establishment of photoauxotrophic growth. The activity of genes encoding enzymes required for lipid mobilisation is regulated largely at the level of transcription, but our knowledge of how this regulation occurs is extremely limited. After germination the rate of lipid reserve mobilisation is determined by the carbohydrate status of the seedling and by the osmotic potential of the growth substrate. The plant response to both of these requires the action of the hormone abscisic acid (ABA). We have shown that this regulation is tissue specific (Penfield et al., 2004 Plant Cell 16, 2705-2718), and that although lipid breakdown in the embryo is inhibited by ABA, lipid breakdown in the endosperm tissues is not. Furthermore, in many species the action of the endosperm is central to the processes controlling seed germination, yet very little is known about gene expression in this tissue, or of the function of the endosperm in mature Arabidopsis seeds. Mature Arabidopsis seeds can be dissected into embryo and endosperm/seed coat fractions, with the latter fraction containing RNA only from the endosperm as the seed coat cells undergo programmed cell death during the latter stages of seed development. In this experiment we divide seeds into embryo and endosperm tissues and transcript profile both shortly after germination, or when germination and lipid reserve mobilisation are inhibited by ABA or by the gibberellin biosynthesis inhibitor paclobutrazol. In this way we can discover the endosperm transcriptome and uncover candidate regulators of lipid mobilisation by searching for genes showing differential expression between embryo and endosperm before and after ABA treatment. Experimenter name = Steven Penfield Experimenter phone = 01904 328759 Experimenter fax = 01904 328762 Experimenter department = Department of Biology Experimenter institute = Centre for Novel Agricultural Products Experimenter address = University of York Experimenter address = PO BOX 373 Experimenter address = York Experimenter zip/postal_code = YO10 5YW Experimenter country = UK Keywords: organism_part_comparison_design
2007-01-08 | GSE5751 | GEO
Project description:The seeds of angiosperms are comprised of three main tissues--the seed coat, embryo, and endosperm--whose coordinated development will enable the next generation to disperse with sufficient maternal resources and germinate when conditions are favorable. We use high-throughput RNA sequencing technology to characterize the developmental dynamics of gene expression in whole seeds resulting from a compatible cross between two species of the Mimulus guttatus complex.We find that development in ovules and seeds involves the activation of the majority of annotated genes in M. guttatus (64-67%), and the differential expression over time of 6,691 genes, including 424 transcription factors. Most of the genes we detected (69%) were expressed at all stages, from ovules to heart-stage embryo seeds. We also detected and validated four genes exhibiting paternally-biased expression (MDB13, ATXR5, DnaJ and BGAL11). Intriguingly, three of our validated PEGs are have imprinted homologues in other plant species, suggesting that these proteins perform a shared role in endosperm development among distantly related plant taxa. Additionally, the overlap in gene expression profiles between stages of development suggests that most genes fulfill multiple developmental and biological roles. Future analyses should examine whether different regions of the seed (embryo, endosperm, and seed coat) have unique patterns of gene expression, and the extent to which spatial coordination and regulation of gene expression may play a role in regulating seed development.
2019-09-27 | GSE123424 | GEO
Project description:Tissues were isolated from the globular seed using laser microdissection. At least two bioreplicates are included for each tissue. Tissues examined are : the embryo proper (EP), micropylar endosperm (MCE), peripheral endosperm (PEN), chalazal endosperm (CZE), chalazal proliferating tissue (CPT), chalazal seed coat (CZSC), inner seed coat (ISC), and outer seed coat (OSC).
2019-01-15 | GSE120360 | GEO
Project description:Arabidopsis seed germination is coordinated with the strong induction of metabolic pathways required for the mobilisation and utilization of seed storage reserves. These are essential to support the seedling before the establishment of photoauxotrophic growth. The activity of genes encoding enzymes required for lipid mobilisation is regulated largely at the level of transcription, but our knowledge of how this regulation occurs is extremely limited. After germination the rate of lipid reserve mobilisation is determined by the carbohydrate status of the seedling and by the osmotic potential of the growth substrate. The plant response to both of these requires the action of the hormone abscisic acid (ABA). We have shown that this regulation is tissue specific (Penfield et al., 2004 Plant Cell 16, 2705-2718), and that although lipid breakdown in the embryo is inhibited by ABA, lipid breakdown in the endosperm tissues is not. Furthermore, in many species the action of the endosperm is central to the processes controlling seed germination, yet very little is known about gene expression in this tissue, or of the function of the endosperm in mature Arabidopsis seeds. Mature Arabidopsis seeds can be dissected into embryo and endosperm/seed coat fractions, with the latter fraction containing RNA only from the endosperm as the seed coat cells undergo programmed cell death during the latter stages of seed development. In this experiment we divide seeds into embryo and endosperm tissues and transcript profile both shortly after germination, or when germination and lipid reserve mobilisation are inhibited by ABA or by the gibberellin biosynthesis inhibitor paclobutrazol. In this way we can discover the endosperm transcriptome and uncover candidate regulators of lipid mobilisation by searching for genes showing differential expression between embryo and endosperm before and after ABA treatment. Experimenter name = Steven Penfield; Experimenter phone = 01904 328759; Experimenter fax = 01904 328762; Experimenter department = Department of Biology; Experimenter institute = Centre for Novel Agricultural Products; Experimenter address = University of York; Experimenter address = PO BOX 373; Experimenter address = York; Experimenter zip/postal_code = YO10 5YW; Experimenter country = UK Experiment Overall Design: 18 samples were used in this experiment
2008-06-14 | E-GEOD-5751 | biostudies-arrayexpress
Project description:Cultivation of canola at temperatures above the optimum growth temperature of 21°C for prolonged periods, especially during the flowering stage, resulted in several adverse effects, including rapid vegetative growth, reduced viability of female gametophytes, increased seed abortion rate, accelerated embryo development, and a reduction in seed oil composition (Young et al., 2004; Mácová et al., 2022; Secchi et al., 2023). One of the distinctive phenotypes observed during the seed development of certain canola cultivars subjected to prolonged heat stress affecting the seed yield is the occurrence of the pre-harvest sprouting phenotype (PHS) (Mácová et al., 2022). Misregulation of seed dormancy by abscisic acid and dormancy-related genes is thought to be the primary cause of PHS in many cereal crops (Benech-Arnold & Rodríguez, 2018; Tai et al., 2021). This phenotype is associated with seed coat rupture (SCR), observed in seeds during the early stages of maturation. In this study, we employed a multi-methodological approach to investigate the occurrence of SCR phenotype in seeds of Brassica napus cv. Topas. The results demonstrate that SCR occurs in seeds around 20 days after pollination (20DAP) when the plants are cultivated in elevated temperatures over an extended period. The unrestricted embryonic growth exerts pressure on the seed coat, as evidenced by a reduction in the thickness of the seed coat cell layers. This results in an early alteration to the cell wall composition, with an increased proportion of demethylesterified pectin, which is likely to stiffen the seed coat, thereby rendering it more susceptible to rupture. The precise mechanism by which accelerated embryo development influences heat stress-mediated seed development in canola plants has yet to be elucidated.
2024-11-26 | GSE282385 | GEO
Project description:Seeds are comprised of three major parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed part undergoes distinct developmental programs during seed development. What methylation changes occur in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of two major parts of Arabidopsis mature green stage seeds, the seed coat and embryo, using Illumina sequencing.
2014-05-17 | GSE57755 | GEO
Project description:Seed coat colour is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds, such as seed dormancy, longevity, oil content, protein content and fibre content. In Brassica napus, inheritance of seed coat colour is related to maternal effects and pollen effects (xenia effects). In this research, we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus with pollen effect. Microcopy of transverse sections of the mature seed shows pigment is deposited only in the epidermal cells, the first cell layer of seed coat. By Illumina Hiseq 2000 sequencing technology, a total of 12 G clean data, 116x coverage of coding sequences of B. napus, was achieved from 26-day old brown and yellow seeds. It was assembled into 172,238 independent transcripts and 55,637 unigenes by Trinity. A total of 150 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcripted in seeds. However transcription of all the orthologs was independent of the embryonal control of seed coat colour. Of all the Trinity-assembled unigenes, only 55 genes were found to be differentially expressed between the brown seeds and yellow mutant. Among them 50 were up-regulated and 5 were down-regulated in the yellow seeds as compared to the brown counterpart. By KEGG classification, 14 metabolic pathways were enriched significantly. Of these, 5 pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were produced at higher levels in the embryo of yellow seeds as compared to brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the 26-day embryo of yellow seeds. Pigment indispensable substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe and disappearance of pigment in the yellow seeded mutant indicate that embryonal control of seed coat colour is related with Phe and Ala metabolism in the embryo of B. napus.
2018-05-19 | GSE69137 | GEO
Project description:MYB-bHLH-TTG1 regulates Arabidopsis seed coat biosynthesis pathways directly and indirectly via multiple tiers of transcription factors
2020-04-08 | GSE148210 | GEO
Project description:The molecular mechanism of seed morphophysiological dormancy of Epimedium pseudowushanense B.L.Guo. remains largely unknown. The endogenous ABA and GA content of E. pseudowushanense seeds at three developmental stages was quantitatively determined. The result showed the levels of ABA in E. pseudowushanense seeds decreased during the seed embryo growing and development, levels of GA3 increased during seed embryo growing, and levels of GA4 increased during seed dormancy releasing and seed sprouting. High-throughput sequencing method was used for reveal the E. pseudowushanense seed transcriptome. The transcriptome data were assembled as 178,613 unigenes and the numbers of differentially expressed unigenes between the seed development stages were compared. By computer analysis of the KEGG reference pathways, twelve candidate genes were likely to be involved in metabolism and signaling of abscisic acid and gibberellins. The expression patterns of these genes were revealed by real-time quantitative RT-PCR. Phylogenetic relationships among the deduced E. pseudowushanense proteins and their homologous in other plant species were analyzed. The results indicate EpNCED1, EpNCED2, EpCYP707A1 and EpCYP707A2 are likely to be involved in ABA biosynthesis and catabolism. EpSnRK2 is likely implicated in ABA signaling during seed dormancy. EpGA3ox is likely to be involved in gibberellin biosynthesis, and EpDELLA1 and EpDELLA2 are likely implicated in GA signaling. This study was the first to provide the E. pseudowushanense seed transcriptome and the key genes involved in metabolism and signaling of abscisic acid and gibberellins, and so it is valuable for studies on seed morphophysiological dormancy mechanism
2018-05-21 | GSE79474 | GEO