Genome-wide transcriptional profiling in relation to seed storage compounds in tetralocular Brassica rapa
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica rapa
PROVIDER: GSE85725 | GEO | 2017/03/09
SECONDARY ACCESSION(S): PRJNA339187
REPOSITORIES: GEO
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Project description:Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression in about 10 % of all matched genes, with a total abundance of 44 %, showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6 % of A. thaliana genes were matched by Brassica ESTs detected by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development. Seeds from 2 developmental stages of B. napus were used to construct 2 LongSAGE libraries, 23 days after pollination (23 DAP) and 35 days after pollination (35 DAP). Biological replicates and confirmation: Cloning of tag-amplified RT-PCR products, Real-time RT-PCR
2009-02-15 | E-GEOD-14313 | biostudies-arrayexpress
Project description:Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression in about 10 % of all matched genes, with a total abundance of 44 %, showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6 % of A. thaliana genes were matched by Brassica ESTs detected by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development.
2009-02-16 | GSE14313 | GEO
Project description:During seed growth, sugar and nitrogen compounds confer regulatory control on storage activities. Thus, seed storage production could be regulated by the supply of nutrients. In order to improve nitrogen flux into the embryo, transgenic pea lines were created where ADP-glucose pyrophosphorylase (AGP) from Pisum sativum has been repressed by RNAi approach in the seeds under control of the seed-specific LeB4 promotor (Bäumlein et al. Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within legumin box is essential for tissue-specific expression of a legumin gene. Plant J 1992 2: 233-239). The plastidial enzyme AGP catalyzes the reaction of glucose-1-phosphate and ATP to pyrophosphate and ADP-glucose, which is the substrate for starch synthase. The AGP activity and transcript levels were strongly decreased in three independent transgenic lines. Repression of AGP results in a wrinkled seed phenotype obviously due to transient accumulation of free sugars during maturation. Mature seeds have reduced starch content whereas the protein concentration is higher due to increased fractions of albumins and globulins. Repression of AGP interferes with storage protein metabolism and alters fluxes of nitrogen during seed growth. The influence of decreased AGP on altered gene expression in developing cotyledons was analysed using a 6k-Oligo-microarray. Ps6kOLI1 microarray hybridization were performed using three independent biological replicates of four developmental stages (20, 25, 30 and 35 DAP) from seeds of the transgenic line iAGP-3.
2008-09-01 | E-MEXP-1749 | biostudies-arrayexpress
Project description:Beech trees produce seeds irregularly, necessitating the storage of these seeds for forestation. Despite the acquisition of desiccation tolerance during development, beech seeds lose viability during long-term storage faster than orthodox-type seeds. Seeds stored for short (3 years) and long (20 years) periods under optimal conditions were compared. Aged seeds characterized with germination capacity reduced to 30% displayed increased membrane damage, manifested as electrolyte leakage and lipid peroxidation levels. Analyses have been based on embryonic axes containing higher levels of reactive oxygen species (ROS) and higher levels of protein-bound methionine sulfoxide (MetO) in aged seeds. Using gel-free shotgun proteomics, 3,949 proteins were identified and 2,442 were reliably quantified to indicate 25 proteins with upregulated abundance and 35 with downregulated abundance in beech seeds under long-term storage compared to those under short-term storage. Functional analyses based on gene ontology annotations revealed that nucleic acid binding activity (biological process), hydrolases (molecular function), ribosome organization or biogenesis and transmembrane transport (cellular processes), and ATP synthesis (pathway) were affected in aged seeds. To verify whether MetO the oxidative posttranslational modification of proteins reversed via the action of methionine sulfoxide reductase (Msr) enzymes is involved in ageing of beech seeds we identified 316 and reliably quantified 226 MetO-containing proteins, among which 9 and 19 exhibited significantly up- and downregulated MetO levels, respectively, in beech seeds under long-term storage. Several Msr isoforms were identified and recognized as MsrA1-like, MsrA4, MsrB5 and MsrB5-like in beech seeds. Only MsrA1-like displayed decreased abundance in aged seeds. We demonstrated that the loss of membrane integrity reflected in elevated abundance of membrane proteins had higher impact on seed ageing progress rather than MetO/Msr system.
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Project description:To identify α-null-related transcriptional changes, the gene expressions of cgy-2-NIL and its recurrent parent DN47 were compared using Illumina high-throughput RNA-sequencing on samples at 25, 35, 50, and 55 days after flowering (DAF). Seeds at 18 DAF served as the control.
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Project description:RNA sequencing in sunflower for detect mRNA expression of developmental seeds. The two cultivars (86-1, L-1-OL-1) with significant difference in oleic acid content in two different seed developmental stages (oleic acid accumulated rapidly at 17 DAF, and kept relatively stable at 27 DAF) for transcriptome sequencing
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Project description:Nitrogen application to legume seeds regulates seed metabolism and composition. In order to improve nitrogen flux into the embryo, the Vicia faba amino acid permease VfAAP1 (Miranda et al. Amino acid permeases in developing seeds of Vicia faba L.: expression precedes storage protein synthesis and is regulated by amino acid supply. Plant J 2001 28: 61-72) was expressed in pea under control of the seed-specific LeB4 promotor (Bäumlein et al. Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within legumin box is essential for tissue-specific expression of a legumin gene. Plant J 1992 2: 233-239). Several transgenic lines have been generated. Mature seeds of the homozygous marker gene-free line AAP14/10 showed an increase in amino acid supply, seed nitrogen and protein content due to higher globulin fraction. The effect of VfAAP1 was tested under field conditions in two growing periods, 2005 and 2006, and the data could be confirmed. Over-expression of VfAAP1 interferes with storage protein metabolism and alters fluxes of nitrogen during seed growth. The influence of VfAAP1 on altered gene expression in developing cotyledons was analysed using a 6k-Oligo-microarray. Four developmental stages (18, 22, 26 and 30 DAP) from seeds, grown 2006, of the transgenic line AAP14/10 were hybridized against wildtype control.
2008-05-01 | E-MEXP-1557 | biostudies-arrayexpress
Project description:Seed development is a complex process controlled by many factors, including genetics, plant growth regulators, and the environment. Understanding the different compositions and abundances of proteins in various types of seeds at different developmental stages is fundamental for improving seed quality and enhancing nutritional and food security. In this study, we applied label-free quantitative proteomics to analyze round and wrinkled pea seeds at five different growth stages: 4, 7, 12, 15 days after anthesis (DAA), and at maturity. Wrinkled peas had lower starch content (29.5%) compared to round peas (~47-55%). Proteomic analysis identified 3,659 protein groups, of which approximately 21-24% proteins were shared across growth stages. Relatively more proteins were identified during early seed development compared to later stages, and the protein profiles were also drastically different between early and late stages. Statistical analysis identified 735 significantly different proteins between wrinkled and round seeds, regardless of the growth stage. These detected proteins were characterized into different functional classes including metabolic enzymes, proteins involved in protein biosynthesis and homeostasis, carbohydrate metabolism, vesicle trafficking, cell division, and cell wall organization. Cell division-related proteins were more abundant in the early stages of seed development, whereas storage proteins and proteins implicated in lipid metabolism were more abundant at the later stages. Wrinkled seeds had a significantly lower abundance of starch-branching enzyme than did round seeds. This enzyme is involved in the biosynthesis of the amylopectin component of starch. Seed storage proteins such as legumin and a form of albumin (PA2) accumulated more in round pea genotypes, whereas vicilin was more abundant in the wrinkled pea genotype. In summary, this study can enhance our understanding of pea seed development, highlighting key differences in protein profiles between round and wrinkled pea seeds.
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Project description:Apple seeds were subjected to accelerated aging. After 7, 14, and 21 days of aging, embryos were isolated. Part of the embryos were shortly fumigated with nitric oxide (NO). After 48 h of embryos culture (aged embryos or aged embryos treated with NO), embryonic axes were used to extract the total RNA. RT-qPCR were done to analyze the changes in the expression of genes related to seed aging. Short-term (3 h) treatment of embryos isolated from accelerated aged apple seeds (Malus domestica Borkh.) with NO partially reduced the effects of aging. The aim of the study was to investigate the impact of the short-term NO treatment of embryos isolated from apple seeds subjected to accelerated aging on the expression of genes potentially linked to the regulation of seed aging. Apple seeds were artificially aged for 7, 14, or 21 days. Then the embryos were isolated from the seeds, treated with NO, and cultured for 48 h. Progression of seeds aging was associated with the decreased transcript levels of most of the analyzed genes (Lea1, Lea2a, Lea4, Hsp70b, Hsp20a, Hsp20b, ClpB1, ClpB4, Cpn60a, Cpn60b, Raptor, and Saur). The role of NO in the mitigation of seed aging depended on the duration of the aging. After 7 and 14 days of seed aging, a decreased expression of genes potentially associated with the promotion of aging (Tor, Raptor, Saur) was noted. NO-dependent regulation of seed aging was associated with the stimulation of the expression of genes encoding chaperones and proteins involved in the repair of damaged proteins. After NO application, the greatest upregulation of ClpB, Pimt was noted in the embryos isolated from seeds subjected to 7-day long accelerated aging, Hsp70b, Hsp70c, Cpn in the embryos of seeds aged for 14 days, and Lea2a in the embryos of seeds after 21 days of aging.
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