Transcriptome analysis of the seed weight plasticity in Brassica napus
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ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE169511 | GEO | 2021/03/25
REPOSITORIES: GEO
Similar Datasets
Project description:Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. In this study, we employed a microarray analysis with high oleic acid line and low oleic acid line from the developing seeds (27 days after flowering) of Brassica napus.
2018-09-20 | GSE120223 | GEO
Project description:MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play crucial regulatory roles in various developmental processes. Silique length indirectly influences seed yield in rapeseed (Brassica napus); however, the molecular roles of miRNAs in silique length are largely unknown. Here, backcross progenies of rapeseed with long siliques (LS) and short siliques (SS) were used to elucidate this role. Four small RNA libraries from early developing siliques were sequenced, and a total of 814 non-redundant miRNA precursors were identified, representing 65 known miRNAs, and 394 novel miRNAs. Expression analyses revealed 12 known miRNAs and 5 novel miRNAs that were differentially expressed in LS and SS lines. Furthermore, though two degradome sequencing, we annotated 522 cleavage events. An analysis of correlated expression between differentially expressed miRNAs and their targets demonstrated that some transcription factors might repress cell proliferation or auxin signal transduction to control silique length, and that a Pi/Cu deficiency might also restrict silique development. More significantly, the overexpression of miR160 in rapeseed may repress auxin response factors and result in increased silique length, illustrating that silique length could be regulated via an auxin-response pathway. These results will serve as a foundation for future research in B. napus.
2019-08-01 | GSE107056 | GEO
Project description:MicroRNAs and siRNAs are important regulators of plant development and seed formation, yet their population and abundance in the oil crop Brassica napus are still less understood, especially at different developmental stages and among cultivars with varied seed oil contents. Here, we systematically analyzed the small RNA expression profiles of Brassica napus seeds at early embryonic developmental stages in a high oil content and a low oil content Brassica napus cultivars, both cultured in two environments. A total of 50 conserved miRNAs and 11 new miRNAs were identified, together with some new miRNA targets. Expression analysis revealed some miRNAs with varied expression levels in different seed oil content cultivars or at different embryonic developmental stages. A large amount of 23-nt small RNAs with specific nucleotide composition preference were also identified, which may present new classes of functional small RNAs. Examination of small RNA profiles in 2 different seed oil content rapeseed culvitars at 2 locations.
2011-12-28 | E-GEOD-34727 | biostudies-arrayexpress
Project description:Gene expression profiles during seed development and fatty acid (FA) metabolism, as well as the relevant regulation, of Brassica napus were studied through multiple high-throughput genomic approaches. Serial Analysis of Gene Expression (SAGE) using seed materials obtained a total of 68,718 tags, of which 23,897 were unique and 503 tags were functionally identified, and revealed the transcriptome of approximately 35,000 transcripts in B. napus developing seeds. Further, ~22,000 independent ESTs were obtained by large-scale sequencing using immature embryos at different stages, and 8343 uni-ESTs and 3355 full-length cDNAs were identified respectively, resulting in the systemic identification of B. napus FA biosynthesis-related genes. Gene expression profiles were further studied employing cDNA chip hybridization to reveal the global regulatory network of FA metabolism in developing seeds. Together with the analysis on FA amounts and composition, it was shown that 17-21 days after pollination (DAP) was a crucial stage for transition of seed to sink tissue. High expressions of FA biosynthesis-related genes and transition of FA components are mainly at stages 21 DAP or 21-25 DAP respectively. In addition, compared to Arabidopsis, more critical roles of starch metabolism are detected for B. napus seed FA metabolism and storage components accumulation. Crucial effects of starch metabolism, carbon flux, oxidative pentose phosphate pathway (OPPP), photosynthesis, and other regulators in FA metabolism were discussed. Keywords: Brassica napus, immature seed, SAGE, EST, cDNA microarray
2008-02-26 | GSE7204 | 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:Waterlogging is one major stress for crops and causes multiple problems for plants, for example low gas diffusion, reducing conditions in the soil and accumulation of toxic metabolites. Brassica napus is an important oil crop with high waterlogging sensitivity, which may cause severe yield losses. Its reactions to the stress are not fully understood. In this work the transcriptional response of rapeseed to one aspect of waterlogging, hypoxia in the root zone, was analyzed, including two rapeseed cultivars from different origin, Avatar from Europe and Zhongshuang 9 from Asia. Both cultivars showed a high number of differentially expressed genes in roots after 4 and 24 h of hypoxia. The response included many well-known hypoxia-induced genes such as genes coding for glycolytic and fermentative enzymes. Leaves hardly responded to the root stress after a 24-h-stress treatment, and photosynthesis seemed to be not affected by the stress applied to roots. There was no clear difference in either gene expression or tolerance to waterlogging between the two genotypes used in this study.
2022-05-03 | GSE180262 | GEO
Project description:C3-C4 intermediate Moricandia suffruticosa showed tolerance to drought and heat stresses, and high photosynthetic capacity under these abiotic stresses as comparing with C3 relative crop rapeseed (Brassica napus). In our study, systematic analysis was conducted to reveal photosynthetic difference between C3-C4 Moricandia suffruticosa and its relative C3 rapeseed from the same Brassiceae tribe. It was found that Moricandia leaf photosynthesis and anatomy were significantly changed compared to rapeseed under drought and heat stress conditions. De novo transcriptome of Moricandia was assembled by next generation sequencing, and unigenes were mapped to respective rapeseed gene locus. Then comparative transcriptome analysis was conducted in leaf tissues of Moricandia and rapeseed under both drought and heat stresses. Main pathways and candidate genes were revealed from this analysis, which may be associated with the stress induced change in Moricandia.
2020-08-12 | GSE156029 | GEO
Project description:We profiled the gene regulatory landscape of Brassica napus reproductive development using RNA sequencing. Comparative analysis of this nascent allotetraploid across the plant lifecycle revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling across reproductive development revealed lower accumulation of C subgenome transcripts relative to the A subgenome. Subgenome-specific transcriptional networks identified distinct transcription factor families enriched in each of the A and C subgenome in early seed development. Analysis of a tissue specific transcriptome of early seed development revealed transcription factors predicted to be regulators encoded by the A subgenome are expressed primarily in the seed coat whereas regulators encoded by the C subgenome were expressed primarily in the embryo. Whole genome transcription factor networks identified BZIP11 as an essential regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in knockdown of predicted target genes, and a reproductive-lethal phenotype. Our data indicate that subgenome bias are characteristic features of the B. napus seed throughout its development, and that such bias might not be universal across the embryo, endosperm, and seed coat of the developing seed. We also find that examining transcriptional networks spanning both the A and C genomes of the whole B. napus seed can identify valuable targets for seed development research. We suggest that-omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.
2021-08-31 | GSE144771 | GEO
Project description:High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress.
2015-01-05 | GSE57697 | GEO
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38018 | biostudies-arrayexpress