Brassica napus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA645178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12440724_1.fastq.gz | Fastqsanger.gz | |||
| SRR12440724_2.fastq.gz | Fastqsanger.gz | |||
| SRR12440725_1.fastq.gz | Fastqsanger.gz | |||
| SRR12440725_2.fastq.gz | Fastqsanger.gz | |||
| SRR12440726_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial to the regulation of various developmental processes. Plant architecture is a collection of genetically controlled agronomic traits that determine crop production and mechanized harvesting. Although several genes had been found to regulate plant architecture, the mechanisms whereby miRNAs regulate plant architecture in the rapeseed Brassica napus remain unknown. Results: In this study, we characterized a rod-like rapeseed mutant with an ideal plant architecture that substantially enhanced its breeding potential. To explore miRNAs that contribute to the rapeseed plant architecture, backcross progenies that developed into small plants (rod-like) and tall plants (normal) were used for study. Four small RNA (sRNA) libraries and two degradome libraries from the shoot apex of normal and rod-like plants were sequenced. A total of 925 non-redundant B. napus miRNA precursors were identified, representing 315 precursors for 74 known miRNAs and 610 precursors for 327 novel miRNAs. Expression analysis revealed that 10 known miRNAs and 7 novel miRNAs were differentially expressed between the normal and rod-like plants. In addition, 408 targets were identified through degradome sequencing and 14 targets were further validated via RNA ligase-mediated 5′ rapid amplification of cDNA ends. Furthermore, the functions of miR319 and its target gene TCP4 were studied and provided a novel insight into how miR319 regulates plant architecture. Conclusions: Correlation analysis between differentially expressed miRNAs and their targets demonstrated that nutrition and metal deprivation, energy supply deficiency, senescence and TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCPs) contributed to the premature termination of shoot development in rod-like mutant. The work further elucidates the mechanism of miRNAs participate in the regulation of plant architecture.
2024-10-31 | GSE102050 | GEO
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: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:The libraries of RNA extracted from the seeds on the 30th, 40th and 50th days (30d, 40d, and 50d) after drought treatment were employed for sequencing and analysis. Our results demonstrated the reasons of the oil content decreased by RNA-seq. These results may help to establish a theoretical foundation for breeding excellent varieties of rapeseed with high oil content in areas with frequent droughts.
2020-10-29 | GSE160342 | GEO
Project description:Global climate changes on one aspect of extreme temperature records would suddenly reset environmental growth conditions for field-grown crops, which severely affects agronomic and commercial traits. Taking the cold-season preferable crop rapeseed Brassica napus L. for example, low-temperature shocks change endogenous regulatory networks and cause phenotypic damages during most lifespan. Here we screened out two genetic breeding elites with different temperature-dependent germination rates, core germplasms with good germination performance and genetic loci and candidate genes potentially involved in low-temperature tolerant functions for the pre-breeding purpose of cold-tolerant germination. By using the phenotype of the germination index of 273 core germplasms under normal temperature and 10 transcriptomic datasets of cold-tolerant Jia You (JY) 1621 and cold-sensitive JY1605 elite cultivars on three timepoints during germination process, we successfully identified clustered genes of early and late temperature response germination (ETRG and LTRG) genes and several cold-tolerant (CDT) and temperature-insensitive (TPI) candidate regulators. This study performed comprehensive multi-omics research on potential cold-responsive genes for the rapeseed improvement of cold tolerance germination.
2024-09-21 | GSE277254 | GEO
Project description:A critical barrier for improving crops yield is the compensatory effect between seed weight (SW) and seed number (SN), which has been widely reported in several crops including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source-sink (S-S) ratios in order to modify the relationship between SW and SN under field conditions.
2021-03-25 | GSE169511 | GEO