Brassica napus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA416679 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18051100_1.fastq.gz | Fastqsanger.gz | |||
| SRR18051100_2.fastq.gz | Fastqsanger.gz | |||
| SRR18051200_1.fastq.gz | Fastqsanger.gz | |||
| SRR18051200_2.fastq.gz | Fastqsanger.gz | |||
| SRR18051300_1.fastq.gz | Fastqsanger.gz |
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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.
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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.
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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.
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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.
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Project description:QTLs detection for low-temperature germination in rapeseed
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Project description:Heavy rainfall causes flooding of natural ecosystems as well as farmland, negatively affecting crop performance and yield. While the response of the wild model organism Arabidopsis thaliana to such stress conditions is well understood, we hardly know anything about the response of its relative, the important oil crop plant Brassica napus. Here, we analyzed the molecular response of leaves of rapeseed seedlings to full submergence under illumination. RNAseq experiments revealed a strong carbon starvation response under submergence, but no indication for a low-oxygen response. We used two cultivars in this study, one Asian flooding-tolerant cultivar and one European hybrid cultivar, but those genotypes did not show strong differences in their responses to submergence.
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