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Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [ChIP-seq]

ABSTRACT: We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique).Histone modifications analysis suggested there was histone modifications reprogramming in the B. napus hybrids compeared with parents.

ORGANISM(S): Brassica napus

PROVIDER: GSE218583 | GEO | 2023/07/18

REPOSITORIES: GEO

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Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids [RNA-seq]

Project description:We integrated data of transcriptome and histone modifications (H3K4me3 and H3K27me3) for HZ62 in three tissue types (seedling, flower bud and silique). Transcriptome analysis suggested that gene expression level altered in hybrids compared with parents.

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Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids

Project description:Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

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Project description:We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

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Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-reChIP]

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Brassica napus control vs. heat stress

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.

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Brassica napus control vs. heat stress

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Brassica napus differentially expressed genes in seeds and silique walls

Project description:Identification of differentially expressed genes in seeds and silique walls at the seed-filling stage in Brassica napus through transcriptional profiling

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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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