Dataset Information

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa.

ABSTRACT:

Background

Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported.

Results

Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid.

Conclusions

This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.

SUBMITTER: Zhang L

PROVIDER: S-EPMC6694508 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa.

Zhang Libin L Zou Jun J Li Shisheng S Wang Baoshan B Raboanatahiry Nadia N Li Maoteng M

BMC genomics 20190814 1

<h4>Background</h4>Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported.<h4>Results</h4>Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel ...[more]

PMID: 31412776

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Project description:The family Brassicaceae is a source of important crop species, including Brassica napus (oilseed rape), Brassica oleracea, and B. rapa, that is used globally for oil production or as a food source (e.g., pak choi or turnip). However, despite advances in recent years, including genome sequencing, a lack of established tools tailored to the study of Brassica crop species has impeded efforts to understand their molecular processes in greater detail. Here, we describe the use of a simple Agrobacterium-mediated transient expression system adapted to B. rapa and B. napus that could facilitate study of molecular and biochemical events in these species. We also demonstrate the use of this method to characterize the N-degron pathway of protein degradation in B. rapa. The N-degron pathway is a subset of the ubiquitin-proteasome system and represents a mechanism through which proteins may be targeted for degradation based on the identity of their N-terminal amino acid residue. Interestingly, N-degron-mediated processes in plants have been implicated in the regulation of traits with potential agronomic importance, including the responses to pathogens and to abiotic stresses such as flooding tolerance. The stability of transiently expressed N-degron reporter proteins in B. rapa indicates that its N-degron pathway is highly conserved with that of Arabidopsis thaliana. These findings highlight the utility of Agrobacterium-mediated transient expression in B. rapa and B. napus and establish a framework to investigate the N-degron pathway and its roles in regulating agronomical traits in these species. Significance statement:We describe an Agrobacterium-mediated transient expression system applicable to Brassica crops and demonstrate its utility by identifying the destabilizing residues of the N-degron pathway in B. rapa. As the N-degron pathway functions as an integrator of environmental signals, this study could facilitate efforts to improve the robustness of Brassica crops.

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Project description:Key messageTranscriptomic and epigenomic profiling of gene expression and small RNAs during seed and seedling development reveals expression and methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance of hybrids through heterosis remains a key aspect in plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate the potential role of transcriptomic and epigenomic patterns in early expression of hybrid vigor, we investigated gene expression, small RNA abundance and genome-wide methylation in hybrids from two distant Brassica napus ecotypes during seed and seedling developmental stages using next-generation sequencing. A total of 31117, 344, 36229 and 7399 differentially expressed genes, microRNAs, small interfering RNAs and differentially methylated regions were identified, respectively. Approximately 70% of the differentially expressed or methylated features displayed parental dominance levels where the hybrid followed the same patterns as the parents. Via gene ontology enrichment and microRNA-target association analyses during seed development, we found copies of reproductive, developmental and meiotic genes with transgressive and paternal dominance patterns. Interestingly, maternal dominance was more prominent in hypermethylated and downregulated features during seed formation, contrasting to the general maternal gamete demethylation reported during gametogenesis in angiosperms. Associations between methylation and gene expression allowed identification of putative epialleles with diverse pivotal biological functions during seed formation. Furthermore, most differentially methylated regions, differentially expressed siRNAs and transposable elements were in regions that flanked genes without differential expression. This suggests that differential expression and methylation of epigenomic features may help maintain expression of pivotal genes in a hybrid context. Differential expression and methylation patterns during seed formation in an F1 hybrid provide novel insights into genes and mechanisms with potential roles in early heterosis.

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Dataset Information

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa.

Background

Results

Conclusions

Publications

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa.

Similar Datasets

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