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

doi:10.1186/s12864-019-6001-x

. 2019 Aug 14;20(1):649.

doi: 10.1186/s12864-019-6001-x.

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

Libin Zhang¹, Jun Zou², Shisheng Li³, Baoshan Wang⁴, Nadia Raboanatahiry⁵, Maoteng Li^{6

7}

Affiliations

¹ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
² College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
³ Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
⁴ College of Life Science, Shandong Normal University, Jinan, 250000, China.
⁵ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. nadia_raboana@hust.edu.cn.
⁶ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. limaoteng426@hust.edu.cn.
⁷ Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China. limaoteng426@hust.edu.cn.

PMID: 31412776
PMCID: PMC6694508
DOI: 10.1186/s12864-019-6001-x

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

Libin Zhang et al. BMC Genomics. 2019.

. 2019 Aug 14;20(1):649.

doi: 10.1186/s12864-019-6001-x.

Authors

Libin Zhang¹, Jun Zou², Shisheng Li³, Baoshan Wang⁴, Nadia Raboanatahiry⁵, Maoteng Li^{6

7}

Affiliations

¹ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
² College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
³ Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China.
⁴ College of Life Science, Shandong Normal University, Jinan, 250000, China.
⁵ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. nadia_raboana@hust.edu.cn.
⁶ College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China. limaoteng426@hust.edu.cn.
⁷ Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang, 438000, China. limaoteng426@hust.edu.cn.

PMID: 31412776
PMCID: PMC6694508
DOI: 10.1186/s12864-019-6001-x

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.

Keywords: B. napus; B. rapa; Hybrid; MicroRNAs; Small RNA sequencing.

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Conflict of interest statement

The authors declare that they have no conflict of interests.

Figures

**Fig. 1**
Bioinformatics analysis of small RNA sequencing. a The length distribution of small RNAs in *B. napus*, *B. rapa* and F1 hybrid. b MiRNA distribution in the genome of hybrid of *B. napus* and *B. rapa* hybrid. From outer to inter circles: (1) chromosomes of hybrid (Yellow indicates the chromosomes of *B. napus*; Purple indicates the chromosomes of *B. rapa*); (2) small RNA reads; (3) 24 nt small RNA reads; (4) mature miRNA reads. c The percentage of small RNAs of *B. napus*, *B. rapa* and F1 hybrid

**Fig. 2**
miRNA identification and differentially expressed miRNA analysis in *B. napus*, *B. rapa* and F1 hybrid. a The correlation analysis of the clean reads. b TPM distribution of the clean reads. c Venn diagram analysis of the identified conserved miRNAs in *B. napus*, *B. rapa* and F1 hybrid. d Venn diagram analysis of the identified novel miRNAs in *B. napus*, *B. rapa* and F1 hybrid. e Heatmap analysis of the differentially expressed miRNAs in *B. napus*, *B. rapa* and F1 hybrid

**Fig. 3**
Quantitative RT-PCR Validation of differentially miRNAs between *B. napus*, *B. rapa* and the F1 hybrid

**Fig. 4**
KEGG pathway analysis of the differentially expressed miRNAs in *B. napus*, *B. rapa* and F1 hybrid (Top 20 pathways pathways)

**Fig. 5**
MiRNA-mRNA interaction network analysis in *B. napus*, *B. rapa* and F1 hybrid (Red indicates the miRNAs; Blue indicates the target genes; Yellow indicates the important transcription factors)

**Fig. 6**
Non-additive miRNA expression analysis between *B. napus*, *B. rapa* and F1 hybrid. a. The number of upregulated and downregulated non-additively expressed miRNAs in F1 hybrid. b. Expression pattern analysis of 134 down-regulated miRNAs in F1 hybrid

**Fig. 7**
MiRNA synteny analysis between F1 hybrid (AⁿA^rCⁿ) and two progenitors AⁿAⁿCⁿCⁿ and A^rA^r. The miRNAs of AⁿAⁿCⁿCⁿ and A^rA^r were mapped to F1 genome. The lines indicate the matches of miRNAs from two progenitors to F1 genome. a. Yellow indicates the Aⁿ and Cⁿ genomes of F1 hybrid; Purple indicates the A^r genome of F1 hybrid; Orange indicates the *B. napus* genome. b. Yellow indicates the Aⁿ and Cⁿ genomes of F1 hybrid; Purple indicates the A^r genome of F1 hybrid; Blue indicates the *B. rapa* genome

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References

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[1] Otto SP, Whitton J. Polyploid incidence and evolution. Annu Rev Genet. 2000;34:401–437. doi: 10.1146/annurev.genet.34.1.401. - DOI - PubMed

[2] Otto SP, Whitton J. Polyploid incidence and evolution. Annu Rev Genet. 2000;34:401–437. doi: 10.1146/annurev.genet.34.1.401. - DOI - PubMed

[3] Ng DWK, Lu J, Chen ZJ. Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr Opin Plant Biol. 2012;15:154–161. doi: 10.1016/j.pbi.2012.01.007. - DOI - PubMed

[4] Ng DWK, Lu J, Chen ZJ. Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr Opin Plant Biol. 2012;15:154–161. doi: 10.1016/j.pbi.2012.01.007. - DOI - PubMed

[5] Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature. 2009;457:327. doi: 10.1038/nature07523. - DOI - PMC - PubMed

[6] Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature. 2009;457:327. doi: 10.1038/nature07523. - DOI - PMC - PubMed

[7] Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol. 2007;58:377–406. doi: 10.1146/annurev.arplant.58.032806.103835. - DOI - PMC - PubMed

[8] Chen ZJ. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol. 2007;58:377–406. doi: 10.1146/annurev.arplant.58.032806.103835. - DOI - PMC - PubMed

[9] Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploidy plants. Science. 2008;320:481–483. doi: 10.1126/science.1153585. - DOI - PubMed

[10] Leitch AR, Leitch IJ. Genomic plasticity and the diversity of polyploidy plants. Science. 2008;320:481–483. doi: 10.1126/science.1153585. - DOI - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

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