Plant Growth Regulation

, Volume 85, Issue 1, pp 27–39 | Cite as

Comparative transcriptome discovery and elucidation of the mechanism of long noncoding RNAs during vernalization in Brassica rapa

  • Tongkun Liu
  • Peng Wu
  • Qian Wang
  • Wenli Wang
  • Changwei Zhang
  • Feifei Sun
  • Zhaokun Liu
  • Ying Li
  • Xilin Hou
Original paper
  • 109 Downloads

Abstract

Flowering time is an important agronomic trait in Brassica rapa (B. rapa). However, our current understanding of the role of long noncoding RNAs (lncRNAs) in flowering time responded to vernalization is limited. The rapid development of the omics sequencing technology has facilitated the identification of thousands of lncRNAs in various plant species. Here, we used comparative transcriptome analysis between control and vernalized B. rapa to identify differentially expressed genes (DEGs) and lncRNAs (DELs). A total of 300 DEGs and 254 DELs were identified. Co-localization networks consisting of 128 DEGs and 127 DELs were established, followed by analyses of hierarchical categories, functional annotations, and correlation from mRNA-to-lncRNA. We found that the BraZF-HD21 (Bra026812) gene which responds to photoperiods and vernalization is correlated with lncRNA TCONS_00035129. The correlated genes that were mapped to the plant hormone signal transduction pathway and increased gibberellin A3 (GA3) content demonstrated that vernalization influences plant hormone levels. These findings suggest that vernalization alters the process of hormone biosynthesis, which in turn regulates flowering. This study provides an approach to elucidation of the regulatory mechanism of lncRNAs during vernalization in B. rapa.

Keywords

Comparative transcriptome Brassica rapa Vernalization LncRNA Conetworks Hormones 

Notes

Acknowledgements

This work was supported by the Fundamental Research Funds for the Central Universities (Y0201700179), the Natural science of Jiangsu Province (BK20171374), and the National Natural Science Foundation of China (No. 31330067). We thank Mr. Hua-wei Tan in Nanjing Hua-Seq Biotechnologies Co, Ltd., China for assistance on bioinformatics analysis.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10725_2018_371_MOESM1_ESM.jpg (389 kb)
Supplementary Fig. 1 The statistical analysis for the composition of raw reads for each sample. The statistical data include the reads containing adapter, “N”, low quality and clean reads (JPG 389 KB)
10725_2018_371_MOESM2_ESM.jpg (788 kb)
Supplementary Fig. 2 The sequencing saturation of each sample in NHCC (JPG 787 KB)
10725_2018_371_MOESM3_ESM.jpg (682 kb)
Supplementary Fig. 3 Exon coverage statistics of each sample (JPG 681 KB)
10725_2018_371_MOESM4_ESM.jpg (297 kb)
Supplementary Fig. 4 Secondary structure of known pre-miRNA (JPG 296 KB)
10725_2018_371_MOESM5_ESM.jpg (763 kb)
Supplementary Fig. 5 The distribution of genes that were mapped to the pathway of plant hormone signal transduction in NHCC (JPG 762 KB)
10725_2018_371_MOESM6_ESM.jpg (29 kb)
Supplementary Fig. 6 Bioinformatics analysis pipeline of LncRNA (JPG 29 KB)
10725_2018_371_MOESM7_ESM.jpg (368 kb)
Supplementary Fig. 7 Expression leves of DEG and DEL under vernalization (JPG 368 KB)
10725_2018_371_MOESM8_ESM.xls (7.4 mb)
Supplementary material 8 (XLS 7610 KB)

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Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Tongkun Liu
    • 1
  • Peng Wu
    • 1
  • Qian Wang
    • 2
  • Wenli Wang
    • 1
  • Changwei Zhang
    • 1
  • Feifei Sun
    • 3
  • Zhaokun Liu
    • 4
  • Ying Li
    • 1
  • Xilin Hou
    • 1
  1. 1.Department of HorticultureNanjing Agricultural UniversityNanjingChina
  2. 2.Jinling Institute of TechnologyNanjingChina
  3. 3.Nanjing Institute of Vegetable ScienceNanjingChina
  4. 4.Suzhou Institute of VegetableNanjingChina

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