Comparative transcriptome discovery and elucidation of the mechanism of long noncoding RNAs during vernalization in Brassica rapa
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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.
KeywordsComparative transcriptome Brassica rapa Vernalization LncRNA Conetworks Hormones
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.
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Conflict of interest
The authors declare no conflict of interest.