Integrative Analysis of mRNA and miRNA Expression Profiles of the Tuberous Root Development at Seedling Stages in Turnips

Abstract

The tuberous root of Brassica rapa L. (turnip) is an important modified organ for nutrition storage. A better understanding of the molecular mechanisms involved in the process of tuberous root development is of great value in both economic and biological context. In this study, we analyzed the expression profiles of both mRNAs and miRNAs in tuberous roots at an early stage before cortex splitting (ES), cortex splitting stage (CSS), and secondary root thickening stage (RTS) in turnip based on high-throughput sequencing technology. A large number of differentially expressed genes (DEGs) and several differentially expressed miRNAs (DEMs) were identified. Based on the DEG analysis, we propose that metabolism is the dominant pathway in both tuberous root initiation and secondary thickening process. The plant hormone signal transduction pathway may play a predominant role in regulating tuberous root initiation, while the starch and sucrose metabolism may be more important for the secondary thickening process. These hypotheses were partially supported by sequential DEM analyses. Of all DEMs, miR156a, miR157a, and miR172a exhibited relatively high expression levels, and were differentially expressed in both tuberous root initiation and the secondary thickening process with the expression profiles negatively correlated with those of their target genes. Our results suggest that these miRNAs play important roles in tuberous root development in turnips.

Genome-wide survey indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) calcium-dependent protein kinase genes

“…Transcriptional profiles are typically closely related to a gene function. To investigate the link between evolutionary and functional divergence of 55 BrrCDPK genes in turnip development and growth, the expression levels of turnip CDPK genes were analyzed in four different tissues (root, stem, leaf, and flower) by quantitative real-time polymerase chain reaction (qRT-PCR) and using publicly available qRT-PCR expression profiles of three root development stages 39 . A heatmap was created using Genesis 1.7.7.0 software.…”

“…To analyze gene expression in different stages of tuberous root development, a heat map of different root development stages was made using the transcriptional data generated by Jingjuan Li 39 . Samples were collected on day 18 (the early stage before cortex splitting, ES), day 28 (the cortex splitting stage, CSS), and day 64 (the stage of root thickening, RTS) after sowing, respectively.…”

“…For the three root developmental stages, the expression levels from RNA-Seq data were obtained from previous research 39 . Samples were collected on day 18 (the early stage before cortex splitting, ES), day 28 (the cortex splitting stage, CSS), and day 64 (the stage of root thickening, RTS) after sowing.…”

Cassava microRNAs and storage root development

“…Cytokinins and auxins have been involved in thickening of storage roots (tuberization) in sweet potato, whose storage roots develop from some of fibrous roots similarly as observed in cassava (Noh et al 2010). The signal transduction pathway of auxin was also reported to play a great role in tuberous root initiation in Brassica rapa (Li et al 2015). It should be noted that in cassava, NAC, but not NAC1, was found to be the target of miR164 though miR164/NAC showed a negative correlation with SR development.…”

Comparative Transcriptome Analysis Reveals Effects of Exogenous Hematin on Anthocyanin Biosynthesis during Strawberry Fruit Ripening

“…Quantitative real-time PCR (qRT-PCR) experiments were conducted to assess the reliability of the RNA-Seq data [34]. Eleven pairs of gene specific primers were designed to verify the DEGs in the strawberry fruit (Table S1).…”