Identification of miRNAs and their targets in regulating tuberous root development in radish using small RNA and degradome analyses

Abstract

High-throughput small RNA sequencing and degradome analysis were used in this study to thoroughly investigate the role of miRNA-mediated regulatory network in tuberous root development of radish. Samples from the early seedling stage (RE) and the cortex splitting stage (RL) were used for the construction of six small RNA libraries and one degradome library. A total of 518 known and 976 novel miRNAs were identified, of which, 338 known and 18 novel miRNAs were expressed in all six libraries, respectively. A total of 52 known and 57 novel miRNAs were identified to be significantly differentially expressed between RE and RL, and 195 mRNAs were verified to be the targets of 194 miRNAs by degradome sequencing. According to the degradome analysis, 11 differentially expressed miRNAs had miRNA-mRNA targets, and 13 targets were identified for these 11 miRNAs. Of the 13 miRNA-mRNA targets, 4 genes (RSG11079.t1, RSG11844.t1, RSG16775.t1, and RSG42419.t1) were involved in hormone-mediated signaling pathway, 2 gens (RSG11079.t1 and RSG16775.t1) were related to post-embryonic root development, and 1 gene (RSG23799.t1) was involved in anatomical structure morphogenesis, according to the GO function analysis for biological process. Target Genes participated in these processes are important candidates for further studies. This study provides valuable information for a better understanding of the molecular mechanisms involved in radish tuberous root formation and development.

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway

“…MicroRNAs (miRNAs) represent an extensive class of small (usually 21–24 nucleotides length), non-coding, single-stranded, endogenous RNAs which are abundant in all eukaryotes. Since the direct cloning of first plant miRNA from Arabidopsis ( Arabidopsis thaliana L.) ( Park et al, 2002 ; Llave et al, 2002 ; Reinhart et al, 2002 ), more and more miRNAs and their putative targets were identified in different plant species, such as maize ( Zea mays L.) ( Zhang et al, 2009a ), rice ( Oryza sativa L.) ( Zhang et al., 2017b ; Peng et al, 2011 ), barley ( Hordeum vulgare L.) ( Curaba et al, 2012 ), switchgrass ( Panicum virgatum L.) ( Xie et al, 2014 ), wheat ( Triticum aestivum L.) ( Han et al, 2014 ), sweet potato ( Ipomoea babatas L.) ( Bian et al, 2016 ), rapeseed ( Brassica napus L.) ( Jian et al, 2018 ), sesame ( Sesamum indicu L.) ( Marakli, 2018 ) and radish ( Raphanus sativus L.) ( Liu et al, 2018 ), and so on. In plants, the stem-loop secondary structure of RNA Polymerase II transcript (pri-miRNA) was cleaved by Dicer-like 1 (DCL1) protein to produce a hairpin RNA molecule (pre-miRNA), which further cleaved by DCL1 to result in a double stranded intermediate RNA ( Jones-Rhoades, Bartel & Bartel, 2006 Zhu et al, 2013 ).…”

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

“…microRNAs (miRNAs) are small, endogenous, noncoding RNAs that have essential functions in many biological processes, such as the regulations of growth and development, stress response, and metabolism. Many studies have shown that miRNAs play essential roles in root and tuber formation or development [27][28][29]. miR165/166 regulated root growth by determining the fate of root cells in Arabidopsis combined with phytohormone crosstalk, by negatively regulating its target genes auxin response factor ARF10, ARF16 and ARF17 [30].…”

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita)

“…microRNAs (miRNAs) are small, endogenous, non-coding RNAs that have essential functions in many biological processes, such as the regulations of growth and development, stress response, and metabolism. Many studies have shown that miRNAs play essential roles in root and tuber formation or development [27][28][29]. miR165/166 regulated root growth by determining the fate of root cells in Arabidopsis combined with phytohormone crosstalk, by negatively regulating its target genes auxin response factor ARF10, ARF16 and ARF17 [30].…”