Identification of microRNAs and their targets in inflorescences of an Ogura-type cytoplasmic male-sterile line and its maintainer fertile line of turnip (Brassica rapa ssp. rapifera) via high-throughput sequencing and degradome analysis

Abstract

Cytoplasmic male sterility (CMS) is a widely used trait in angiosperms caused by perturbations in nucleus-mitochondrion interactions that suppress the production of functional pollen. MicroRNAs (miRNAs) are small non-coding RNAs that act as regulatory molecules of transcriptional or post-transcriptional gene silencing in plants. The discovery of miRNAs and their possible implications in CMS induction provides clues for the intricacies and complexity of this phenomenon. Previously, we characterized an Ogura-CMS line of turnip (Brassica rapa ssp. rapifera) that displays distinct impaired anther development with defective microspore production and premature tapetum degeneration. In the present study, high-throughput sequencing was employed for a genome-wide investigation of miRNAs. Six small RNA libraries of inflorescences collected from the Ogura-CMS line and its maintainer fertile (MF) line of turnip were constructed. A total of 120 pre-miRNAs corresponding to 89 mature miR-NAs were identified, including 87 conversed miRNAs and 33 novel miRNAs. Among these miRNAs, the expression of 10 differentially expressed mature miRNAs originating from 12 pre-miRNAs was shown to have changed by more than twofold between inflorescences of the Ogura-CMS line and inflorescences of the MF line, including 8 down-and 2 up-regulated miRNAs. The expression profiles of the differentially expressed miRNAs were confirmed by stem-loop quantitative real-time PCR. In addition, to identify the targets of the identified miR-NAs, a degradome analysis was performed. A total of 22 targets of 25 miRNAs and 17 targets of 28 miRNAs were identified as being involved in the reproductive development for Ogura-CMS and MF lines of turnip, respectively. Negative correlations of expression patterns between partial miRNAs and their targets were detected. Some of these identified targets, such as squamosa promoter-binding-like transcription factor family proteins, auxin response factors and pentatricopeptide repeat-containing proteins, were previously

miRNome profiling reveals differential miRNAs associated with embryogenic potential in the somatic embryogenesis of Araucaria angustifolia

“…The advent of deep sequencing technologies has enabled the identi cation of miRNAs during embryogenesis in non-model plant species, including conifers (Zhang et al 2012;Singh et al 2018;Lin et al 2020). However, only four conifer species have miRNAs deposited in the miRBase (v22.1) database, and few studies addressed this speci c phase of the plant life cycle (Alves et al 2020), illustrating that our understanding of plant embryogenesis by epigenetics and post-transcriptional regulation is still in its initial moment (Zhang et al 2012).…”

“…The plant gene silencing process is mediated by small non-coding classes of RNAs, including miRNAs and small interfering RNA (siRNAs) (Lakhwani et al 2020). miRNAs are a distinct class of single-stranded RNA of ~ 18-25 nucleotides (Zhang et al 2018a,b;Lin et al 2020). MIR genes are endogenously transcribed as long precursor transcripts (pri-miRNAs), forming a fold-back hairpin structure with the small RNA embedded in one of its arms (Rogers and Chen 2013; Chorostecki et al 2017).…”

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

“…Deep sequencing technology has led to the identification of numerous miRNAs in plant genomes from species such as Italian sweet pepper [20], tea, mulberry, Chinese cabbage, turnip, longan (Dimocarpus longan Lour. ), bread wheat, Artemisia annua, Populus euphratica, Moringa oleifera, and Solanum lycopersicum [21][22][23][24][25][26][27][28][29][30]. The following are some examples of these miRNAs, many of which are involved in specific signaling pathways.…”