Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA‐and siRNA‐mediated transcript cleavage involved in somatic embryogenesis

Abstract

SummarySomatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs and their target genes in nonembryogenic and embryogenic tissues of 'Valencia' sweet orange. By high-throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs) derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes. The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, miRNA-and siRNA-mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE.

MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis

“…Auxin/ARF-related functions can also be postulated for miR390 , which had a significantly modulated expression in SE of Arabidopsis (present study) and of other plants (Zhang et al, 2012; Lin and Lai, 2013; Wu et al, 2015). miR390 has been documented as controlling the auxin signaling pathway by triggering the production of tasiARFs which down-regulate expression of ARF2, ARF3 , and ARF4 genes (Allen et al, 2005; Williams et al, 2005).…”

“…Similar to the widely documented involvement of miRNA molecules in plant development in vivo (Jin et al, 2013), the expression of miRNAs was reported during in vitro induced SE in several plant species including Citrus sinensis, Dimocarpus longan, Gossypium hirsutum, Larix kaempferi, Larix leptolepis, Liriodendron tulipifera × L. chinense, Manihot esculenta , and Zea mays (Zhang et al, 2012, 2014; Li et al, 2013; Lin and Lai, 2013; Yang et al, 2013; Chávez-Hernández et al, 2015; Wu et al, 2015; Lin et al, 2015a,b; Khatabi et al, 2016). Thus, the engagement of miRNAs in the embryogenic transition that is induced in vitro is assumed, although knowledge about the function of the specific miRNA in SE induction is very limited.…”

Small RNA and Transcriptome Sequencing Reveal a Potential miRNA-Mediated Interaction Network That Functions during Somatic Embryogenesis in Lilium pumilum DC. Fisch.

“…(Yang et al, 2013), Dimocarpus longan Lour. (Lin and Lai, 2013; Lin et al, 2015a,b) and Citrus sinensis (Wu et al, 2011; Wu X. M. et al, 2015). The same miRNA may participate in different stages of SE in different plants.…”

Cellular and molecular changes associated with competence acquisition during passion fruit somatic embryogenesis: ultrastructural characterization and analysis of SERK gene expression

“…Understanding the fundamental molecular events that trigger SE could guide the improvement of propagation protocols, especially, for plants that are recalcitrant to in vitro culture (Mahdavi-Darvari et al 2015). Additionally, SE is a potential model system for studying the basis of developmental reprogramming among higher eukaryotic organisms (Zimmerman 1993;Lin and Lai 2013;Wu et al 2015), further highlighting the importance of investigating this unique developmental pathway.…”