MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour

Abstract

Trans-acting short-interfering RNAs (tasiRNAs) originate from TAS3 families through microRNA (miRNA) 390-guided cleavage of primary transcripts and target auxin response factors (ARF3/-4), which are involved in the normal development of lateral roots and flowers in plants. However, their roles in embryo development are still unclear. Here, the pathway miR390-TAS3-ARF3/-4 was identified systematically for the first time during somatic embryo development in Dimocarpus longan. We identified the miR390 primary transcript and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, salicylic acid, anaerobic induction, fungal elicitor, circadian control, and heat stress. The longan TAS3 transcript, containing two miR390-binding sites, was isolated; the miR390- guided cleavage site located near the 3′ end of the TAS3 transcript was verified. Eight TAS3-tasiRNAs with the 21-nucleotides phase were found among longan small RNA data, further confirming that miR390-directed TAS3 cleavage leads to the production of tasiRNA in longan. Among them, TAS3_5′D5+ and 5′D6+ tasiRNAs were highly abundant, and verified to target ARF3 and -4, implying that miR390-guided TAS3 cleavage with 21-nucleotides phase leading to the production of tasiRNA-ARF is conserved in plants. Pri-miR390 was highly expressed in friable-embryogenic callus (EC), and less expressed in incomplete compact pro-embryogenic cultures, while miR390 showed its lowest expression in EC and highest expression in torpedo-shaped embryos (TEs). DlTAS3 and DlARF4 both exhibited their lowest expressions in EC, and reached their peaks in the globular embryos stage, which were mainly inversely proportional to the expression of miR390, especially at the globular embryos to cotyledonary embryos (CEs) stages. While DlARF3 showed little variation from the EC to TEs stages, and exhibited its lowest expression in the CEs stage. There was a general lack of correlation between the expressions of DlARF3 and miR390. In addition, pri-miR390, DlTAS3, DlARF3 and -4 were up-regulated by 2,4-D in a concentration-dependent manner. They were also preferentially expressed in roots, pulp, and seeds of ‘Sijimi’ longan, implying their extended roles in the development of longan roots and fruit. This study provided insights into a possible role of miR390-tasiRNAs-ARF in plant somatic embryo development.

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

“…The auxin-related miRNAs frequently target the fundamental components of the auxin signaling pathway, including the ARFs, which are involved in SE induction [27,93]. Accordingly, insights into embryogenic cultures of Arabidopsis and other plants indicated that miR160 could directly regulate the expression of ARF10, ARF16, and ARF17; miR167 seems to the control expression of ARF6 and ARF8, while miR390 possibly downregulates the ARF2, ARF3, ARF4 transcripts [55,63,64,68,81,85,86].…”

MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis

“…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.…”

Association mapping of agronomic traits of canola (Brassica napus L.) subject to heat stress under field conditions

“…Many other genes were found associated with heat stress such as gibberellin 2-oxidase 8 which regulates plant growth (Lo et al, 2008), ethylene-regulated nuclear protein (ERT2), which regulates plant growth and development through cell elongation and cell division (Sakai et al, 1998), ABC-2 type transporter family protein is involved in plant growth, development and response to abiotic stresses (Kang et al, 2011). Other genes associated with plant growth and development such as C2H2-like zinc finger protein (Chrispeels et al, 2000), iron regulated 2 , and core-2/I-branching beta-1,6-Nacetylglucosaminyltransferase family protein (Lin et al, 2015) were also identified.…”

“…Many candidate genes were identified that are associated with raceme height and are involved in different physiological process. Of these candidate genes, Core-2/Ibranching beta-1,6-N-acetylglucosaminyltransferase family proteins involved in plant development (Lin et al, 2015), plant calmodulin-binding protein is associated with Ca2+ binding and plant growth (Ranty et al, 2006), indoleacetic acid-induced protein 10 which enhances plant growth under drought stress condition (Yasin et al, 2006), protein kinase family protein involved in stem elongation and vascular development (Matschi et al, 2013), auxin response factor 1 regulates plant growth and development (Li et al, 2016), mitogen-activated protein kinase acts as signal transporter for cell division and plant growth (Sinha et al, 2011), AP2/B3-like transcriptional factor family protein is involved in plant growth , ACC oxidase 1 is involved in plant growth and lowering stress susceptibility ( Van de Poel and Van Der Straeten, 2014).…”