MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice

Abstract

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.

Cytological observation and RNA-seq analysis reveal novel miRNAs high expression associated with the pollen fertility of neo-tetraploid rice

“…4 ). Short Tandem Target Mimic (STTM) has provided effective tools to block endogenous mature miRNA activity, making it technically possible to undertake large-scale genome-wide studies model and crop plants [ 55 , 56 ]. The STTM vectors of osa-miR528-5p , osa-MIR397b-p3 , osa-miR5492 , and osa-MIR5495-p5 were constructed and transformed osa-miR528-5p- STTM into neo-tetraploid rice Huaduo1 and osa-MIR397b-p3- STTM, osa-miR5492- STTM, and osa-MIR5495-p5- STTM into the japonica variety Nipponbare.…”

G‐U base‐paired hpRNA confers potent inhibition of small RNA function in plants

“…However, while sRNAs can be readily identified using RNA sequencing technologies, functional analysis of these molecules using existing mutagenesis approaches is not as easy due to their small size and noncoding nature as well as functional redundancy among homologous members of sRNAs. Currently, the most useful approach for sRNA function analysis is the sRNA decoy technologies developed based on the features of naturally occurring miRNA target mimics in plants and animals (Chen et al., 2021; Ebert et al., 2007). The first of the sRNA decoy technologies in plants, miRNA target MIMICs ( MIM ), was derived from the naturally occurring non–protein‐coding RNA of IPS1 ( INDUCED BY PHOSPHATE STARVATION1 ) in Arabidopsis thaliana , which binds to and sequesters miR399 due to high sequence complementarity with a mismatched 3‐nt bulge at the miRNA cleavage site (Franco‐Zorrilla et al., 2007; Todesco et al., 2010).…”

“…SPONGEs are synthetic RNAs containing up to 15 miRNA binding sequences with mismatches at the miRNA cleavage sites, with each binding site separated by 4 nts (Reichel et al., 2015). All three approaches, MIMs, STTMs, and SPONGEs can confer effective repression of some individual miRNAs, but high variabilities in their efficacies exist when targeting different miRNA families (Chen et al., 2021; Reichel et al., 2015).…”

Prediction of MicroRNAs Involved in Lignan and Cyanogenic Glycosides Biosynthesis of Flax (Linum usitatissimum L.)

“…Among its main antinutrients belong cyanogenic glycosides for whose is the breeding program set up to minimizing by contrast to lignan´s content (Fofana et al, 2017b, Kazachkov et al, 2020. For these purposes the microRNAs represent a valuable tool in agronomic trait analysis and innovative in silico approaches are necessary in successful breeding process (Chen et al, 2021, Tan et al, 2022.…”