Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)

Abstract

MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology. A total of 88 conserved and 124 novel miRNAs were identified, of which 50 were proven to be salinity-responsive miRNAs, with 32 significantly up-regulated and 18 down-regulated. miR172b and miR1120a, as well as mi393a, were the most significantly differently expressed. Targets of these miRNAs were computationally predicted, then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the targets of salinity-responsive miRNAs were enriched in transcription factors and stress-related proteins. Finally, we investigated the expression profiles of seven miRNAs ranging between salt-tolerant and sensitive genotypes, and found that they played critical roles in salinity tolerance in wild emmer. Our results systematically identified the salinity-responsive miRNAs in wild emmer, not only enriching the miRNA resource but also laying the foundation for further study on the biological functions and evolution of miRNAs in wild wheat and beyond.

MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower

“…During this investigation, qRT-PCR indicated that seven miRNAs have different expression models in both leaves and root of plants under stress and normal conditions. This is in accordance to prior results reported in wheat and rice [38,39]. In fact, miRNAs are expressed only in some organs and in response to environmental stresses [40,41].…”

“…The miR408 family was suggested as Cu-miRNA [37]. In Arabidopsis at low and high Cu concentration, Cu-miRNA accumulated and disappeared, respectively [38,39].The main target genes of miR408 encode blue copper proteins, including those in the phycocyanin family [53,54]. The biological function of Cu is entirely related to the reconstruction of its properties.…”

Identification and characterization of circRNAs involved in the regulation of low nitrogen-promoted root growth in hexaploid wheat

“…Moreover, all the seven DECs had 2–13 miRNA-binding sites, which was similar with previous reports in human and another study in wheat [ 23 , 26 ], but was significantly higher than that reported in rice and tomato [ 18 , 19 ]. Interestingly, some putative circRNA-binding miRNAs have been reported that involved in the response to low nitrogen and other abiotic stresses [ 37 , 38 ]. For example, miR530 is differentially expressed in response to low nitrogen stress in rice, suggesting that it may play an important role in plant nitrogen utilization [ 37 ].…”

Alfalfa response to heat stress is modulated by microRNA156

“…In alfalfa, miR156 regulates shoot branching, stem thickness, trichome density, flowering time and forage yield (Aung et al , ). In addition to growth and development, miR156 has been associated with response to salinity and drought in A. thaliana , Brachypodium distachyon, cotton, rice, barley, wheat and alfalfa (Wang et al , Cui et al , Mondal and Ganie , Deng et al , Arshad et al , Feng et al ); aluminum stress in rice (Lima et al ); and immunity to bacterial infection in Nicotiana benthamiana (Padmanabhan et al ). The above‐mentioned observations suggest that miR156 could also be an effective molecular tool to improve heat stress in plants (Aung et al , Gao et al , Arshad et al ).…”