Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops

Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.


INTRODUCTION
Salinity, as a major environmental stress factor, restricts crop growth and yield globally. It is reported that salinity affected a land area as large as 800 million hectares across the globe, accounting for 6% of the land (Abdel Attia et al., 2021). Approximately 20% of the irrigated soils are affected by salinity stress , and 50% of arable land will be affected by 2050 (Butcher et al., 2016). Salt stress leads to changes in metabolic activity, cell wall damage, and cytoplasmic dissolution; it reduces the photosynthetic efficiency, accelerates aging, increases respiratory consumption and toxin accumulation, and eventually results in plant death (Osman et al., 2020;Abdel Latef et al., 2021). It is estimated that salinity can result in $27.3 billion in agricultural damage every year (Qadir et al., 2014). On the other hand, regional food scarcity will persist continually, particularly in South Asia, sub-Saharan Africa, the Middle East, and where population increase is rapid but agricultural outputs are low (FAO, 2017). Therefore, breeding and growing salt-tolerant crops to utilize the marginal and high-salinity soils are one of the most important strategies to meet the increase in food demand required by the estimated population in 2050 of 10 billion people (Mekonnen and Hoekstra, 2016;FAO, 2017;Morton et al., 2019).
MicroRNA (miRNA) is a non-coding single-stranded small RNA with a length of 21-24 nucleotides, and it acts as gene regulators to control the transcript abundance of its target gene. In the wild, miRNA exists in diverse organisms, including plants, animals, and microorganisms, and it regulates growth, development, signal transduction, response to adversity, and other biological processes. It was firstly discovered in Caenorhabditis (Lee and Ambros, 2001) and was then detected in four laboratories at approximately the same time in Llave et al. (2002), Mette et al. (2002), Park et al. (2002), Reinhart et al. (2002). After that, more and more plant miRNAs have been identified and functionally characterized in various plant species. MiRNA family names are listed in the order of publication, and miRNAs with similar sequences (usually fewer than 3 nt in difference) and common functions are classified as members of the same miRNA family . Both the intraspecific conservation and interspecific differences of miRNAs are environmentally adaptive and evolve with the change in environment . However, the evolution of miRNAs is conservative because some key target genes of miRNAs are conservative (Gramzow and Theißen, 2019).
Various enzymes and functional proteins are involved in the plant's miRNA biosynthesis and functions. The primary miRNA transcripts for plants are produced by RNA polymerase II from miRNA genes, and these then pair with complementary bases to form special hairpin structures (Budak and Akpinar, 2015). Then, the stem ring secondary structure is generated by the DICER-LIKE1 (Bielewicz et al., 2013). After the methylation catalyzed by HUA Enhance 1 at the 3 end, the double strand was transferred to the cytoplasm with the help of the transport protein HST. In the cytoplasm, this double-stranded miRNA is decomposed into mature single-stranded miRNA and integrated into RNA-induced silencing complex (RISC) cells, where miRNA interacts with the complementary target mRNA and activates the catalytic RISC with the assistance of Argonaute 1 (AGO1) (Koroban et al., 2016). There are two modes for miRNA to regulate gene expression: RNA cleavage and translation inhibition. The first mode is that miRNAs guide the Argonaute component of RISC to cleave a single phosphodiester bond opposite to the 10th and 11th nucleotides of the miRNA within complementary RNA. Then, the RISC will be free by releasing the fragments, and it then subsequently recognizes and cleaves another transcript (Jones-Rhoades et al., 2006). Afterward, the cleavage fragments are released to make the RISC competent for other RNA recognization and cleavage (Jones-Rhoades et al., 2006). MiRNA-mediated translational repression requires the participation of P-body components, a microtubulesevering enzyme, AGO1, and AGO10 (Brodersen et al., 2008). In addition, miRNA possibly prevents translation by triggering the sequestration of miRNA target in P-bodies (Chen, 2009). In addition, each miRNA can control multiple target genes (Haas et al., 2012). For instance, miR156 promotes floral meristem identity transformation by targeting SPL3, SPL4, and SPL5 in Arabidopsis thaliana (Xu et al., 2016). A gene can also be regulated by multiple miRNAs. For example, miR31 and miR143 affect steroid hormone synthesis by targeting the FSHR receptor .
MiRNAs can regulate plant growth, development, pathogens, and abiotic stress responses. MiR160, miR169, peu-miRn68, and 477b are involved in the hormone signaling crosstalk model of root growth and development in apple rootstock, A. thaliana and Populus (Sorin et al., 2014;Lian et al., 2018;Meng et al., 2020). Cs-miR414 and cs-miR828 are involved in tea bud dormancy (Jeyaraj et al., 2014). For pathogen stress regulations, miR397 plays a negative regulatory role in apple resistance to hepatitis B virus , miR396 affects the susceptibility to rice blast (Chandran et al., 2019), and miR528 increases the viral defense ability of Oryza sativa (Wu et al., 2017). In the aspect of abiotic stress regulations, miR399 and miR827 are important for the resistance to phosphorus deficiency (Hackenberg et al., 2013;Du et al., 2018). The lack of sulfur induces the expression of miR395 for the regulation of genes in the sulfur assimilation pathway (Kawashima et al., 2009). The expression of miR319 is crucial for the cold tolerance of rice . MiR399 regulates Arabidopsis flowering at different temperatures (Kim et al., 2011). Recently, the comparative antagonistic expression profile of miR169 indicates that the miR169 family is a general regulator of various abiotic stresses (Rao et al., 2020). In addition, the over-expression of miR156 changes the expression level of other miRNAs, thus increasing the contents of anthocyanins, flavonoids, and flavonols and decreasing the total lignin content, suggesting the essential role of miRNAs in nutritional processes .
Noticeably, it is demonstrated that miRNA plays important roles in plant salinity responses and adaptation through various miRNA-mediated biological processes, including signal transduction, membrane transport, protein biosynthesis and degradation, photosynthesis, and transcription. In the present review, we mainly discuss the recent research progress on saltstress-related miRNA in plants and the future research direction about miRNA in the salinity stress research field to come up with a strategy to improve the agronomic traits of stress tolerance through the manipulation of miRNAs.

IDENTIFICATION AND EXPRESSION OF PLANT MIRNAS UNDER SALT STRESS
In recent years, with the rapid development of biotechnology, such as microarray and high-throughput deep sequencing, thousands of plant miRNAs were identified under salt stress. As shown in Table 1, different concentrations (80-600 mM) of NaCl and treatment time (3 h to 15 days) were applied for salt stress treatments for identifying salt-responsive miRNA ( Table 1). MiRNAs were detected in leaf, root, stem, and flower separately or in the whole seedling ( Table 1). Fu et al. identified 1,077 miRNAs in Zea mays, comprising the highest number of identified miRNAs in various crops among the reports (Fu et al., 2017). Moreover, 882, 876, 693, and 650 miRNAs were identified in Mesembryanthemum indicates the plant name of halophyte; -indicates no related information.
Frontiers in Plant Science | www.frontiersin.org crystallinum, Medicago truncatula, Vicia faba, and Ipomoea batatas, respectively (Jian et al., 2016;Cao et al., 2018;Alzahrani et al., 2019;Yang et al., 2020). The numbers of identified miRNA vary from dozens to hundreds, which may be due to the plant species, tissue specificity, development stage, and salt stress treatment methods. However, the large-scale identification of miRNAs under salt stress is very necessary and essential, and it lays a solid foundation for the further illumination of the miRNA network. The expression levels of miRNA are up-or down-regulated by salinity stress. For instance, the expression of miR167 in panicle is negatively correlated with the increase of salt concentration (Jodder et al., 2018). In cotton, miR156, miR157, and miR172 are up-regulated at 0.25% NaCl, but their expression decreases with increasing salt concentration . The expression of miR164 also decreases with the increase of salt stress in maize (Shan et al., 2020). Macovei et al. found that the expression levels of Osa-miR414, -miR164e, and -miR408 significantly decrease with increased salt stress and further regulate the occurrence of genes to resist external salt stress by increasing the content of helicases (Macovei and Tuteja, 2012). In addition, some miRNAs are expressed differently in the early and late stages of salt stress treatment. For example, zma-miR169 displays initial up-regulation and subsequent down-regulation under salt stress . MiRNAs and their targets, such as cotton miR156-SPL2, miR159-TCP3, miR162-DCL1, miR395-APS1, and miR396-GRF1, exhibit negative correlation on expression levels . Table 2 shows the expression levels of some representative miRNAs in plants under salt stress. MiR156, miR319, and miR528 are induced by salinity stress Stief et al., 2014;Zhou and Luo, 2014;Xie F. et al., 2015;Yuan et al., 2015), while miR164 and miR397 are repressed (Macovei and Tuteja, 2012;Wang et al., 2013;Gupta et al., 2014;Qin et al., 2015;Xie F. et al., 2015;Lu et al., 2017), which were confirmed at least in two plant species (Table 2). Interestingly, the expression levels of nine miRNAs (e.g., miR159, miR168, miR169, miR172, miR393, miR395, miR396, miR399, and miR408) were promoted in some plant species but were inhibited in the other plant species. For instance, salinity stress increases the expression of miR393 in Arabidopsis thaliana, Triticum aestivum, and Agrostis stolonifera, but decreases the expression of miR393 in Oryza sativa, Gossypium sp., and Spartina alterniflora (Xia et al., 2012;Gupta et al., 2014;Iglesias et al., 2014;Qin et al., 2015;Xie F. et al., 2015;Zhao et al., 2019). Similarly, the expression of miR396 is increased by salinity in Solanum lycopersicum, Nicotiana tabacum, and Agrostis stolonifera but decreased in Arabidopsis thaliana, Oryza sativa, and Spartina alterniflora (Gao et al., 2010;Qin et al., 2015;Cao et al., 2016;Yuan et al., 2019). Up-or down-regulated gene expression usually suggests potential positive or negative functional role. However, the same miRNA has an opposite expression pattern in different plant species under salinity stress conditions, suggesting the same miRNA may play a diverse role in different plant species under salt stress. Moreover, the expression levels of some miRNAs, including miR167, miR390, miR394, miR402, and miR414 were only investigated in very few plant species under salinity stress ( Table 2). Considering some miRNAs displayed totally different expressions in different species, their expression patterns need to be investigated in more plant species under salinity stress conditions.

MiRNA STUDIES IN HALOPHYTE PALNTS
Glycophyte plants, such as Arabidopsis and rice, can only survive at salinity levels 0-100 mM NaCl without any capability to adapt to high salt stress (Horie et al., 2012), whereas some remarkable halophytes can tolerate salinity levels as high as >1000 mM NaCl (Flowers and Colmer, 2008;Munns and Tester, 2008). To an extent, the salt-sensitive glycophytes may not provide enough insights into salt tolerance mechanisms, and the halophytes may have more value for expanding our knowledge about salt resistance mechanisms. Therefore, the exploration of the role of halophyte miRNAs in salinity adaptation can offer compelling contributions for devising strategies of resistance improvement in crops through genetic engineering and plant selection programs. However, there are not many reports on the discovery of saltresponsive miRNAs in halophytes ( Table 1).
The halophyte plant Suaeda maritima grows naturally along the seashore. The expression of S. maritima sma-miR2 and sma-miR5 increases under the influence of seawater, suggesting their metabolic regulatory roles specific to saline environments (Gharat and Shaw, 2015). Eutrema salsugineum, a close relative of A. thaliana, can thrive in high salt conditions ranging from 100 to 500 mM (Amtmann, 2009). E. salsugineum has been developed as a valuable model plant for salt stress-tolerance study because its salinity tolerance is extreme, its lifetime is short, its seed production is copious, and its transformation is easy (Zhu, 2000;Amtmann et al., 2005). Zhang et al. (2013) identified 246 miRNAs candidates in E. salsugineum. In addition, 26 conserved miRNAs and 4 novel miRNAs were found to display a significant response to salt stress in E. salsugineum Wu et al., 2016). Recently, 88 conserved miRNAs and 13 novel miRNAs were identified from Reaumuria soongorica seeds treated with various NaCl concentrations, providing a useful reference for salt resistance improvement of seed germination . A total of 135 conserved miRNAs and the hairpin precursor of 12 novel mcr-miRNAs were found from M. crystallinum seedlings treated with 200 mM NaCl (Chiang et al., 2016). Oryza coarctata is a wild relative of rice and grown in saline water. Mondal et al. found 338 known and 95 novel miRNAs in salt-treated O. coarctata leaves, providing a miRNA-target networking that is involved in salt stress adaption (Mondal et al., 2015). Halostachys caspica (Bieb.), a salt-tolerant short shrub, can be naturally grown on the field with a salt concentration as high as 100 g/kg dry soil (Song et al., 2006).  found that 31 conserved miRNAs and 12 novel miRNAs were significantly up-regulated, and 48 conserved miRNAs and 13 novel miRNAs were significantly down-regulated by salinity stress in H. caspica. A set of miRNAs were also identified in a salt marsh monocot halophyte smooth cordgrass (Spartina alterniflora Loisel) and another plant named salt cress Leaf ( Gao et al., 2016 (Thellungiella salsuginea) Zandkarimi et al., 2015). These identified miRNAs in halophytes can be further projected as potential miRNAs for developing salt tolerance in glycophyte crops.

FUNCTIONS OF MIRNA UNDER SALT STRESS
Numerous plant miRNAs have been identified under salt stress, but not many miRNAs have been functionally characterized in detail. Table 3 shows us the miRNAs responsive to salt stress, and these which were functionally studied by transgenetic approaches, such as overexpression and knocked down/out of the miRNA itself or its targets ( Table 3). For instance, miR394a/b over-expression and lcr (functional loss of miR394 target LCR) mutant plants are hypersensitive to salt stress, but LCR over-expressing plants display the salt-tolerant phenotype (Song et al., 2013). MiR393 is a comparative well-studied plant miRNA in different plant species, including Arabidopsis, rice, and creeping bentgrass. MiR393ab mutant shows reduced inhibition of LR (lateral root) number and length, increased levels of ROS in LRs, and reduced APX enzymatic activity (Iglesias et al., 2014). Over-expressing Osa-mR393 in rice and Arabidopsis reduces tolerance to salt and drought and increases tillers and early flowering (Gao et al., 2011;Xia et al., 2012), while over-expressing miR393-resistant form mTIR1 in Arabidopsis enhances salt tolerance in mTIR1 transgenic plant . However, over-expressing Osa-miR393a in creeping bentgrass improves salt stress tolerance associated with the increased uptake of potassium , suggesting that the same miRNA or different miRNA from the same miRNA family may have different promotion and inhibition effects on salt tolerance in different plants. A similar situation was found for miRNA396, that is, over-expressing Osa-miR396c reduced salt and alkali stress tolerance in rice and Arabidopsis (Gao et al., 2010), but enhanced salt tolerance associated with improved water retention, increased chlorophyll content, cell membrane integrity, and Na + exclusion during high salinity exposure in creeping bentgrass . Additionally, over-expressing Sp-miR396a-5p in tobacco enhanced its tolerance to salt, drought, and cold stresses . The overexpression of miR395c or miR395e retarded and accelerated, respectively, the seed germination of Arabidopsis under high salt or dehydration stress conditions (Kim et al., 2010b). Over-expressing miR156a weakens salt resistance in apples, whereas its target gene MdSPL13 strengthens salt resistance (Ma et al., 2020). Transgenic Arabidopsis plants over-expressing the target gene PeNAC070 of miR164 exhibits promoted LR development, delayed stem elongation, and increased sensitivity to salt stress (Lu et al., 2017). Over-expressing the target gene GmNFYA3 of miR169 reduces leaf water loss, enhances drought tolerance, and increases sensitivity to high salinity and exogenous ABA (Ni et al., 2013). Over-expression of miR172c substantially increased the sensitivity of plant roots to salt stress, and the removal of miR172c would decrease the sensitivity of plant roots to salt stress, respectively Sahito et al., 2017). Osa-miR319a and mi319b positively regulate salt tolerance in creeping bentgrass and swithgrass, respectively (Zhou et al., 2013;Zhou and Luo, 2014;Liu et al., 2019). MiR390 increases LR growth under salt stress via the auxin pathway (He et al., 2018). Additionally, over-expressing miR399f, miR402, and miR408 in Arabidopsis, Tae-miR408 and Sm-MIR408 in tobacco, and Osa-miR528 in creeping bentgrass increases salinity tolerance (Kim et al., 2010a;Feng et al., 2013;Ma et al., 2015;Yuan et al., 2015;Baek et al., 2016;Bai et al., 2018;Guo et al., 2018), indicating that these miRNAs enhance plant salt stress adaptation. By contrast, over-expressing miR414c, miR417, and miRNVL5 increases sensitivity to salinity stress (Jung and Kang, 2007;Gao et al., 2016;Wang et al., 2019). Collectively, these results suggest that the agronomic trait of salinity stress tolerance could be enhanced by the manipulation of miRNA or its target.

DISCUSSION AND FUTURE PROSPECTS
In the face of soil salinization, the cultivation of saline-tolerant plants is one of the most economical and effective technologies for biological improvement. Understanding the molecular mechanisms of miRNAs in abiotic stress provides an effective tool for plant breeding, especially in the context of climate and human-induced environmental changes. The essential regulating role of miRNAs in plant salt stress response reveals that miRNA could be applied for salt resistance improvement in crops. The salinity resistance of transgenic plants can be remarkably increased by over-expressing miRNA or knocking down/out the target gene of miRNA. Alternatively, the salinity resistance can be promoted by knocking down/out miRNA, which has a negative effect on salinity response, or over-expressing the target gene of the miRNA. Considering that one miRNA may have more than one targets that would cause totally different effects on plants, we should carefully consider the miRNA effects on crop growth, development, and the sensitivity to other abiotic stresses when optimizing the salinity resistance by miRNA manipulation.
The homologous tetraploid was more tolerant to salt stress than the diploid. Moreover, novel miRNAs induced by genome replication were identified, suggesting salt-responsive miRNAs could be screened by comparative analysis on the plant materials with different ploidy and salinity stress tolerance to explain the key roles of miRNA in achieving better salt stress tolerance. Generally, miRNAs are evolutionarily conserved in their functions in response to salt stress. However, the same miRNAs or different miRNAs from the same miRNA family may have different promotion and inhibition effects on salt tolerance in different plants. Therefore, the function of some miRNAs should be widely studied in different species, especially in crops.
Moreover, considering the significant number of salt-stressresponsive miRNAs identified by using powerful technology (such as high throughput sequencing), only a few miRNAs have been functionally characterized. Therefore, after the identification of plant miRNAs under salinity stress, further studies should be focused on the exploration of function, which will be very crucial for the salt tolerance improvement through miRNA manipulation in crops. Additionally, miRNAs may affect the plant stress tolerance through their interaction with ABA biosynthesis and the regulation of auxin response factors, The investigation of the crosstalk between miRNA and plant hormone will thus expand our knowledge and understanding of the role of plant miRNAs under stress conditions. Finally, the construction of the plant miRNA network in salt stress response will shed light on the salinity resistance improvement through miRNA manipulation in crops.

AUTHOR CONTRIBUTIONS
TX conceived and designed this manuscript. TX, LZ, and ZY wrote the manuscript. YW and TD helped to revise the manuscript. All authors read and approved the manuscript.