Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture

Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos

KEY MESSAGE

This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.

Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants

The increasing demand for food is the result of an increasing population. It is crucial to enhance crop yield for sustainable production. Recently, microRNAs (miRNAs) have gained importance because of their involvement in crop productivity by regulating gene transcription in numerous biological processes, such as growth, development and abiotic and biotic stresses. miRNAs are small, non-coding RNA involved in numerous other biological functions in a plant that range from genomic integrity, metabolism, growth, and development to environmental stress response, which collectively influence the agronomic traits of the crop species. Additionally, miRNA families associated with various agronomic properties are conserved across diverse plant species. The miRNA adaptive responses enhance the plants to survive environmental stresses, such as drought, salinity, cold, and heat conditions, as well as biotic stresses, such as pathogens and insect pests. Thus, understanding the detailed mechanism of the potential response of miRNAs during stress response is necessary to promote the agronomic traits of crops. In this review, we updated the details of the functional aspects of miRNAs as potential regulators of various stress-related responses in agronomic plants.

Tae-miR397 Negatively Regulates Wheat Resistance to Blumeria graminis

MicroRNA (miRNA) plays a crucial role in the interactions between plants and pathogens, and identifying disease-related miRNAs could help us understand the mechanisms underlying plant disease pathogenesis and breed resistant varieties. However, the role of miRNA in wheat defense responses remains largely unexplored. The miR397 family is highly conserved in plants and involved in plant development and defense response. Therefore, the purpose of this study was to investigate the function of tae-miR397 in wheat resistance to powdery mildew. The expression pattern analysis revealed that tae-miR397 expression was higher in young leaves than in other tissues and was significantly decreased in wheat Bainong207 leaves after Blumeria graminis (Bgt) infection and chitin treatment. Additionally, the expression of tae-miR397 was significantly down-regulated by salicylic acid and induced under jasmonate treatment. The overexpression of tae-miR397 in common wheat Bainong207 enhanced the wheat's susceptibility to powdery mildew in the seedling and adult stages. The rate of Bgt spore germination and mycelial growth in transgenic wheat plants overexpressing tae-miR397 was faster than in the untransformed wild-type plants. The target gene of tae-miR397 was predicted to be a wound-induced protein (Tae-WIP), and the function was investigated. We demonstrated that silencing of Tae-WIP via barley-stripe-mosaic-virus-induced gene silencing enhanced wheat's susceptibility to powdery mildew. qRT-PCR indicated that tae-miR397 regulated wheat immunity by controlling pathogenesis-related gene expressions. Moreover, the transgenic plants overexpressing tae-miR397 exhibited more tillers than the wild-type plants. This work suggests that tae-miR397 is a negative regulator of resistance against powdery mildew and has great potential for breeding disease-resistant cultivars.

Regulatory roles of noncoding RNAs in callus induction and plant cell dedifferentiation

Plant regulatory noncoding RNAs (ncRNAs) have emerged as key modulators of gene expression during callus induction. Their further study may promote the design of innovative plant tissue culture protocols. The use of plants by humans has recently taken on a new and expanding insight due to the advent of genetic engineering technologies. In this context, callus cultures have shown remarkable potential for synthesizing valuable biomolecules, crop improvement, plant micropropagation, and biodiversity preservation. A crucial stage in callus production is the conversion of somatic cells into totipotent cells; compelling evidence indicates that stress factors, transcriptional regulators, and plant hormones can trigger this biological event. Besides, posttranscriptional regulators of gene expression might be essential participants in callus induction. However, research related to the analysis of noncoding RNAs (ncRNAs) that modulate callogenesis and plant cell dedifferentiation in vitro is still at an early stage. During the last decade, some relevant studies have enlightened the fact that different classes of ncRNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs) are implicated in plant cell dedifferentiation through regulating the expression levels of diverse gene targets. Hence, understanding the molecular relevance of these ncRNAs in the aforesaid biological processes might represent a promising source of new biotechnological approaches for callus culture and plant improvement. In this current work, we review the experimental evidence regarding the prospective roles of ncRNAs in callus induction and plant cell dedifferentiation to promote this field of study.

Wheat Long Noncoding RNAs from Organelle and Nuclear Genomes Carry Conserved microRNA Precursors Which May Together Comprise Intricate Networks in Insect Responses

Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs at a large scale. Wheat is among the leading food staples worldwide whose production is threatened by both biotic and abiotic stressors. Here, we identified putative lncRNAs from durum wheat varieties that differ in stem solidness, a major source of defense against wheat stem sawfly, a devastating insect pest. We also analyzed and annotated lncRNAs from two bread wheat varieties, resistant and susceptible to another destructive pest, orange wheat blossom midge, with and without infestation. Several putative lncRNAs contained potential precursor sequences and/or target regions for microRNAs, another type of regulatory noncoding RNAs, which may indicate functional networks. Interestingly, in contrast to lncRNAs themselves, microRNAs with potential precursors within the lncRNA sequences appeared to be highly conserved at the sequence and family levels. We also observed a few putative lncRNAs that have perfect to near-perfect matches to organellar genomes, supporting the recent observations that organellar genomes may contribute to the noncoding transcript pool of the cell.

Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN ( https://pmiren.com ) does not include root tissues and root-associated miRNAs might thus be missing, we performed first the prediction of novel miRNAs using the sRNAbench tool. We found a total of 150 putatively novel miRNA genes with expression of both arms from 289 unique mature sequences and nearly 30% of all miRNA reads in roots corresponded to novel miRNAs. In contrast, this figure in leaves dropped to under 3%, confirming the undersampling of roots in the complement of known miRNAs. By using 120 publicly available wheat datasets, 598 Zea mays small RNA libraries, 64 plant species genomes, wheat degradome library, and functional enrichment analysis, a subset of novel miRNAs were confirmed as bona-fide miRNAs. Of the total 605 miRNAs identified in this study inclusive of 316 known miRNAs, 528 miRNAs were shared by both cultivars, 429 miRNAs were shared by both root tissues and 329 miRNAs were shared by both leaf tissues. In addition, 32 miRNAs were specific to Kukri while 45 miRNAs were specific to RAC875. These miRNAs had diverse functions, such as regulation of gene transcription, protein translation, energy metabolism, and cell cycle progression. Our data provide a genome-wide miRNA expression profile in these two wheat cultivars and help functional studies of wheat genomics.

Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton

The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 JmjC genes (GhJMJs) were identified by genome-wide analysis in upland cotton (Gossypium hirsutum), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between G. hirsutum and Theobroma cacao. We have further explored the putative molecular regulatory mechanisms of the JmjC gene family in cotton. GhJMJ24 and GhJMJ49 were both preferentially expressed in embryogenic callus compared to nonembryogenic callus in cotton tissue culture, which might be regulated by transcription factors and microRNAs to some extent. Further experiments indicated that GhJMJ24 and GhJMJ49 might interact with SUVH4, SUVH6, DDM1, CMT3, and CMT1 in the nucleus, potentially in association with demethylation of H3K9me2. Taken together, our results provide a foundation for future research on the biological functions of GhJMJ genes in cotton, especially in somatic embryogenesis in cotton tissue culture, which is crucial for the regeneration of transgenic plants.

MicroRNA Zma-miR528 Versatile Regulation on Target mRNAs during Maize Somatic Embryogenesis

MicroRNAs (miRNAs) are small non-coding RNAs that regulate the accumulation and translation of their target mRNAs through sequence complementarity. miRNAs have emerged as crucial regulators during maize somatic embryogenesis (SE) and plant regeneration. A monocot-specific miRNA, mainly accumulated during maize SE, is zma-miR528. While several targets have been described for this miRNA, the regulation has not been experimentally confirmed for the SE process. Here, we explored the accumulation of zma-miR528 and several predicted targets during embryogenic callus induction, proliferation, and plantlet regeneration using the maize cultivar VS-535. We confirmed the cleavage site for all tested zma-miR528 targets; however, PLC1 showed very low levels of processing. The abundance of zma-miR528 slightly decreased in one month-induced callus compared to the immature embryo (IE) explant tissue. However, it displayed a significant increase in four-month sub-cultured callus, coincident with proliferation establishment. In callus-regenerated plantlets, zma-miR528 greatly decreased to levels below those observed in the initial explant. Three of the target transcripts (MATE, bHLH, and SOD1a) showed an inverse correlation with the miRNA abundance in total RNA samples at all stages. Using polysome fractionation, zma-miR528 was detected in the polysome fraction and exhibited an inverse distribution with the PLC1 target, which was not observed at total RNA. Accordingly, we conclude that zma-miR528 regulates multiple target mRNAs during the SE process by promoting their degradation, translation inhibition or both.

Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants

Small non-coding RNAs (sncRNAs) are molecules with important regulatory functions during development and environmental responses across all groups of terrestrial plants. In seed plants, the development of a mature embryo from the zygote follows a synchronized cell division sequence, and growth and differentiation events regulated by highly regulated gene expression. However, given the distinct features of the initial stages of embryogenesis in gymnosperms and angiosperms, it is relevant to investigate to what extent such differences emerge from differential regulation mediated by sncRNAs. Within these, the microRNAs (miRNAs) are the best characterized class, and while many miRNAs are conserved and significantly represented across angiosperms and other seed plants during embryogenesis, some miRNA families are specific to some plant lineages. Being a model to study zygotic embryogenesis and a relevant biotechnological tool, we systematized the current knowledge on the presence and characterization of miRNAs in somatic embryogenesis (SE) of seed plants, pinpointing the miRNAs that have been reported to be associated with SE in angiosperm and gymnosperm species. We start by conducting an overview of sncRNA expression profiles in the embryonic tissues of seed plants. We then highlight the miRNAs described as being involved in the different stages of the SE process, from its induction to the full maturation of the somatic embryos, adding references to zygotic embryogenesis when relevant, as a contribution towards a better understanding of miRNA-mediated regulation of SE.

miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato

Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.

Analysis of miRNA expression associated with the Lr46 gene responsible for APR resistance in wheat (Triticum aestivum L.)

Lr46/Yr29/Pm39 (Lr46) is a gene for slow rusting resistance in wheat. The aim of the study was to analyze the miRNA expression in selected common wheat cultivars carrying resistance genes, Lr46 among others (HN Rod, Pavon‘S’, Myna‘S’, Frontana‘S’, and Sparrow’S’) in response to leaf rust infection caused by Puccinia triticina Erikss. In the Pavon ‘S’, Myna ‘S’, Frontana‘S’, and Sparow‘S’ varieties a product with a length of 242 bp has been identified, which is specific to the Xwmc44 marker linked to the brown rust resistance gene Lr46. In the next step, the differences in the expression of microRNA (miR5085 and miR164) associated with the Lr46 gene, which is responsible for different resistance of selected wheat cultivars to leaf rust, were examined using emulsion PCR (ddPCR). In the experiment, biotic stress was induced in mature plants by infecting them with fungal spores under controlled conditions in a growth chamber. For analysis the plant material was collected before inoculation and 6, 12, 24, and 48 h after inoculation. The experiments also showed that plant infection with Puccinia triticina resulted in an increase in miR164 expression in cultivars carrying the Lr46 gene. The expression of miR164 remained stable in a control cultivar (HN ROD) lacking this gene. This has proved that miR164 can be involved in leaf rust resistance mechanisms.

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.

Dynamic changes in the expression pattern of miRNAs and associated target genes during coconut somatic embryogenesis

Genome-wide analysis of small RNAs identifies somatic embryogenesis- specific miRNAs and their targets and provides novel insights into the mechanisms governing somatic embryogenesis in coconut, a highly in vitro recalcitrant species. Coconut, a major plantation crop of the tropics is recalcitrant to in vitro culture with a very low rate of somatic embryo turnover. Clonal propagation to enhance the production of high yielding, disease-free planting material in coconut has remained a distant reality. To better understand the molecular basis of this recalcitrance and to throw light on the complex regulatory network involved in the transition of coconut somatic cells to embryogenic calli, genome-wide profiling of small RNAs from embryogenic (EC) and non-embryogenic calli (NEC) was undertaken using Illumina Hiseq 2000 platform. We have identified a total of 110 conserved miRNAs (representing 46 known miRNA families) in both types of calli. In addition, 97 novel miRNAs (48 specific to EC, 21 specific to NEC and 28 common to both the libraries) were also identified. Among the conserved miRNAs, 10 were found to be differentially expressed between NEC and EC libraries with a log2 fold change > 2 following RPM-based normalization. miR156f, miR167c, miR169a, miR319a, miR535a, and miR5179 are upregulated and miR160a, miR166a, miR171a, and miR319b are down-regulated in NEC. To confirm the differential expression pattern and their regulatory role in SE, the expression patterns of miRNAs and their putative targets were analyzed using qRT- PCR and most of the analyzed miRNA-target pairs showed inverse correlation during somatic embryogenesis. Selected targets were further validated by RNA ligase mediated rapid amplification of 5' cDNA ends (5'RLM-RACE). Our data suggest that a few conserved miRNAs and species-specific miRNAs act in concert to regulate the process of somatic embryogenesis in coconut. The results of this study provide the first overview into the regulatory landscape of somatic embryogenesis in coconut and possible strategies for fine-tuning or reprogramming to enhance somatic embryo turn over in coconut.

Identification of microRNAs in developing wheat grain that are potentially involved in regulating grain characteristics and the response to nitrogen levels

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in the regulation of plant development and growth, but little information is available concerning their roles during grain development under different nitrogen (N) application levels. Our objective was to identify miRNAs related to the regulation of grain characteristics and the response to different N fertilizer conditions.

RESULTS

A total of 79 miRNAs (46 known and 33 novel miRNAs) were identified that showed significant differential expression during grain development under both high nitrogen (HN) and low nitrogen (LN) treatments. The miRNAs that were significantly upregulated early in grain development target genes involved mainly in cell differentiation, auxin-activated signaling, and transcription, which may be associated with grain size; miRNAs abundant in the middle and later stages target genes mainly involved in carbohydrate and nitrogen metabolism, transport, and kinase activity and may be associated with grain filling. Additionally, we identified 50 miRNAs (22 known and 28 novel miRNAs), of which 11, 9, and 39 were differentially expressed between the HN and LN libraries at 7, 17, and 27 days after anthesis (DAA). The miRNAs that were differentially expressed in response to nitrogen conditions target genes involved mainly in carbohydrate and nitrogen metabolism, the defense response, and transport as well as genes that encode ubiquitin ligase. Only one novel miRNA (PC-5p-2614_215) was significantly upregulated in response to LN treatment at all three stages, and 21 miRNAs showed significant differential expression between HN and LN conditions only at 27 DAA. We therefore propose a model for target gene regulation by miRNAs during grain development with N-responsive patterns.

CONCLUSIONS

The potential targets of the identified miRNAs are related to various biological processes, such as carbohydrate/nitrogen metabolism, transcription, cellular differentiation, transport, and defense. Our results indicate that miRNA-mediated networks, via posttranscriptional regulation, play crucial roles in grain development and the N response, which determine wheat grain weight and quality. Our study provides useful information for future research of regulatory mechanisms that focus on improving grain yield and quality.

Development-Related miRNA Expression and Target Regulation during Staggered In Vitro Plant Regeneration of Tuxpeño VS-535 Maize Cultivar

In vitro plant regeneration addresses basic questions of molecular reprogramming in the absence of embryonic positional cues. The process is highly dependent on the genotype and explant characteristics. However, the regulatory mechanisms operating during organ differentiation from in vitro cultures remain largely unknown. Recently, miRNAs have emerged as key regulators during embryogenic callus induction, plant differentiation, auxin responses and totipotency. Here, we explored how development-related miRNA switches the impact on their target regulation depending on physiological and molecular events taking place during maize Tuxpeño VS-535 in vitro plant regeneration. Three callus types with distinctive regeneration potential were characterized by microscopy and histological preparations. The embryogenic calli (EC) showed higher miRNA levels than non-embryogenic tissues (NEC). An inverse correlation for miR160 and miR166 targets was found during EC callus induction, whereas miR156, miR164 and miR394 displayed similar to their targets RNA accumulation levels. Most miRNA accumulation switches took place early at regenerative spots coincident with shoot apical meristem (SAM) establishment, whereas miR156, miR160 and miR166 increased at further differentiation stages. Our data uncover particular miRNA-mediated regulation operating for maize embryogenic tissues, supporting their regulatory role in early SAM establishment and basipetala growth during the in vitro regeneration process.

Transcriptome analysis of callus from melon

OBJECTIVE

To identify the key genes promoting the differentiation of melon non-embryogenic callus into embryogenic callus.

METHODS

The transcriptome sequencing analysis was used to analyze the mRNA sequence in embryogenic callus (Z) and non-embryogenic callus (F); transcript mapping, gene expression analysis, cluster analysis, classification analysis and enrichment analysis were then used to detect the differentially expressed genes and enriched pathways.

RESULTS

The correlation coefficient between sample Z and sample F was 0.929 after transcript mapping. The overall gene expression levels in sample Z were higher as compared with sample F. Furthermore, cluster analysis showed that the expression of genes involved in photosynthesis was increased in sample Z when comparing to F. Besides, the classification of differential Gene Ontology (GO) showed that many metabolic processes were affected with the metabolism enhanced in embryogenic callus. Interestingly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis further demonstrated the high metabolic activity and active secondary metabolite formation in the embryogenic callus.

CONCLUSION

The genes associated with photosynthesis, metabolic pathways and biosynthesis of secondary metabolites may promote the differentiation of callus into embryogenic callus.

Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes

MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, have been shown to play essential roles in the regulation of gene expression at the post-transcriptional level. Although Paulownia tomentosa is an ecologically and economically important timber species due to its rapid growth, few efforts have focused on small RNAs (sRNAs) in the cambial tissues during winter and summer transition. In the present study, we identified 33 known miRNA families and 29 novel miRNAs which include 20 putative novel miRNAs* in P. tomentosa cambial tissues during winter and summer transition. Through differential expression analysis, we showed that 15 known miRNAs and 8 novel miRNAs were preferentially abundant in certain stage of cambial tissues. Based on the P. tomentosa mRNA transcriptome database, 1667 and 78 potential targets were predicted for 29 known and 20 novel miRNAs, respectively and the predicted targets are mostly transcription factors and functional genes. The targets of these miRNAs were enriched in "metabolic process" and "transcription regulation" by using Gene Ontology enrichment analysis. In addition, KEGG pathway analyses revealed the involvement of miRNAs in starch and sucrose metabolism and plant-pathogen interaction metabolism pathways. Noticeably, qRT-PCR expression analysis demonstrated that 9 miRNAs and their targets were existed a negative correlation in P. tomentosa cambial tissues. This study is the first to examine known and novel miRNAs and their potential targets in P. tomentosa cambial tissues during winter and summer transition and identify several candidate genes potentially regulating cambial phase transition, and thus provide a framework for further understanding of miRNAs functions in the regulation of cambial phase transition and wood formation in trees.