Control of sulfate concentration by miR395-targeted APS genes in Arabidopsis thaliana

Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar

Secondary xylem produced by stem secondary growth is the main source of tree biomass and possesses great economic and ecological value in papermaking, construction, biofuels, and the global carbon cycle. The secondary xylem formation is a complex developmental process, and the underlying regulatory networks and potential mechanisms are still under exploration. In this study, using hybrid poplar (Populus alba × Populus glandulosa clone 84K) as a model system, we first ascertained three representative stages of stem secondary growth and then investigated the regulatory network of secondary xylem formation by joint analysis of transcriptome and miRNAs. Notably, 7507 differentially expressed genes (DEGs) and 55 differentially expressed miRNAs (DEMs) were identified from stage 1 without initiating secondary growth to stage 2 with just initiating secondary growth, which was much more than those identified from stage 2 to stage 3 with obvious secondary growth. DEGs encoding transcription factors and lignin biosynthetic enzymes and those associated with plant hormones were found to participate in the secondary xylem formation. MiRNA-target analysis revealed that a total of 85 DEMs were predicted to have 2948 putative targets. Among them, PagmiR396d-PagGRFs, PagmiR395c-PagGA2ox1/PagLHW/PagSULTR2/PagPolyubiquitin 1, PagmiR482d-PagLAC4, PagmiR167e-PagbHLH62, and PagmiR167f/g/h-PagbHLH110 modules were involved in the regulating cambial activity and its differentiation into secondary xylem, cell expansion, secondary cell wall deposition, and programmed cell death. Our results give new insights into the regulatory network and mechanism of secondary xylem formation.

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain

Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.

MicroRNAs Mediated Plant Responses to Salt Stress

One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.

Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants

MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.

The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees

Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.

Genome-wide miRNAs profiles of pearl millet under contrasting high vapor pressure deficit reveal their functional roles in drought stress adaptations

Pearl millet (Pennisetum glaucum [L.] R. Br.) is an important crop capable of growing in harsh and marginal environments, with the highest degree of tolerance to drought and heat stresses among cereals. Diverse germplasm of pearl millet shows a significant phenotypic variation in response to abiotic stresses, making it a unique model to study the mechanisms responsible for stress mitigation. The present study focuses on identifying the physiological response of two pearl millet high-resolution cross (HRC) genotypes, ICMR 1122 and ICMR 1152, in response to low and high vapor pressure deficit (VPD). Under high VPD conditions, ICMR 1152 exhibited a lower transpiration rate (Tr), higher transpiration efficiency, and lower root sap exudation than ICMR 1122. Further, Pg-miRNAs expressed in the contrasting genotypes under low and high VPD conditions were identified by deep sequencing analysis. A total of 116 known and 61 novel Pg-miRNAs were identified from ICMR 1152, while 26 known and six novel Pg-miRNAs were identified from ICMR 1122 genotypes, respectively. While Pg-miR165, 168, 170, and 319 families exhibited significant differential expression under low and high VPD conditions in both genotypes, ICMR 1152 showed abundant expression of Pg-miR167, Pg-miR172, Pg-miR396 Pg-miR399, Pg-miR862, Pg-miR868, Pg-miR950, Pg-miR5054, and Pg-miR7527 indicating their direct and indirect role in root physiology and abiotic stress responses. Drought responsive Pg-miRNA targets showed upregulation in response to high VPD stress, further narrowing down the miRNAs involved in regulation of drought tolerance in pearl millet.

Identification and Characterization of Csa-miR395s Reveal Their Involvements in Fruit Expansion and Abiotic Stresses in Cucumber

The miR395 plays an indispensable role in biochemical processes by regulating their target genes. However, little is known about the roles of miR395 in cucumber fruit expansion and response to abiotic stresses. Here, 4 Csa-miR395s and 8 corresponding target genes were identified in the cucumber genome. Csa-miR395s were all located on the same chromosome (Chr 5). Csa-miR395a/b/c and Csa-miR395d were distributed in different branches without a closer genetic relationship. Massive cis-acting elements, including light, phytohormone, and stress response elements, were detected in the promoter regions of Csa-MIR395s, indicating that Csa-miR395s might be involved in complex regulatory networks to control cucumber growth and development and stress response. In addition, Csa-miR395a/b/c shared the same target genes, and Csa-miR395d had its specific target genes. Tissue-specific expression analysis showed that Csa-miR395a/b/c were all expressed in the leaf, root, ovary, and expanded fruit of cucumber and highly expressed in the expanded fruits compared to the ovary, while Csa2G215520 and Csa1G502860 (target genes of Csa-miR395a/b/c) presented a downregulated trend in the expanded fruit compared to the ovary. Meanwhile, the protein co-expression network revealed that these target genes had interactions in sulfur metabolism. These results suggested that Csa-miR395a/b/c targeting Csa2G215520 and Csa1G502860 might promote cucumber fruit expansion by affecting sulfur metabolism. Additionally, Quantitative Real-time PCR analysis validated that Csa-miR395s could be regulated by NaCl stress, and Csa-miR395a/b/c could respond to PEG stress, which further confirmed the reliability of cis-acting elements data. Taken together, our results could be helpful for further exploration of the functions of miR395s in cucumber fruit expansion and response to abiotic stresses.

MiR395c Regulates Secondary Xylem Development Through Sulfate Metabolism in Poplar

Secondary xylem development requires the coordination of multiple regulatory factors, including plant hormones, transcription factors, and microRNAs (miRNAs). MiR395 is an important regulator involved in sulfate metabolism, but its function in plant development is unclear. This study investigated the functions of miR395c in the secondary xylem development in Populus alba × P. glandulosa. MiR395c was highly expressed in the shoot apex and secondary xylem. The overexpression of miR395c resulted in an increase in both secondary xylem width and vessel dimension, as well as a decrease in the thickness of the secondary cell wall of the xylem fiber. Further analysis showed that miR395c inhibited biosynthesis of sulfate metabolic products by targeting ATPS genes, which led to the reduction of Abscisic acid (ABA) synthesis and down-regulation of MYB46 expression. Our results indicate that miR395c regulates the secondary xylem development process via sulfate metabolism in Populus.

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

Genome-wide identification of the BURP domain-containing genes in Phaseolus vulgaris

Plant-specific BURP domain-containing proteins have an essential role in the plant's development and stress responses. Although BURP domain-containing proteins have been identified in several plant species, genome-wide analysis of the BURP gene family has not been investigated in the common bean. In the present study, we identified 11 BURP family members in the common bean (Phaseolus vulgaris) genome with a comprehensive in silico analysis. Pairwise alignment and phylogenetic analyses grouped PvBURP members into four subfamilies [RD-22 like (3), PG1β-like (4), BNM2-like (3), and USP-like (1)] according to their amino acid motifs, protein domains and intron-exon structure. The physical and biochemical characteristics of amino acids, motif and intron-exon structure, and cis-regulatory elements of BURPs members were determined. Promoter regions of BURP members included stress, light, and hormone response-related cis-elements. Therefore, expression profiles of PvBURP genes were identified with in silico tools and qRT-PCR analyses under stress (salt and drought) and hormone treatment (ABA, IAA) in the current study. While significant activity changes were not observed in BURP genes in RNA-seq data sets related to salt stress, it was determined that some BURP genes were expressed differently in those with drought stress. We identified 12 different miRNA, including miRNA395, miRNA156, miRNA169, miRNA171, miRNA319, and miRNA390, targeting the nine PvBURP genes using two different in silico tools based on perfect or near-perfect complementarity to their targets. Here we present the first study to identify and characterize the BURP genes in common bean using whole-genome analysis, and the findings may serve as a reference for future functional research in common bean.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01052-9.

The Critical Role of Small RNAs in Regulating Plant Innate Immunity

Plants, due to their sessile nature, have an innate immune system that helps them to defend against different pathogen infections. The defense response of plants is composed of a highly regulated and complex molecular network, involving the extensive reprogramming of gene expression during the presence of pathogenic molecular signatures. Plants attain proper defense against pathogens through the transcriptional regulation of genes encoding defense regulatory proteins and hormone signaling pathways. Small RNAs are emerging as versatile regulators of plant development and act in different tiers of plant immunity, including pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). The versatile regulatory functions of small RNAs in plant growth and development and response to biotic and abiotic stresses have been widely studied in recent years. However, available information regarding the contribution of small RNAs in plant immunity against pathogens is more limited. This review article will focus on the role of small RNAs in innate immunity in plants.

Transcriptome and microRNA Sequencing Identified miRNAs and Target Genes in Different Developmental Stages of the Vascular Cambium in Cryptomeria fortunei Hooibrenk

Cryptomeria fortunei Hooibrenk is an important fast-growing coniferous timber species that is widely used in landscaping. Recently, research on timber quality has gained substantial attention in the field of tree breeding. Wood is the secondary xylem formed by the continuous inward division and differentiation of the vascular cambium; therefore, the development of the vascular cambium is particularly important for wood quality. In this study, we analyzed the transcriptomes of the cambial zone in C. fortunei during different developmental stages using Illumina HiSeq sequencing, focusing on general transcriptome and microRNA (miRNA) data. We performed functional annotation of the differentially expressed genes (DEGs) in the different stages identified by transcriptome sequencing and generated 15 miRNA libraries yielding 4.73 Gb of clean reads. The most common length of the filtered miRNAs was 21nt, accounting for 33.1% of the total filtered reads. We annotated a total of 32 known miRNA families. Some miRNAs played roles in hormone signal transduction (miR159, miR160, and miR166), growth and development (miR166 and miR396), and the coercion response (miR394 and miR395), and degradome sequencing showed potential cleavage sites between miRNAs and target genes. Differential expression of miRNAs and target genes and functional validation of the obtained transcriptome and miRNA data provide a theoretical basis for further elucidating the molecular mechanisms of cellular growth and differentiation, as well as wood formation in the vascular cambium, which will help improve the wood quality of C. fortunei.

Si vis pacem para bellum: A prospective in silico analysis of miRNA-based plant defenses against fungal infections

Fungal pathogens are an important threat for plant crops, being responsible for important reductions of production yields and a consequent economic impact. Among the molecular mediators of fungal infections of plant crops, non-coding RNAs (ncRNAs) have been described as relevant players either in the plant immune responses and mechanism of defense or in the colonization of plant tissues by fungi. Acting as a mechanism of defense, some plant small ncRNAs such as miRNAs and tasiRNAs can be secreted by cells and directed to target the transcriptome of pathogenic fungi, triggering an RNAi-like interference mechanism able to silence the expression of specific fungal genes. The detailed knowledge of this mechanism of defense against fungal pathogens could open new possibilities for the protection of human important crops. To infer putative functional relationships mediated by ncRNA communication, we performed a prospective analysis to determine potential plant miRNAs able to target the genome of fungal pathogens, which resulted in the description of enriched specific plant miRNA families and their putative fungal targets that could be further studied in the context of plant-fungi interactions. The expression profile of specific members of the enriched miRNAs families showed an infection-dependent behavior in laboratory models of infection. Plant miRNAs showed sequence complementarity with coding genes of their cognate fungal pathogens. Plant miRNAs could potentially target fungal genes belonging to functional families related to stress response, membrane architecture, vacuolar transport, membrane traffic, and anabolic processes. Families of specific infection-responsive miRNAs are included in the putative plant defense mechanism.

bHLH104 confers tolerance to cadmium stress in Arabidopsis thaliana

Cd is a non-essential heavy metal that is toxic to both plants and animals. Here, we reveal that the transcription factor bHLH104 positively regulates Cd tolerance in Arabidopsis thaliana. We show that Fe deficiency-responsive genes were induced by Cd treatment, and that their upregulation was suppressed in bhlh104 loss-of-function mutants, but enhanced upon overexpression of bHLH104. Correspondingly, the bhlh104 mutants displayed sensitivity to Cd stress, whereas plants overexpressing bHLH104 exhibited enhanced Cd tolerance. Further analysis suggested that bHLH104 positively regulates four heavy metal detoxification-associated genes, IREG2, MTP3, HMA3 and NAS4, which play roles in Cd sequestration and tolerance. The bHLH104 overexpression plants accumulated high levels of Cd in the root but low levels of Cd in the shoot, which might contribute to the Cd tolerance in those lines. The present study thus points to bHLH104 as a potentially useful tool for genetic engineering of plants with enhanced Cd tolerance.