microRNAs and Their Targets in Apple (Malus domestica cv. "Fuji") Involved in Response to Infection of Pathogen Valsa mali

Genome-wide identification of trihelix transcription factors in the apple genome in silico

Trihelix transcription factors are involved in the growth and development of plants, as well as various stress responses. In the study presented, we identified 37 trihelix family genes in the apple genome (MdTH). The trihelix genes were located on 13 chromosomes. Phylogenetic analysis of these MdTH and the trihelix genes of other species divided them into six subfamilies: GT-1, GT-2, SH4, SIP1, GTγ, and GTδ. The genes of different groups significantly diverged in their gene structure and conserved functional domains. Cis-element analysis showed that promoter sequences of MdTH genes contained light response elements, phytohormone response elements, and stress-related cis-elements. The expression pattern analysis results demonstrated that MdTH were regulated by drought, salinity, as well as high and low temperatures. MdTH4 and MdTH24 were highly regulated by soil salinity, MdTH4-by drought. MdTH30 showed high expression under low temperature; MdTH8, MdTH20, and MdTH36-under high temperature.

Quantitative proteomic sequencing of F 1 hybrid populations reveals the function of sorbitol in apple resistance to Botryosphaeria dothidea

Apple ring rot, which is caused by Botryosphaeria dothidea, is one of the most devastating diseases of apple. However, the lack of a known molecular resistance mechanism limits the development of resistance breeding. Here, the 'Golden Delicious' and 'Fuji Nagafu No. 2' apple cultivars were crossed, and a population of 194 F ₁ individuals was generated. The hybrids were divided into five categories according to their differences in B. dothidea resistance during three consecutive years. Quantitative proteomic sequencing was performed to analyze the molecular mechanism of the apple response to B. dothidea infection. Hierarchical clustering and weighted gene coexpression network analysis revealed that photosynthesis was significantly correlated with the resistance of apple to B. dothidea. The level of chlorophyll fluorescence in apple functional leaves increased progressively as the level of disease resistance improved. However, the content of soluble sugar decreased with the improvement of disease resistance. Further research revealed that sorbitol, the primary photosynthetic product, played major roles in apple resistance to B. dothidea. Increasing the content of sorbitol by overexpressing MdS6PDH1 dramatically enhanced resistance of apple calli to B. dothidea by activating the expression of salicylic acid signaling pathway-related genes. However, decreasing the content of sorbitol by silencing MdS6PDH1 showed the opposite phenotype. Furthermore, exogenous sorbitol treatment partially restored the resistance of MdS6PDH1-RNAi lines to B. dothidea. Taken together, these findings reveal that sorbitol is an important metabolite that regulates the resistance of apple to B. dothidea and offer new insights into the mechanism of plant resistance to pathogens.

A fungal microRNA-like RNA subverts host immunity and facilitates pathogen infection by silencing two host receptor-like kinase genes

Small RNAs (sRNAs) play important roles in various biological processes by silencing their corresponding target genes in most eukaryotes. However, cross-kingdom regulation mediated by fungal microRNA-like RNAs (milRNAs) in plant-pathogen interactions is still largely unknown. Using molecular, genetic, histological, and biochemical approaches, we found that the apple tree Valsa canker pathogen Valsa mali milRNA Vm-milR1 could suppress the host immunity by silencing two host receptor-like kinase genes, MdRLKT1 and MdRLKT2. Vm-milR1 was highly induced during V. mali infection. Deletion of Vm-milR1 precursor abolished the generation of Vm-milR1 and reduced the virulence of V. mali. Inoculation of Vm-milR1 deletion mutants induced the host defence responses, including reactive oxygen species (ROS) accumulation, callose deposition, and high expression of defence-related genes. Furthermore, Vm-milR1 was confirmed to be able to suppress the expression of MdRLKT1 and MdRLKT2 in a sequence-specific manner. Moreover, overexpression of either MdRLKT1 or MdRLKT2 enhanced apple resistance to V. mali by activating the host defence responses. Furthermore, knockdown of MdRLKT1 or MdRLKT2 compromised the host resistance to V. mali. Our study revealed that V. mali was equipped with Vm-milR1 as an sRNA effector to silence host receptor-like kinase genes, suppress the host defence responses, and facilitate pathogen infection.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya

BACKGROUND

MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown.

RESULTS

In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. Thirty-four candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. Hmo-miR157b-HmSPL6-like, Hmo-miR160a-Hpcyt P450-like3, Hmo-miR6020-HmCYP71A8-like, Hmo-novel-2-HmCYP83B1-like, Hmo-novel-15-HmTPST-like, Hmo-miR828a-HmTT2-like, Hmo-miR858-HmMYB12-like, Hmo-miR858-HmMYBC1-like and Hmo-miR858-HmMYB2-like were verified by 5'RACE and transient expression system in tobacco.

CONCLUSIONS

Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and Hmo-miR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.

miRNA and Degradome Sequencing Identify miRNAs and Their Target Genes Involved in the Browning Inhibition of Fresh-Cut Apples by Hydrogen Sulfide

Surface browning is the major limit for the shelf life of fresh-cut apples, and hydrogen sulfide (H₂S) treatment can effectively inhibit the browning. However, the molecular mechanism on how fresh-cut apples respond to H₂S was poorly understood. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs, which regulate multiple crucial biological processes in almost all aspects of the life cycle. Herein, 12 small RNA libraries and one mixed degradome library were constructed from control and H₂S-treated fresh-cut apples immediately after treatment (C0 and S0) and 6 d of storage (C6 and S6) at 4 °C. The results identified nine (three upregulated and six downregulated) and 10 (two upregulated and eight downregulated) differentially expressed miRNAs (DEmiRNAs) in S0 versus C0 and S6 versus C6, respectively. The target genes of DEmiRNAs were transcription factors and functional proteins. The miR156 targeting SPL, miR164 targeting NAC, miR319 targeting TCP4, GAMYB, and acyl-CoA-binding protein 4, and miR6478 targeting patatin-like protein 2 might play important roles in the browning inhibition of fresh-cut apples by H₂S via regulating the ROS, phenylpropanoid, and lipid metabolism. The results give valuable information for further studying the role of miRNA in regulating browning processes and the underlying molecular mechanism of H₂S treatment on browning inhibition.

Transcriptional regulation of MdmiR285N microRNA in apple (Malus x domestica) and the heterologous plant system Arabidopsis thaliana

Malus x domestica microRNA MdmiR285N is a potential key regulator of plant immunity, as it has been predicted to target 35 RNA transcripts coding for different disease resistance proteins involved in plant defense to pathogens. In this study, the promoter region of MdmiR285N was isolated from the apple genome and analyzed in silico to detect potential regulatory regions controlling its transcription. A complex network of putative regulatory elements involved in plant growth and development, and in response to different hormones and stress conditions, was identified. Activity of the β-Glucoronidase (GUS) reporter gene driven by the promoter of MdmiR285N was examined in transgenic apple, demonstrating that MdmiR285N was expressed during the vegetative growth phase. Similarly, in transgenic Arabidopsis thaliana, spatial and temporal patterns of GUS expression revealed that MdmiR285N was differentially regulated during seed germination, vegetative phase change, and reproductive development. To elucidate the role of MdmiR285N in plant immunity, MdmiR285N expression in wild-type apple plants and GUS activity in transgenic apple and Arabidopsis thaliana plants were monitored in response to Erwinia amylovora and Pseudomonas syringae pv. Tomato DC3000. A significant decrease of MdmiR285N levels and GUS expression was observed during host-pathogen infections. Overall, these data suggest that MdmiR285N is involved in the biotic stress response, plant growth, and reproductive development.

Silencing Dicer-Like Genes Reduces Virulence and sRNA Generation in Penicillium italicum, the Cause of Citrus Blue Mold

The Dicer protein is one of the most important components of RNAi machinery because it regulates the production of small RNAs (sRNAs) in eukaryotes. Here, Dicer1-like gene (Pit-DCL1) and Dicer2-like gene (Pit-DCL2) RNAi transformants were generated via pSilent-1 in Penicillium italicum (Pit), which is the causal agent of citrus blue mold. Neither transformant showed a change in mycelial growth or sporulation ability, but the pathogenicity of the Pit-DCL2 RNAi transformant to citrus fruits was severely impaired, compared to that of the Pit-DCL1 RNAi transformant and the wild type. We further developed a citrus wound-mediated RNAi approach with a double-stranded fragment of Pit-DCL2 generated in vitro, which achieved an efficiency in reducing Pi-Dcl2 expression and virulence that was similar to that of protoplast-mediated RNAi in P. italicum, suggesting that this approach is promising in the exogenous application of dsRNA to control pathogens on the surface of citrus fruits. In addition, sRNA sequencing revealed a total of 69.88 million potential sRNAs and 12 novel microRNA-like small RNAs (milRNAs), four of which have been predicated on target innate immunity or biotic stress-related genes in Valencia orange. These data suggest that both the Pit-DCL1 and Pit-DCL2 RNAi transformants severely disrupted the biogenesis of the potential milRNAs, which was further confirmed for some milRNAs by qRT-PCR or Northern blot analysis. These data suggest the sRNAs in P. italicum that may be involved in a molecular virulence mechanism termed cross-kingdom RNAi (ck-RNAi) by trafficking sRNA from P. italicum to citrus fruits.

MdUGT88F1-Mediated Phloridzin Biosynthesis Regulates Apple Development and Valsa Canker Resistance

In apple (Malus domestica), the polyphenol profile is dominated by phloridzin, but its physiological role remains largely elusive. Here, we used MdUGT88F1 (a key UDP-glucose:phloretin 2'-O-glucosyltransferase gene) transgenic apple lines and Malus spp. germplasm to gain more insight into the physiological role of phloridzin in apple. Decreasing phloridzin biosynthesis in apple lines by RNA silencing of MdUGT88F1 led to a series of severe phenotypic changes that included severe stunting, reduced internode length, spindly leaf shape, increased stem numbers, and weak adventitious roots. These changes were associated directly with reduced lignin levels and disorders in cell wall polysaccharides. Moreover, compact organization of tissues and thickened bark enhanced resistance to Valsa canker (caused by the fungus Valsa mali), which was associated with lignin- and cell wall polysaccharide-mediated increases of salicylic acid and reactive oxygen species. Phloridzin was also assumed to be utilized directly as a sugar alternative and a toxin accelerator by V. mali in apple. Therefore, after infection with V. mali, a higher level of phloridzin slightly compromised resistance to Valsa canker in MdUGT88F1-overexpressing apple lines. Taken together, our results shed light on the importance of MdUGT88F1-mediated biosynthesis of phloridzin in the interplay between plant development and pathogen resistance in apple trees.

Genome-wide identification of drought-responsive microRNAs in two sets of Malus from interspecific hybrid progenies

Drought stress can negatively impact apple fruit quality and yield. Apple microRNAs (miRNAs) participate in apple tree and fruit development, as well as in biotic stress tolerance; however, it is largely unknown whether these molecules are involved in the drought response. To identify drought-responsive miRNAs in Malus, we first examined the drought stress tolerance of ten F₁ progenies of R3 (M. × domestica) × M. sieversii. We performed Illumina sequencing on pooled total RNA from both drought-tolerant and drought-sensitive plants. The sequencing results identified a total of 206 known miRNAs and 253 candidate novel miRNAs from drought-tolerant plants and drought-sensitive plants under control or drought conditions. We identified 67 miRNAs that were differentially expressed in drought-tolerant plants compared with drought-sensitive plants under drought conditions. Under drought stress, 61 and 35 miRNAs were differentially expressed in drought-tolerant and drought-sensitive plants, respectively. We determined the expression levels of seven out of eight miRNAs by stem-loop qPCR analysis. We also predicted the target genes of all differentially expressed miRNAs and identified the expression of some genes. Gene Ontology analyses indicated that the target genes were mainly involved in stimulus response and cellular and metabolic processes. Finally, we confirmed roles of two miRNAs in apple response to mannitol. Our results reveal candidate miRNAs and their associated mRNAs that could be targeted for improving drought tolerance in Malus species, thus providing a foundation for understanding the molecular networks involved in the response of apple trees to drought stress.