Synthesis of an artificial Vitis vinifera miRNA 319e using overlapping long primers and its application for gene silencing

Artificial Sweet Cherry miRNA 396 Promotes Early Flowering in Vernalization-Dependent Arabidopsis Edi-0 Ecotype

The flowering and fruiting of sweet cherry (Prunus avium L.) depend on precise synchronization with seasonal events. During harsh autumn and winter conditions, floral buds enter dormancy to protect and prepare for the productive season. Dormancy release occurs after exposure to genotype-specific chilling temperatures, an event in which epigenetic reprogramming triggers further metabolic and gene expression activation. Similarly, several Arabidopsis ecotypes require chilling (vernalization) to transition from vegetative to floral states. At vernalization's end, the decrease in the repressor complex formed by SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS C (FLC) allows FLOWERING LOCUS T (FT) to induce flowering. However, this alone does not fully explain the process. MicroRNAs (miRNAs) play a crucial role in gene regulation during plant development and environmental interactions, and miR396's role during flower development and vernalization has been described in some plant species, although not for sweet cherry dormancy. We used 'Regina', a high-chill sweet cherry variety, to identify candidate small RNA molecules throughout dormancy, resulting in the detection of miR396. The transcript expression levels of the putative miRNA target genes were evaluated through quantitative PCR analyses of dormant buds. Additionally, an artificial sweet cherry miR396 was used to transform Arabidopsis Edi-0, a vernalization-requiring ecotype. Ectopic expression of this artificial molecule partially mirrored the effect on target genes observed in dormant buds and, more importantly, led to vernalization-independent flowering. Artificial miR396 expression also resulted in decreased FLC and increased SVP and FT transcript levels. These results could pave the way for future studies on the involvement of miR396 in the regulation of dormancy and flowering, with potential applications in improving crop resilience and productivity.

The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology

Improving crop yield potential is crucial to meet the increasing demands of a rapidly expanding global population in an ever-changing and challenging environment. Therefore, different technological approaches have been proposed over the last decades to accelerate plant breeding. Among them, artificial microRNAs (amiRNAs) represent an innovative tool with remarkable potential to assist plant improvement. MicroRNAs (miRNAs) are a group of endogenous, small (20-24 nucleotides), non-coding RNA molecules that play a crucial role in gene regulation. They are associated with most biological processes of a plant, including reproduction, development, cell differentiation, biotic and abiotic stress responses, metabolism, and plant architecture. In this context, amiRNAs are synthetic molecules engineered to mimic the structure and function of endogenous miRNAs, allowing for the targeted silencing of specific nucleic acids. The current review explores the diverse applications of amiRNAs in plant biology and agriculture, such as the management of infectious agents and pests, the engineering of plant metabolism, and the enhancement of plant resilience to abiotic stress. Moreover, we address future perspectives on plant amiRNA-based gene silencing strategies, highlighting the need for further research to fully comprehend the potential of this technology and to translate its scope toward the widespread adoption of amiRNA-based strategies for plant breeding.

MicroRNA-mediated bioengineering for climate-resilience in crops

Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.

Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana

Targeted gene silencing using small regulatory RNAs is a widely used technique for genetic studies in plants. Artificial microRNAs are one common approach, as they have the advantage of producing just a single functional small RNA, which can be designed for high target specificity and low off-target effects. Simultaneous silencing of multiple targets with artificial microRNAs can be achieved by producing polycistronic microRNA precursors. Alternatively, specialized trans-acting short interfering RNA (tasiRNA) precursors can be designed to produce several specific tasiRNAs at once. Here we tested several artificial microRNA- and tasiRNA-based methods for multiplexed gene silencing in Solanum lycopersicum (tomato) and Nicotiana benthamiana. All analyses used transiently expressed transgenes delivered by infiltration of leaves with Agrobacterium tumefacians. Small RNA sequencing analyses revealed that many previously described approaches resulted in poor small RNA processing. The 5'-most microRNA precursor hairpins on polycistronic artificial microRNA precursors were generally processed more accurately than precursors at the 3'-end. Polycistronic artificial microRNAs where the hairpin precursors were separated by transfer RNAs had the best processing precision. Strikingly, artificial tasiRNA precursors failed to be processed in the expected phased manner in our system. These results highlight the need for further development of multiplexed artificial microRNA and tasiRNA strategies. The importance of small RNA sequencing, as opposed to single-target assays such as RNA blots or real-time polymerase chain reaction, is also discussed.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production

BACKGROUND

In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. Many S genes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due to Plum pox virus (PPV).

RESULTS

For this purpose, hairpin-inducing silencing constructs based on Prunus persica orthologs were used to generate Prunus salicina (Japanese plum) 4E and 4G silenced plants by Agrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulated eIFiso4E transgenic Japanese plums were not regenerated in our conditions, eIFiso4G11-, but not the eIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka.

CONCLUSIONS

Our results indicate that S gene function of the translation initiation complex isoform is conserved in Prunus species. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.

Agrobacterium-Mediated Transformation of Tree Fruit Crops: Methods, Progress, and Challenges

Genetic engineering based on Agrobacterium-mediated transformation has been a desirable tool to manipulate single or multiple genes of existing genotypes of woody fruit crops, for which conventional breeding is a difficult and lengthy process due to heterozygosity, sexual incompatibility, juvenility, or a lack of natural sources. To date, successful transformation has been reported for many fruit crops. We review the major progress in genetic transformation of these fruit crops made in the past 5 years, emphasizing reproducible transformation protocols as well as the strategies that have been tested in fruit crops. While direct transformation of scion cultivars was mostly used for fruit quality improvement, biotic and abiotic tolerance, and functional gene analysis, transgrafting on genetically modified (GM) rootstocks showed a potential to produce non-GM fruit products. More recently, genome editing technology has demonstrated a potential for gene(s) manipulation of several fruit crops. However, substantial efforts are still needed to produce plants from gene-edited cells, for which tremendous challenge remains in the context of either cell's recalcitrance to regeneration or inefficient gene-editing due to their polyploidy. We propose that effective transient transformation and efficient regeneration are the key for future utilization of genome editing technologies for improvement of fruit crops.

Tyramine and tyrosine decarboxylase gene contributes to the formation of cyanic blotches in the petals of pansy (Viola × wittrockiana)

Tyrosine decarboxylase (TYDC) can catalyze tyrosine into tyramine. Several studies demonstrated its roles in the acidity, salidroside and defense response. Here we found that TYDC from Viola × wittrockiana Gam (VwTYDC) may contribute to the formation of cyaninc blotches in the petal. VwTYDC gene were cloned from Viola × wittrockiana and the cDNA full-length sequences were 1634 bp encoding 494 amino acids. Gene expression of VwTYDC in different tissues and developmental stages showed that they were significantly higher expressed in flowers than stems, leaves and roots. In addition, VwTYDC expression were higher in cyanic blotches than those observed in acyanic blotches of petal. Metabolites analysis showed the contents of tyramine in cyanic blotches were also higher than that in acyanic areas. Furthermore, in vitro assay revealed the absorption peak of anthocyanins had a red shift and an increase when fed tyramine. We speculated that tyramine might contribute to flower color expression of pansy as co-pigment. Our study demonstrated for the first time that the contents of tyramine led to flower blotches formation in cyanic blotches of the petals in plant flowers, and this may due to the higher expression of VwTYDC gene.