The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress

Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Masson pine (Pinus massoniana Lamb.) is a major fast-growing woody tree species and pioneer species for afforestation in barren sites in southern China. However, the regulatory mechanism of gene expression in P. massoniana under drought remains unclear. To uncover candidate microRNAs, their expression profiles, and microRNA-mRNA interactions, small RNA-seq was used to investigate the transcriptome from seedling roots under drought and rewatering in P. massoniana. A total of 421 plant microRNAs were identified. Pairwise differential expression analysis between treatment and control groups unveiled 134, 156, and 96 differential expressed microRNAs at three stages. These constitute 248 unique microRNAs, which were subsequently categorized into six clusters based on their expression profiles. Degradome sequencing revealed that these 248 differentially expressed microRNAs targeted 2069 genes. Gene Ontology enrichment analysis suggested that these target genes were related to translational and posttranslational regulation, cell wall modification, and reactive oxygen species scavenging. miRNAs such as miR482, miR398, miR11571, miR396, miR166, miRN88, and miRN74, along with their target genes annotated as F-box/kelch-repeat protein, 60S ribosomal protein, copper-zinc superoxide dismutase, luminal-binding protein, S-adenosylmethionine synthase, and Early Responsive to Dehydration Stress may play critical roles in drought response. This study provides insights into microRNA responsive to drought and rewatering in Masson pine and advances the understanding of drought tolerance mechanisms in Pinus.

Fruit crops combating drought: Physiological responses and regulatory pathways

Drought is a common stress in agricultural production. Thus, it is imperative to understand how fruit crops respond to drought and to develop drought-tolerant varieties. This paper provides an overview of the effects of drought on the vegetative and reproductive growth of fruits. We summarize the empirical studies that have assessed the physiological and molecular mechanisms of the drought response in fruit crops. This review focuses on the roles of calcium (Ca2+) signaling, abscisic acid (ABA), reactive oxygen species signaling, and protein phosphorylation underlying the early drought response in plants. We review the resulting downstream ABA-dependent and ABA-independent transcriptional regulation in fruit crops under drought stress. Moreover, we highlight the positive and negative regulatory mechanisms of microRNAs in the drought response of fruit crops. Lastly, strategies (including breeding and agricultural practices) to improve the drought resistance of fruit crops are outlined.

Functional Differences of Grapevine Circular RNA Vv-circPTCD1 in Arabidopsis and Grapevine Callus under Abiotic Stress

Circular RNAs (circRNAs) serve as covalently closed single-stranded RNAs and have been proposed to influence plant development and stress resistance. Grapevine is one of the most economically valuable fruit crops cultivated worldwide and is threatened by various abiotic stresses. Herein, we reported that a circRNA (Vv-circPTCD1) processed from the second exon of the pentatricopeptide repeat family gene PTCD1 was preferentially expressed in leaves and responded to salt and drought but not heat stress in grapevine. Additionally, the second exon sequence of PTCD1 was highly conserved, but the biogenesis of Vv-circPTCD1 is species-dependent in plants. It was further found that the overexpressed Vv-circPTCD1 can slightly decrease the abundance of the cognate host gene, and the neighboring genes are barely affected in the grapevine callus. Furthermore, we also successfully overexpressed the Vv-circPTCD1 and found that the Vv-circPTCD1 deteriorated the growth during heat, salt, and drought stresses in Arabidopsis. However, the biological effects on grapevine callus were not always consistent with those of Arabidopsis. Interestingly, we found that the transgenic plants of linear counterpart sequence also conferred the same phenotypes as those of circRNA during the three stress conditions, no matter what species it is. Those results imply that although the sequences are conserved, the biogenesis and functions of Vv-circPTCD1 are species-dependent. Our results indicate that the plant circRNA function investigation should be conducted in homologous species, which supports a valuable reference for further plant circRNA studies.

Physiological and Transcriptome Analyses of Photosynthesis in Three Mulberry Cultivars within Two Propagation Methods (Cutting and Grafting) under Waterlogging Stress

Mulberry is a valuable woody plant with significant economic importance. It can be propagated through two main methods: cutting and grafting. Waterlogging can have a major impact on mulberry growth and can significantly reduce production. In this study, we examined gene expression patterns and photosynthetic responses in three waterlogged mulberry cultivars propagated through cutting and grafting. Compared to the control group, waterlogging treatments reduced levels of chlorophyll, soluble protein, soluble sugars, proline, and malondialdehyde (MDA). Additionally, the treatments significantly decreased the activities of ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) in all three cultivars, except for superoxide dismutase (SOD). Waterlogging treatments also affected the rate of photosynthesis (Pn), stomatal conductance (Gs), and transpiration rate (Tr) in all three cultivars. However, no significant difference in physiological response was observed between the cutting and grafting groups. Gene expression patterns in the mulberry changed dramatically after waterlogging stress and varied between the two propagation methods. A total of 10,394 genes showed significant changes in expression levels, with the number of differentially expressed genes (DEGs) varying between comparison groups. GO and KEGG analysis revealed important DEGs, including photosynthesis-related genes that were significantly downregulated after waterlogging treatment. Notably, these genes were upregulated at day 10 in the cutting group compared to the grafting group. In particular, genes involved in carbon fixation were significantly upregulated in the cutting group. Finally, cutting propagation methods displayed better recovery capacity from waterlogging stress than grafting. This study provides valuable information for improving mulberry genetics in breeding programs.

The role of shoot-derived RNAs transported to plant root in response to abiotic stresses

A large number of RNA molecules are transported over long-distance between shoots and roots via phloem in higher plants. Mobile RNA signals are important for plants to tackle abiotic stresses. Shoot-derived mobile RNAs can be involved in the response to different developmental or environmental signals in the root. Some environmental conditions such as climate change, water deficit, nutrient deficiency challenge modern agriculture with more expeditious abiotic stress conditions. Root architecture determines the ability of water and nutrient uptake and further abiotic stress tolerance, and shoot tissue also determines the balance between shoot-root relationship in plant growth and adaptations. Thus, it is necessary to understand the roles of shoot-derived RNA signals and their potential function in roots upon abiotic stresses in the model plants (Arabidopsis thaliana and Nicotiana benthamiana) and agricultural crops. In this review, we summarize the so-far discovered shoot-derived mobile RNA transportation to the root under abiotic stress conditions, e.g. drought, cold stress and nutrient deficiencies. Furthermore, we will focus on the biological relevance and the potential roles of these RNAs in root development and stress responses which will be an asset for the future breeding strategies.

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.

Insights into Mobile Small-RNAs Mediated Signaling in Plants

In higher plants, small RNA (sRNA)-mediated RNA interfering (RNAi) is involved in a broad range of biological processes. Growing evidence supports the model that sRNAs are mobile signaling agents that move intercellularly, systemically and cross-species. Recently, considerable progress has been made in terms of characterization of the mobile sRNAs population and their function. In this review, recent progress in identification of new mobile sRNAs is assessed. Here, critical questions related to the function of these mobile sRNAs in coordinating developmental, physiological and defense-related processes is discussed. The forms of mobile sRNAs and the underlying mechanisms mediating sRNA trafficking are discussed next. A concerted effort has been made to integrate these new findings into a comprehensive overview of mobile sRNAs signaling in plants. Finally, potential important areas for both basic science and potential applications are highlighted for future research.

WRKY41/WRKY46-miR396b-5p-TPR module mediates abscisic acid-induced cold tolerance of grafted cucumber seedlings

Grafting is one of the key agronomic measures to enhance the tolerance to environmental stresses in horticultural plants, but the specific molecular regulation mechanism in this tolerance largely remains unclear. Here, we found that cucumber grafted onto figleaf gourd rootstock increased cold tolerance through abscisic acid (ABA) activating WRKY41/WRKY46-miR396b-5p-TPR (tetratricopeptide repeat-like superfamily protein) module. Cucumber seedlings grafted onto figleaf gourd increased cold tolerance and induced the expression of miR396b-5p. Furthermore, overexpression of cucumber miR396b-5p in Arabidopsis improved cold tolerance. 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) and transient transformation experiments demonstrated that TPR was the target gene of miR396b-5p, while TPR overexpression plants were hypersensitive to cold stress. The yeast one-hybrid and dual-luciferase assays showed that both WRKY41 and WRKY46 bound to MIR396b-5p promoter to induce its expression. Furthermore, cold stress enhanced the content of ABA in the roots and leaves of figleaf gourd grafted cucumber seedlings. Exogenous application of ABA induced the expression of WRKY41 and WRKY46, and cold tolerance of grafted cucumber seedlings. However, figleaf gourd rootstock-induced cold tolerance was compromised when plants were pretreated with ABA biosynthesis inhibitor. Thus, ABA mediated figleaf gourd grafting-induced cold tolerance of cucumber seedlings through activating the WRKY41/WRKY46-miR396b-5p-TPR module.

Root osmotic sensing from local perception to systemic responses

Plants face a constantly changing environment, requiring fine tuning of their growth and development. Plants have therefore developed numerous mechanisms to cope with environmental stress conditions. One striking example is root response to water deficit. Upon drought (which causes osmotic stress to cells), plants can among other responses alter locally their root system architecture (hydropatterning) or orientate their root growth to optimize water uptake (hydrotropism). They can also modify their hydraulic properties, metabolism and development coordinately at the whole root and plant levels. Upstream of these developmental and physiological changes, plant roots must perceive and transduce signals for water availability. Here, we review current knowledge on plant osmotic perception and discuss how long distance signaling can play a role in signal integration, leading to the great phenotypic plasticity of roots and plant development.

Characterization and bioinformatics analysis of ptc-miR396g-5p in response to drought stress of Paeonia ostii

Drought is one of the main abiotic stress factors affecting yield of Paeonia ostii. In this study, we conducted bioinformatics and differential expression analyses of P. ostii ‘Feng Dan’ ptc-miR396g-5p in leaf samples under different drought stress. ptc-miR396g-5p belongs to the miR396 family. Among the 271 plant species registered in the miRBase database, at least one miR396 member was found in 48 Angiospermae species, 3 in Gymnospermae species, and 1 in Pteridophy. Mature sequence alignment showed that P. ostii ‘Feng Dan’ ptc-miR396g-5p had high sequence similarity with miR396 from other species. Secondary structure prediction showed that the precursor sequence of ‘Feng Dan’ ptc-miR396g-5p could form a stable stem-loop structure, and the mature sequence was located on the 5′ arm of the secondary structure. Phylogenetic tree analysis showed that ‘Feng Dan’ was closely related to 20 species such as Glycine max, Medicago truncatula, Populus trichocarpa, Citrus sinensis, Vitis vinifera, and Theobroma cacao. The predicted target gene of the ‘Feng Dan’ ptc-miR396g-5p encodes a Signal Transducer and Activator of Transcription (STAT) transcription factor. The negative correlation of expression between the miRNA and its target gene was confirmed by qRT-PCR. Our data indicate that ‘Feng Dan’ ptc-miR396g-5p′s expression decreases under drought, leading to an expression increase of the STAT transcription factor.

How do plants remember drought?

Plants develop both short-term and transgenerational memory of drought stress through epigenetic regulation of transcription for a better response to subsequent exposure. Recurrent spells of droughts are more common than a single drought, with intermittent moist recovery intervals. While the detrimental effects of the first drought on plant structure and physiology are unavoidable, if survived, plants can memorize the first drought to present a more robust response to the following droughts. This includes a partial stomatal opening in the watered recovery interval, higher levels of osmoprotectants and ABA, and attenuation of photosynthesis in the subsequent exposure. Short-term drought memory is regulated by ABA and other phytohormone signaling with transcriptional memory behavior in various genes. High levels of methylated histones are deposited at the drought-tolerance genes. During the recovery interval, the RNA polymerase is stalled to be activated by a pause-breaking factor in the subsequent drought. Drought leads to DNA demethylation near drought-response genes, with genetic control of the process. Progenies of the drought-exposed plants can better adapt to drought owing to the inheritance of particular methylation patterns. However, a prolonged watered recovery interval leads to loss of drought memory, mediated by certain demethylases and chromatin accessibility factors. Small RNAs act as critical regulators of drought memory by altering transcript levels of drought-responsive target genes. Further studies in the future will throw more light on the genetic control of drought memory and the interplay of genetic and epigenetic factors in its inheritance. Plants from extreme environments can give queues to understanding robust memory responses at the ecosystem level.

Conservation and Diversity of miR166 Family Members From Highbush Blueberry (Vaccinium corymbosum) and Their Potential Functions in Abiotic Stress

MicroRNA166 (miR166) is highly conserved and has diverse functions across plant species. The highbush blueberry (Vaccinium corymbosum) genome is thought to harbor 10 miRNA166 loci (Vco-miR166), but the extent of their evolutionary conservation or functional diversification remains unknown. In this study, we identified six additional Vco-miR166 loci based on conserved features of the miR166 family. Phylogenetic analyses showed that mature Vco-miR166s and their precursor cluster in several clades are evolutionary conserved with diverse species. The cis-regulatory elements in the Vco-miR166 promoters indicated functions related to different phytohormones and defense responses. We also identified putative targets of vco-miR166s, which targeted the same gene families, suggesting the functional conservation and diversification of Vco-miR166 family members. Furthermore, we examined the accumulation patterns of six mature Vco-miR166s in response to abiotic stresses by stem-loop reverse RT-qPCR, which revealed their upregulation under freezing, cold, and heat stress, while they were downregulated by drought compared to control growth conditions. However, Vco-miR166 members showed different expression patterns when exposed to salt stress. These results showed that conserved Vco-miR166 family members display functional diversification but also coordinately influence plant responses to abiotic stress.

Physiological, biochemical, and molecular aspects of grafting in fruit trees

Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.

Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine

Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.

Small RNA populations reflect the complex dialogue established between heterograft partners in grapevine

Grafting is an ancient method that has been intensively used for the clonal propagation of vegetables and woody trees. Despite its importance in agriculture the physiological and molecular mechanisms underlying phenotypic changes of plants following grafting are still poorly understood. In the present study, we analyse the populations of small RNAs in homo and heterografts and take advantage of the sequence differences in the genomes of heterograft partners to analyse the possible exchange of small RNAs. We demonstrate that the type of grafting per se dramatically influences the small RNA populations independently of genotypes but also show genotype specific effects. In addition, we demonstrate that bilateral exchanges of small RNAs, mainly short interfering RNAs, may occur in heterograft with the preferential transfer of small RNAs from the scion to the rootstock. Altogether, the results suggest that small RNAs may have an important role in the phenotype modifications observed in heterografts.

The miR169n-NF-YA8 regulation module involved in drought resistance in Brassica napus L

As an ancient and conserved plant microRNA (miRNA) family, miR169 targets nuclear factor Y subunit alpha (NF-YA) family members. The miR169-NF-YA module is associated with plant development and various stress responses. However, the function of miR169 in response to drought stress in rapeseed (Brassica napus L.) is unclear. In the present study, we showed that miR169n acted as a negative regulator of drought resistance in rapeseed by targeting a nuclear factor Y-A gene, NF-YA8. miR169n was strongly down-regulated by drought stress. Expression of a miR169n target mimicry construct (MIM169n) which functioned as a sponge to trap miR169n resulted in enhanced resistance of transgenic plants to both osmotic stress at the post-germination stage and drought stress at the seedling stage. MIM169n plants had a higher relative water content (RWC) and proline content, lower relative electrolyte leakage (REL), and showed higher antioxidative capability compared with those of control (CK) plants under drought stress. Moreover, NF-YA8 was verified as a target of miR169n, and overexpression of NF-YA8 led to improved tolerance of rapeseed to osmotic stress at the post-germination stage. Overall, our findings implied that the miR169n-NF-YA8 regulatory module could serve as a potential target for genetic improvement of drought resistance in B. napus.

Non-Coding RNAs in Response to Drought Stress

Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.

Strigolactones affect phosphorus acquisition strategies in tomato plants

Strigolactones (SLs) are plant hormones that modulate morphological, physiological and biochemical changes as part of the acclimation strategies to phosphorus (P) deficiency, but an in-depth description of their effects on tomato P-acquisition strategies under P shortage is missing. Therefore, in this study, we investigate how SLs impact on root exudation and P uptake, in qualitative and quantitative terms over time, in wild-type and SL-depleted tomato plants grown with or without P. Under P shortage, SL-depleted plants were unable to efficiently activate most mechanisms associated with the P starvation response (PSR), except for the up-regulation of P transporters and increased activity of P-solubilizing enzymes. The reduced SL biosynthesis had negative effects also under normal P provision, because plants over-activated high-affinity transporters and enzymatic activities (phytase, acidic phosphatase) to sustain elevated P uptake, at great carbon and nitrogen costs. A shift in the onset of PSR was also highlighted in these plants. We conclude that SLs are master kinetic regulators of the PSR in tomato and that their defective synthesis might lead both to suboptimal nutritional outcomes under P depletion and an unbalanced control of P uptake when P is available.

Oxalic Acid Preharvest Treatment Improves Colour and Quality of Seedless Table Grape 'Magenta' Upregulating on-Vine Abscisic Acid Metabolism, Relative VvNCED1 Gene Expression, and the Antioxidant System in Berries

The effect of oxalic acid (OA) in determining poorly coloured table grape quality remains relatively unknown. Some red cultivars, such as seedless table grape 'Magenta' are characterised by a poor berry colour, an attribute highly demanded by the consumer. The aim of this research was to elucidate the effect of a preharvest OA treatment (5 mM) on berry colour and quality of table grape by investigating its role in berry development, on-vine ripening, and postharvest senescence. We found that OA significantly increased abscisic acid (ABA) and ABA glucose ester (ABA-GE) content in treated berries. This increase was mediated by changes in the ABA biosynthetic pathway, specifically by the upregulation of the 9-cis-epoxycarotenoid dioxygenase (VvNCED1) gene. The accumulation of ABA in treated berries resulted in colour improvement and a higher individual and total anthocyanins content at harvest compared with control; whereas at harvest, OA-treated table grapes showed a significantly lower glucose and fructose content and a higher content of tartaric, ascorbic, and succinic acids. Furthermore, antioxidant enzyme activity was increased during berry development in OA-treated berries. On the other hand, those berries treated with OA showed a delay in loss of firmness and colour during cold storage, as well as less susceptibility to postharvest decay incidence. This effect of OA delaying the senescence process was also related to enzymatic antioxidant system stimulation. For the first time, the role of OA on increasing quality, mainly colour, in table grapes was elucidated, highlighting that this treatment upregulated ABA metabolism, relative VvNCED1 gene expression and antioxidant system, delaying postharvest berry senescence.

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.

Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress

Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.

High-throughput miRNA deep sequencing in response to drought stress in sugarcane

Drought is a major factor which reduces cane growth and productivity. In the present study, we sequenced drought susceptible (V1) and drought tolerant (V2) sugarcane varieties using high-throughput miRNA deep sequencing method to study the regulation of gene expression by miRNAs during drought stress in sugarcane. A total of 1224 conserved miRNAs which belong to 89 miRNA families were identified and 38% of the differentially regulated miRNAs were common for both varieties. Additionally 435 novel miRNAs were also identified from four small RNA libraries. We identified 145 miRNAs that were differentially expressed in susceptible variety (V1-31) and 143 miRNAs differentially expressed in the tolerant variety (V2-31). Target prediction revealed that the genes mainly encoded transcription factors, proteins, phosphatase and kinases involved in signal transduction pathways, integral component of membrane and inorganic ion transport metabolism, enzymes involved in carbohydrate transport and metabolism and drought-stress-related proteins involved in defense mechanisms. Pathway analysis of targets revealed that "General function prediction only" was the most significant pathway observed in both tolerant and susceptible genotypes followed by "signal transduction mechanisms". Functional annotation of the transcripts revealed genes like calcium-dependent protein kinase, respiratory burst oxidase, caffeic acid 3-O-methyltransferase, peroxidase, calmodulin, glutathione S-transferase and transcription factors like MYB, WRKY that are involved in drought tolerant pathways. qRT-PCR was used to verify the expression levels of miRNAs and their potential targets obtained from RNA sequencing results.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-021-02857-x.

Cold Hardiness Dynamics and Spring Phenology: Climate-Driven Changes and New Molecular Insights Into Grapevine Adaptive Potential

Climate change has become a topic of increasing significance in viticulture, severely challenged by this issue. Average global temperatures are increasing, but frost events, with a large variability depending on geographical locations, have been predicted to be a potential risk for grapevine cultivation. Grape cold hardiness encompasses both midwinter and spring frost hardiness, whereas the avoidance of spring frost damage due to late budbreak is crucial in cold resilience. Cold hardiness kinetics and budbreak phenology are closely related and affected by bud's dormancy state. On the other hand, budbreak progress is also affected by temperatures during both winter and spring. Genetic control of bud phenology in grapevine is still largely undiscovered, but several studies have recently aimed at identifying the molecular drivers of cold hardiness loss and the mechanisms that control deacclimation and budbreak. A review of these related traits and their variability in different genotypes is proposed, possibly contributing to develop the sustainability of grapevine production as climate-related challenges rise.

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine

Transition of grapevine buds from paradormancy to endodormancy is coordinated by changes in gene expression, phytohormones, transcription factors, and other molecular regulators, but the mechanisms involved in transcriptional and post-transcriptional regulation of dormancy stages are not well delineated. To identify potential regulatory targets, an integrative analysis of differential gene expression profiles and their inverse relationships with miRNA abundance was performed in paradormant (long day (LD) 15 h) or endodormant (short day (SD), 13 h) Vitis riparia buds. There were 400 up- and 936 downregulated differentially expressed genes in SD relative to LD budsGene set and gene ontology enrichment analysis indicated that hormone signaling and cell cycling genes were downregulated in SD relative to LD buds. miRNA abundance and inverse expression analyses of miRNA target genes indicated increased abundance of miRNAs that negatively regulate genes involved with cell cycle and meristem development in endodormant buds and miRNAs targeting starch metabolism related genes in paradormant buds. Analysis of interactions between abundant miRNAs and transcription factors identified a network with coinciding regulation of cell cycle and epigenetic regulation related genes in SD buds. This network provides evidence for cross regulation occurring between miRNA and transcription factors both upstream and downstream of MYB3R1.

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.

Increased water use efficiency in miR396-downregulated tomato plants

MicroRNAs regulate plant development and responses to biotic and abiotic stresses but their impact on water use efficiency (WUE) is poorly known. Increasing WUE is a major task in crop improvement programs aimed to meet the challenges posed by the reduction in water availability associated with the ongoing climatic change. We have examined the physiological and molecular response to water stress of tomato (Solanum lycopersicum L.) plants downregulated for miR396 by target mimicry. In water stress conditions, miR396-downregulated plants displayed reduced transpiration and a less then proportional decrease in the photosynthetic rate that resulted in higher WUE. The increase in WUE was associated with faster foliar accumulation of abscisic acid (ABA), with the induction of several drought-protective genes and with the activation of the jasmonic acid (JA) and γ-aminobutyric acid (GABA) pathways. We propose a model in which the downregulation of miR396 leads to the activation of a complex molecular response to water stress. This response acts synergistically with a set of leaf morphological modifications to increase stomatal closure and preserve the efficiency of the photosynthetic activity, ultimately resulting in higher WUE.

Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment

Plant grafting is an ancient agricultural practice widely employed in crops such as woody fruit trees, grapes, and vegetables, in order to improve plant performance. Successful grafting requires the interaction of compatible scion and rootstock genotypes. This involves an intricate network of molecular mechanisms operating at the graft junction and associated with the development and the physiology of the scion, ultimately leading to improved agricultural characteristics such as fruit quality and increased tolerance/resistance to abiotic and biotic factors. Bidirectional transfer of molecular signals such as hormones, nutrients, proteins, and nucleic acids from the rootstock to the scion and vice versa have been well documented. In recent years, studies on rootstock-scion interactions have proposed the existence of an epigenetic component in grafting reactions. Epigenetic changes such as DNA methylation, histone modification, and the action of small RNA molecules are known to modulate chromatin architecture, leading to gene expression changes and impacting cellular function. Mobile small RNAs (siRNAs) migrating across the graft union from the rootstock to the scion and vice versa mediate modifications in the DNA methylation pattern of the recipient partner, leading to altered chromatin structure and transcriptional reprogramming. Moreover, graft-induced DNA methylation changes and gene expression shifts in the scion have been associated with variations in graft performance. If these changes are heritable they can lead to stably altered phenotypes and affect important agricultural traits, making grafting an alternative to breeding for the production of superior plants with improved traits. However, most reviews on the molecular mechanisms underlying this process comprise studies related to vegetable grafting. In this review we will provide a comprehensive presentation of the current knowledge on the epigenetic changes and transcriptional reprogramming associated with the rootstock-scion interaction focusing on woody plant species, including the recent findings arising from the employment of advanced-omics technologies as well as transgrafting methodologies and their potential exploitation for generating superior quality grafts in woody species. Furthermore, will discuss graft-induced heritable epigenetic changes leading to novel plant phenotypes and their implication to woody crop improvement for yield, quality, and stress resilience, within the context of climate change.

Candidate genes and SNPs associated with stomatal conductance under drought stress in Vitis

BACKGROUND

Understanding the complexity of the vine plant's response to water deficit represents a major challenge for sustainable winegrowing. Regulation of water use requires a coordinated action between scions and rootstocks on which cultivars are generally grafted to cope with phylloxera infestations. In this regard, a genome-wide association study (GWAS) approach was applied on an 'ad hoc' association mapping panel including different Vitis species, in order to dissect the genetic basis of transpiration-related traits and to identify genomic regions of grape rootstocks associated with drought tolerance mechanisms. The panel was genotyped with the GrapeReSeq Illumina 20 K SNP array and SSR markers, and infrared thermography was applied to estimate stomatal conductance values during progressive water deficit.

RESULTS

In the association panel the level of genetic diversity was substantially lower for SNPs loci (0.32) than for SSR (0.87). GWAS detected 24 significant marker-trait associations along the various stages of drought-stress experiment and 13 candidate genes with a feasible role in drought response were identified. Gene expression analysis proved that three of these genes (VIT_13s0019g03040, VIT_17s0000g08960, VIT_18s0001g15390) were actually induced by drought stress. Genetic variation of VIT_17s0000g08960 coding for a raffinose synthase was further investigated by resequencing the gene of 85 individuals since a SNP located in the region (chr17_10,497,222_C_T) was significantly associated with stomatal conductance.

CONCLUSIONS

Our results represent a step forward towards the dissection of genetic basis that modulate the response to water deprivation in grape rootstocks. The knowledge derived from this study may be useful to exploit genotypic and phenotypic diversity in practical applications and to assist further investigations.

Abscisic Acid Mediates Drought and Salt Stress Responses in Vitis vinifera-A Review

The foreseen increase in evaporative demand and reduction in rainfall occurrence are expected to stress the abiotic constrains of drought and salt concentration in soil. The intensification of abiotic stresses coupled with the progressive depletion in water pools is a major concern especially in viticulture, as most vineyards rely on water provided by rainfall. Because its economical relevance and its use as a model species for the study of abiotic stress effect on perennial plants, a significant amount of literature has focused on Vitis vinifera, assessing the physiological mechanisms occurring under stress. Despite the complexity of the stress-resistance strategy of grapevine, the ensemble of phenomena involved seems to be regulated by the key hormone abscisic acid (ABA). This review aims at summarizing our knowledge on the role of ABA in mediating mechanisms whereby grapevine copes with abiotic stresses and to highlight aspects that deserve more attention in future research.

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality

Background

In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigating the effect of two different rootstocks (1103 Paulsen - P - and Mgt 101–14 - M) in comparison with not grafted plants - NGC - on transcriptome (RNA-seq and small RNA-seq) and chemical composition of berry skin in Pinot noir, and exploring the influence of rootstock-scion interaction on grape quality. Berry samples, collected at veraison and maturity, were investigated at transcriptional and biochemical levels to depict the impact of rootstock on berry maturation.

Results

RNA- and miRNA-seq analyses highlighted that, at veraison, the transcriptomes of the berry skin are extremely similar, while variations associated with the different rootstocks become evident at maturity, suggesting a greater diversification at transcriptional level towards the end of the ripening process. In the experimental design, resembling standard agronomic growth conditions, the vines grafted on the two different rootstocks do not show a high degree of diversity. In general, the few genes differentially expressed at veraison were linked to photosynthesis, putatively because of a ripening delay in not grafted vines, while at maturity the differentially expressed genes were mainly involved in the synthesis and transport of phenylpropanoids (e.g. flavonoids), cell wall loosening, and stress response. These results were supported by some differences in berry phenolic composition detected between grafted and not grafted plants, in particular in resveratrol derivatives accumulation.

Conclusions

Transcriptomic and biochemical data demonstrate a stronger impact of 1103 Paulsen rootstock than Mgt 101–14 or not grafted plants on ripening processes related to the secondary metabolite accumulations in berry skin tissue. Interestingly, the MYB14 gene, involved in the feedback regulation of resveratrol biosynthesis was up-regulated in 1103 Paulsen thus supporting a putative greater accumulation of stilbenes in mature berries.

A novel strigolactone-miR156 module controls stomatal behaviour during drought recovery

miR156 is a conserved microRNA whose role and induction mechanisms under stress are poorly known. Strigolactones are phytohormones needed in shoots for drought acclimation. They promote stomatal closure ABA-dependently and independently; however, downstream effectors for the former have not been identified. Linkage between miR156 and strigolactones under stress has not been reported. We compared ABA accumulation and sensitivity as well as performances of wt and miR156-overexpressing (miR156-oe) tomato plants during drought. We also quantified miR156 levels in wt, strigolactone-depleted and strigolactone-treated plants, exposed to drought stress. Under irrigated conditions, miR156 overexpression and strigolactone treatment led to lower stomatal conductance and higher ABA sensitivity. Exogenous strigolactones were sufficient for miR156 accumulation in leaves, while endogenous strigolactones were required for miR156 induction by drought. The "after-effect" of drought, by which stomata do not completely re-open after rewatering, was enhanced by both strigolactones and miR156. The transcript profiles of several miR156 targets were altered in strigolactone-depleted plants. Our results show that strigolactones act as a molecular link between drought and miR156 in tomato, and identify miR156 as a mediator of ABA-dependent effect of strigolactones on the after-effect of drought on stomata. Thus, we provide insights into both strigolactone and miR156 action on stomata.

LncRNA improves cold resistance of winter wheat by interacting with miR398

One of the important functions of long non-coding RNA (lncRNA) is to be competing endogenous RNAs (ceRNAs). As miR398 is reported to respond to different stressors, it is necessary to explore its relationship with lncRNA in the cold resistance mechanism of winter wheat. Tae-miR398-precursor sequence was isolated from the winter wheat (Triticum aestivum). RLM-RACE verified that tae-miR398 cleaved its target CSD1. Quantitative detection at 5°C, -10°C and -25°C showed that the expression of tae-miR398 decreased in response to low temperatures, whereas CSD1 showed an opposite expression pattern. LncR9A, lncR117 and lncR616 were predicted and verified to interact with miR398. tae-miR398 and three lncRNAs were transferred into Arabidopsis thaliana respectively. The lncR9A were transferred into Brachypodium distachyom. Transgenic plants were cultivated at -8°C and assessed for the expression of malondialdehyde, chlorophyll, superoxide dismutase and miR398-lncRNA-target mRNA. The results demonstrate that tae-miR398 regulates low temperature tolerance by downregulating its target, CSD1. lncRNA regulates the expression of CSD1 indirectly by competitively binding miR398, which, in turn, affects the resistance of Dn1 to cold. miR398-regulation triggers a regulatory loop that is critical to cold stress tolerance in wheat. Our findings offer an improved strategy to crop plants with enhanced stress tolerance.

A constitutive and drought-responsive mRNA undergoes long-distance transport in pear (Pyrus betulaefolia) phloem

Pear is one of the most commercially important fruit trees worldwide and is widely cultivated in temperate zones. Drought stress can greatly limit pear fruit yield and quality. Pyrus betulaefolia Bunge, a drought-resistant pear rootstock that is commonly used in northern China, confers favourable characteristics to pear scions, allowing them to respond rapidly to drought stress via the transport of macromolecules such as phloem-mobile mRNAs. How drought-responsive mRNAs function as phloem-mobile signals remains unknown, however. Here, we used RNA sequencing (RNA-seq) combined with SNP analysis to identify mobile mRNAs in P. betulaefolia. We focused on mobile mRNAs that respond to drought stress and found that the abundance of a novel mRNA named PbDRM (P. betulaefoliaDROUGHT-RESPONSIVE MOBILE GENE) significantly increased in several different scion cultivars when they were grafted onto P. betulaefolia rootstock under drought conditions. In addition, downregulating PbDRM by virus-induced gene silencing (VIGS) increased the drought sensitivity of P. betulaefolia. CAPS RT-PCR analysis confirmed that PbDRM mRNA moves from rootstock to scion in micrografting systems. Therefore, PbDRM mRNA acts as a phloem-mobile signal in pear under drought stress.

Water relations of two Sicilian grapevine cultivars in response to potassium availability and drought stress

We investigated the response of two Sicilian grapevine cultivars, Catarratto and Nero d'Avola, to potassium deficiency and drought stress. Two-year-old plants grafted on 1103 Paulsen were grown in agriperlite, with or without potassium in the fertigation solution for six weeks, and subjected to moderate drought stress by suspending irrigation for one week. Potassium content of leaves, roots and xylem sap were measured with an ion-selective electrode. Changes in stomatal conductance, stem and leaf water potential and hydraulic conductance were compared between genotypes and treatments. Potassium deficiency led to significant decreases in leaf potassium content in both cultivars and under both well-watered and drought stress conditions. Potassium content in xylem sap showed no significant differences between cultivars and was correlated with stem hydraulic conductance, particularly in the drought stress treatments. Under drought stress conditions, potassium availability led to an increase in stomatal conductance, particularly in Nero d'Avola. Both cultivars showed a rather isohydric behavior under these experimental conditions, and the level of isohydry varied with potassium availability. These results can be useful for the development of optimal fertigation practices and the selection of drought tolerant varieties.

Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants

Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications.

Scion control of miRNA abundance and tree maturity in grafted avocado

BACKGROUND

Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown.

RESULTS

Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1.

CONCLUSION

Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.

Scion control of miRNA abundance and tree maturity in grafted avocado

BACKGROUND

Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown.

RESULTS

Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1.

CONCLUSION

Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.

Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution

Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.

Drought Response in Rice: The miRNA Story

As a semi-aquatic plant, rice requires water for proper growth, development, and orientation of physiological processes. Stress is induced at the cellular and molecular level when rice is exposed to drought or periods of low water availability. Plants have existing defense mechanisms in planta that respond to stress. In this review we examine the role played by miRNAs in the regulation and control of drought stress in rice through a summary of molecular studies conducted on miRNAs with emphasis on their contribution to drought regulatory networks in comparison to other plant systems. The interaction between miRNAs, target genes, transcription factors and their respective roles in drought-induced stresses is elaborated. The cross talk involved in controlling drought stress responses through the up and down regulation of targets encoding regulatory and functional proteins is highlighted. The information contained herein can further be explored to identify targets for crop improvement in the future.

Grafting improves tomato drought tolerance through enhancing photosynthetic capacity and reducing ROS accumulation

Drought is the main meteorological threat to plants and limits plant growth, development, and adaptation to environmental changes. However, root-shoot communication plays a vital role in improving tomato plant drought tolerance, especially when cultivars are grafted onto drought-tolerant rootstock. In this study, the relationship between photosynthetic capacity and reactive oxygen species (ROS) in response to drought stress was studied in tomato grafted with different drought-resistant tomato seedlings. To determine the drought-relieving effect of drought-tolerant rootstocks, we measured the effects of grafting on plant growth, net photosynthetic rate (Pn), ROS accumulation, and antioxidant enzyme activities in tomato leaves and roots under drought stress. Plant growth and Pn were significantly inhibited by drought, but ROS accumulation and antioxidant enzyme activities were significantly increased. Treatment with drought-tolerant tomato seedlings significantly increased plant growth and increased Pn under water-deficit conditions compared with those grafted with drought-susceptible rootstock. In addition, the plants grafted with drought-tolerant seedlings had increased activities of partial antioxidant enzymes, leading to decreased ROS production. Our results indicate that tomato grafted with drought-tolerant seedlings alleviated the phytotoxicity and oxidative damage caused by drought by regulating antioxidant enzymes under drought stress.

Identification and characterization of drought responsive miRNAs in a drought tolerant upland rice cultivar KMJ 1-12-3

Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.

The Role of UV-B light on Small RNA Activity During Grapevine Berry Development

We explored the effects of ultraviolet B radiation (UV-B) on the developmental dynamics of microRNAs and phased small-interfering-RNA (phasi-RNAs)-producing loci by sequencing small RNAs in vegetative and reproductive organs of grapevine (Vitis vinifera L.). In particular, we tested different UV-B conditions in in vitro-grown plantlets (high-fluence exposition) and in berries from field-grown (radiation filtering) and greenhouse-grown (low- and high-fluence expositions) adult plants throughout fruit development and ripening. The functional significance of the observed UV-coordinated miRNA responses was supported by degradome evidences of ARGONAUTE (AGO)-programmed slicing of mRNAs. Co-expression patterns of the up-regulated miRNAs miR156, miR482, miR530, and miR828 with cognate target gene expressions in response to high-fluence UV-B was tested by q-RT-PCR. The observed UV-response relationships were also interrogated against two published UV-stress and developmental transcriptome datasets. Together, the dynamics observed between miRNAs and targets suggest that changes in target abundance are mediated transcriptionally and, in some cases, modulated post-transcriptionally by miRNAs. Despite the major changes in target abundance are being controlled primarily by those developmental effects that are similar between treatments, we show evidence for novel miRNA-regulatory networks in grape. A model is proposed where high-fluence UV-B increases miR168 and miR530 that target ARGONAUTE 1 (AGO1) and a Plus-3 domain mRNA, respectively, while decreasing miR403 that targets AGO2, thereby coordinating post-transcriptional gene silencing activities by different AGOs. Up-regulation of miR3627/4376 could facilitate anthocyanin accumulation by antagonizing a calcium effector, whereas miR395 and miR399, induced by micronutrient deficiencies known to trigger anthocyanin accumulation, respond positively to UV-B radiation. Finally, increases in the abundance of an anthocyanin-regulatory MYB-bHLH-WD40 complex elucidated in Arabidopsis, mediated by UV-B-induced changes in miR156/miR535, could contribute to the observed up-regulation of miR828. In turn, miR828 would regulate the AtMYB113-ortologues MYBA5, A6 and A7 (and thereby anthocyanins) via a widely conserved and previously validated auto-regulatory loop involving miR828 and phasi TAS4abc RNAs.

Characterization of genome-wide microRNAs and their roles in development and biotic stress in pear

Using a genome-wide analysis of miRNAs in 'Yali' pear (Pyrus bretschneideri) via the next-generation high-throughput sequencing of small RNAs with a bioinformatics analysis, we found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 and their target genes function in viral defense in 'Duli' and 'Hongbaoshi'. pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319 and their targets function in auxin signaling pathways in 'Zhongai 4' and 'Zhongai 5'. Successful fruit production in pear (Pyrus spp.) depends on the use of optimal combinations of rootstocks and scions. Deciphering plant-pathogen defense mechanisms and hormone signaling pathways is an important step towards developing pear rootstocks and varieties with improved qualities. In the current study, we combined next-generation sequencing of small RNAs with a bioinformatics analysis to systematically identify and characterize 298 miRNAs in the pear scion cultivar 'Yali' (Pyrus bretschneideri). We also analyzed miRNAs in three rootstock varieties ('Duli', 'Zhongai 4', and 'Zhongai 5') and one scion cultivar ('Hongbaoshi'). We found that pbr-miR156, pbr-miR164, pbr-miR399, and pbr-miR482 are induced following infection with the pear virus Apple stem pitting virus (ASPV), and identified their target genes (pbRPS6, pbNAC, pbTLR, and pbRX-CC, respectively), which participate in viral defense pathways in 'Duli' and 'Hongbaoshi'. Furthermore, we identified pbr-miR160, pbr-miR168, pbr-miR171, and pbr-miR319, and found that the production of these miRNAs was suppressed under low levels of synthetic auxin. The targets of these miRNAs (pbARF, pbAEC, pbSCL, and pbTCP4) respond to auxin signaling pathways in 'Zhongai 4' and 'Zhongai 5'. Our results lay the foundation for breeding improved pear cultivars.

Rootstock-induced molecular responses associated with drought tolerance in sweet orange as revealed by RNA-Seq

Background

Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available for citrus propagation, ‘Rangpur’ lime is known to confer enhanced tolerance to drought as compared to other citrus rootstocks. The objective of this study was to investigate the poorly understood molecular responses underlying the rootstock-induced drought tolerance in sweet orange.

Results

RNA-Seq transcriptome analysis was carried out in leaves of sweet orange grafted on ‘Rangpur’ lime subjected to control and drought-stress treatments, under greenhouse conditions, using the Illumina HiSeq platform. A total of 41,827 unique transcripts were identified, among which 1764 transcripts showed significant variation (P ≤ 0.001) between the treatments, with 1081 genes induced and 683 repressed by drought-stress treatment. The transcripts were distributed in 44 different categories of cellular component, molecular function and biological process. Several genes related to cell metabolism, including those involved in the metabolisms of cell wall, carbohydrates and antioxidants, light reactions, biotic and abiotic stress responses, as well as genes coding for transcription factors (TFs), protein kinases (PKs) and proteins involved in the abscisic acid (ABA) and ethylene signaling pathways, were differentially regulated by drought stress. RNA-Seq data were validated by quantitative real-time PCR (qPCR) analysis and comparative analysis of expression of the selected genes between sweet orange grafted on drought-tolerant and -sensitive rootstocks revealed new candidate genes for drought tolerance in citrus.

Conclusions

In conclusion, our results showed that only a relatively small but functionally diverse fraction of the sweet orange transcriptome, with functions in metabolism, cellular responses and regulation, was differentially regulated by drought stress. The data suggest that the rootstock-induced drought tolerance in sweet orange includes the transcriptional activation of genes related to the cell wall, soluble carbohydrate and antioxidant metabolisms, biotic and abiotic stress responses, TFs, PKs and ABA signaling pathway, and the downregulation of genes involved in the starch metabolism, light reactions and ethylene signaling. Future efforts to elucidate their functional roles and explore their potential in the citrus genetic improvement should benefit from this data.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5481-z) contains supplementary material, which is available to authorized users.

Transcription Factor CsWIN1 Regulates Pericarp Wax Biosynthesis in Cucumber Grafted on Pumpkin

Pericarp wax of cucumber is an important economic trait, determining sales and marketing. Grafting of cucumber onto pumpkin rootstock (Cucurbita moschata) is an effective way to produce glossy cucumber fruits. However, the molecular regulation mechanism of this phenomenon remains largely unknown. In the present study, transcriptome analyses, genome-wide DNA methylation sequencing, and wax metabolite analysis were performed on the pericarp of self-rooted versus grafted cucumber. We identified the AP2/ERF-type transcription factor CsWIN1 as methylated and significantly upregulated in grafted cucumber compared to self-rooted cucumber. The increased expression of CsWIN1 was also positively correlated with several key wax biosynthesis genes, including CsCER1, CsCER1-1, CsCER4, CsKCS1, and the wax transporter gene CsABC. The transcriptome expression level of these genes was validated through qRT-PCR profiles. Furthermore, wax metabolite analysis showed that more wax ester (C20 fatty acid composition), but fewer alkanes (C29 and C31) were deposited in grafted cucumber pericarp. The higher expression of CsWIN1 and wax biosynthesis genes was reflected in the glossier appearance of grafted pericarp, possibly the result of higher wax ester content and higher integration of small trichomes in the pericarp. This study demonstrates that grafting can affect the content and composition of pericarp wax in cucumber grafted on pumpkin, and a unique regulation model of CsWIN1 for wax biosynthesis may exist in cucumber.

Dissecting interplays between Vitis vinifera L. and grapevine virus B (GVB) under field conditions

Plant virus infections are often difficult to characterize as they result from a complex molecular and physiological interplay between a pathogen and its host. In this study, the impact of the phloem-limited grapevine virus B (GVB) on the Vitis vinifera L. wine-red cultivar Albarossa was analysed under field conditions. Trials were carried out over two growing seasons by combining agronomic, molecular, biochemical and ecophysiological approaches. The data showed that GVB did not induce macroscopic symptoms on 'Albarossa', but affected the ecophysiological performances of vines in terms of assimilation rates, particularly at the end of the season, without compromising yield and vigour. In GVB-infected plants, the accumulation of soluble carbohydrates in the leaves and transcriptional changes in sugar- and photosynthetic-related genes seemed to trigger defence responses similar to those observed in plants infected by phytoplasmas, although to a lesser extent. In addition, GVB activated berry secondary metabolism. In particular, total anthocyanins and their acetylated forms accumulated at higher levels in GVB-infected than in GVB-free berries, consistent with the expression profiles of the related biosynthetic genes. These results contribute to improve our understanding of the multifaceted grapevine-virus interaction.

Transcriptome and miRNAs analyses enhance our understanding of the evolutionary advantages of polyploidy

Polyploid organisms have more than two sets of chromosomes, including autopolyploid via intraspecific genome doubling, and allopolyploid via merging genomes of distinct species by hybridization. Polyploid organisms are widespread in plants, indicating that polyploidy has some evolutionary advantages over its diploid ancestor. Actually, polyploidy is always tightly associated with hybrid vigor and adaptation to adverse environmental conditions. However, why polyploidy can develop such advantages is poorly known. MicroRNAs (miRNAs) are endogenous ∼21 nt small RNAs which can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. MicroRNAs are essential for cell development, differentiation, signal transduction, and show an adaptive response to biotic and abiotic stresses. Environmental stresses cause plants to over- or under-express certain miRNAs or synthesize new miRNAs to cope with stress. We have here reviewed our current knowledge on the molecular mechanisms, which can account for the evolutionary advantages of polyploidy over its diploid ancestor from genome-wide gene expression and microRNAs expression perspectives.

miRVIT: A Novel miRNA Database and Its Application to Uncover Vitis Responses to Flavescence dorée Infection

Micro(mi)RNAs play crucial roles in plant developmental processes and in defense responses to biotic and abiotic stresses. In the last years, many works on small RNAs in grapevine (Vitis spp.) were published, and several conserved and putative novel grapevine-specific miRNAs were identified. In order to reorganize the high quantity of available data, we produced "miRVIT," the first database of all novel grapevine miRNA candidates characterized so far, and still not deposited in miRBase. To this aim, each miRNA accession was renamed, repositioned in the last version of the grapevine genome, and compared with all the novel and conserved miRNAs detected in grapevine. Conserved and novel miRNAs cataloged in miRVIT were then used for analyzing Vitis vinifera plants infected by Flavescence dorée (FD), one of the most severe phytoplasma diseases affecting grapevine. The analysis of small RNAs from healthy, recovered (plants showing spontaneous and stable remission of symptoms), and FD-infected "Barbera" grapevines showed that FD altered the expression profiles of several miRNAs, including those involved in cell development and photosynthesis, jasmonate signaling, and disease resistance response. The application of miRVIT in a biological context confirmed the effectiveness of the followed approach, especially for the identification of novel miRNA candidates in grapevine. miRVIT database is available at http://mirvit.ipsp.cnr.it. Highlights: The application of the newly produced database of grapevine novel miRNAs to the analysis of plants infected by Flavescence dorée reveals key roles of miRNAs in photosynthesis and jasmonate signaling.