Characterization of Environmental Effects on Flowering and Plant Architecture in an Everbearing Strawberry F1-Hybrid by Meristem Dissection and Gene Expression Analysis

Floral transition in the cultivated everbearing strawberry is a hot topic because these genotypes flower perpetually and are difficult to maintain in a non-flowering state. However, it has rarely been studied using morphogenetic and molecular analyses simultaneously. We therefore examined the morphogenetic effects and the activation of genes involved in floral induction and initiation in seedlings of an everbearing F1-hybrid. Seedlings were grown at 12, 19, and 26 degrees C under 10 h SD and 20 h LD conditions. We observed a strong environmental influence on meristem development and a FLOWERING LOCUS T1 (FaFT1)-SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (FaSOC1) pathway similar to that in the everbearing woodland strawberry. The everbearing cultivar showed typical features of a quantitative LD plant, flowering earlier under LD than SD conditions at all temperatures. We also found that floral induction is facilitated by FaFT1 upregulation under LD conditions, while FaSOC1 upregulation in the apex leads to photoperiod-independent floral initiation. Moreover, we confirmed the strawberry meristem identity gene FaFUL can also be used as an early indicator of floral initiation in EB cultivars. This study also highlights the advantages of seed-propagated F1-hybrids in genetic studies, namely that they are genetically identical and not biased by a previous flowering history

Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants

The use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains: Pseudomonas fluorescens SLU99, Serratia plymuthica S412, S. rubidaea AV10, and S. rubidaea EV23. Greenhouse and in vitro experiments showed that P. fluorescens SLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield

Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens

Simple Summary Microbial bio-stimulants are attracting increasing attention in agricultural research. In particular, plant growth-promoting rhizobacteria (PGPR) have great potential to improve crops' productivity and tolerance of biotic and abiotic stresses. It is anticipated that PGPR could eventually replace synthetic fungicides in agriculture. This research evaluated Pseudomonas aeruginosa strain FG106-which was isolated from tomato plants- as a potential biocontrol agent against several plant pathogens. This strain displayed multiple plant growth-promoting attributes and high in vitro and in vivo inhibition of growth and pathogenicity of tested phytopathogens. It is thus a multifunctional PGPR with potential applications as a biocontrol agent to control fungal and bacterial pathogens. P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent

Metabolic Processes and Biological Macromolecules Defined the Positive Effects of Protein-Rich Biostimulants on Sugar Beet Plant Development

Protein-based biostimulants (PBBs) have a positive effect on plant development, although the biological background for this effect is not well understood. Here, hydrolyzed wheat gluten (HWG) and potato protein film (PF) in two levels (1 and 2 g/kg soil) and in two different soils (low and high nutrient; LNC and HNC) were used as PBBs. The effect of these PBBs on agronomic traits, sugars, protein, and peptides, as well as metabolic processes, were evaluated on sugar beet in comparison with no treatment (control) and treatment with nutrient solution (NS). The results showed a significant growth enhancement of the plants using HWG and PF across the two soils. Sucrose and total sugar content in the roots were high in NS-treated plants and correlated to root growth in HNC soil. Traits related to protein composition, including nitrogen, peptide, and RuBisCO contents, were enhanced in PBB-treated plants (mostly for HWG and PF at 2 g/kg soil) by 100% and >250% in HNC and LNC, respectively, compared to control. The transcriptomic analysis revealed that genes associated with ribosomes and photosynthesis were upregulated in the leaf samples of plants treated with either HWG or PP compared to the control. Furthermore, genes associated with the biosynthesis of secondary metabolites were largely down-regulated in root samples of HWG or PF-treated plants. Thus, the PBBs enhanced protein-related traits in the plants through a higher transcription rate of genes related to protein- and photosynthesis, which resulted in increased plant growth, especially when added in certain amounts (2 g/kg soil). However, sucrose accumulation in the roots of sugar beet seemed to be related to the easy availability of nitrogen

Potato mop-top virus: variability, movement and suppression of host defence

Potato mop-top virus (PMTV) causes an economically damaging disease called potato spraing. Despite being reported across the potato growing regions in the world, very little genetic variability has been reported for the virus. Also, the knowledge on how PMTV suppresses host defence mechanism, and how it interacts with the host during the cellto-cell and long-distance movement is still insufficient to develop successful preventive measures against the PMTV infection. This thesis work identified high diversity of the PMTV in the Andean region of Peru compared to the rest of the world. Among the PMTV genome, CP-RT and 8K genomic regions accumulated the largest number of mutations. Through phylogenetic analysis of the RNA-CP segment we identified two prevailing genotypes around the world. Based on the pathobiological differences, we named these lineages as S (severe), and M (mild) types. The phylogenetic relationship determined in this study helped us to propose a novel classification of PMTV isolates. Our analysis to address the selection pressure on the PMTV genome revealed that the ORF encoding the 8K protein, a viral suppressor of RNA silencing (VSR) is under strong positive selection. Characterization of the RNA silencing suppression activity of the 8K protein from seven highly diverse isolates revealed that the 8K encoded by a Peruvian isolate, P1 exhibits stronger RNA silencing suppression activity compared to that of other isolates. Through mutational analysis, we identified that Ser-50 is necessary for these differences. Through deep sequencing for sRNAs, we identified that VSRs reduce the sRNA accumulation. We observed lower amount of siRNAs with U residue at the 5’-terminus suggesting that P1 8K might affect AGO1-mediated RNA silencing. The present work also identified key host factors necessary for the cell-to-cell and long distance movement of the virus. We showed that the actin network and certain class VIII myosins motors are important for the cell-to-cell movement of PMTV. The dependency on the acto-myosin network for PMTV movement was further demonstrated by the fluorescence recovery after photo bleaching experiments that resulted in compromised delivery of the TGB1 at the plasmodesmata upon disrupting actin and inhibiting two class VIII myosins. In contrast, class XI myosins did not have a significant effect on the cell-to-cell movement of the PMTV, although they appear to be important viral long-distance movement. Analysis of PMTV TGB1 interactions the with host proteins revealed that TGB1 interacts with Nicotiana benthamiana HIPP26 protein, a vascular expressed, metallochaperone that acts as a plasma membrane to nucleus stress signalling relay. PMTV infection upregulated the expression of HIPP26 and altered its subcellular localization from plasmodesmata to the nucleus. Knockdown of NbHIPP26 expression resulted in inhibition of virus long-distance movement, but not the cell-to-cell movement. Together, this data suggests that PMTV hijacks NbHIPP26 to facilitate the long-distance movement of the virus

Spray-Induced Gene Silencing as a Potential Tool to Control Potato Late Blight Disease

Phytophthora infestans causes late blight disease on potato and tomato and is currently controlled by resistant cultivars or intensive fungicide spraying. Here, we investigated an alternative means for late blight control by spraying potato leaves with double-stranded RNAs (dsRNA) that target the P. infestans genes essential for infection. First, we showed that the sporangia of P. infestans expressing green fluorescent protein (GFP) can take up in vitro synthesized dsRNAs homologous to GFP directly from their surroundings, including leaves, which led to the reduced relative expression of GFP. We further demonstrate the potential of spray-induced gene silencing (SIGS) in controlling potato late blight disease by targeting developmentally important genes in P. infestans such as guanine-nucleotide binding protein β-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-β-glucanase (PiEndo3). Our results demonstrate that SIGS can potentially be used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes

Spray-Induced Gene Silencing as a Potential Tool to Control Potato Late Blight Disease

Phytophthora infestans causes late blight disease on potato and tomato and is currently controlled by resistant cultivars or intensive fungicide spraying. Here, we investigated an alternative means for late blight control by spraying potato leaves with double-stranded RNAs (dsRNA) that target the P. infestans genes essential for infection. First, we showed that the sporangia of P. infestans expressing green fluorescent protein (GFP) can take up in vitro synthesized dsRNAs homologous to GFP directly from their surroundings, including leaves, which led to the reduced relative expression of GFP. We further demonstrate the potential of spray-induced gene silencing (SIGS) in controlling potato late blight disease by targeting developmentally important genes in P. infestans such as guanine-nucleotide binding protein beta-subunit (PiGPB1), haustorial membrane protein (PiHmp1), cutinase (PiCut3), and endo-1,3(4)-beta-glucanase (PiEndo3). Our results demonstrate that SIGS can potentially be used to mitigate potato late blight; however, the degree of disease control is dependent on the selection of the target genes

Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control

Modern plant breeding is still a time-consuming and costly process, even with the most advanced technologies such as gene editing. Hence, there is an urgent need to develop alternative means for plant trait manipulation and plant protection. RNA interference (RNAi) is a conserved cellular mechanism mediated by naturally occurring double-stranded RNA (dsRNA) and small RNAs (sRNAs) that can target mRNAs for destruction or transcript reduction. Here, we review the potential of technology based on RNAi, called spray-induced gene silencing (SIGS), as an alternative or adjunct to breeding for manipulation of endogenous gene expression in plants or pathogen control. SIGS based on exogenous application of RNA molecules in plants may be especially useful in reducing pest or pathogen impacts, thereby ameliorating biotic stresses and increasing the agronomic performance of crops

Role of Dicer-Dependent RNA Interference in Regulating Mycoparasitic Interactions

Dicer-like proteins (DCLs) play a vital role in RNA interference (RNAi), by cleaving RNA filament into small RNAs. Although DCL-mediated RNAi can regulate interspecific communication between pathogenic/mutualistic organisms and their hosts, its role in mycoparasitic interactions is yet to be investigated. In this study, we deleted dcl genes in the mycoparasitic fungus Clonostachys rosea and characterize the functions of DCL-dependent RNAi in mycoparasitism. Deletion of dcl2 resulted in a mutant with reduced secondary metabolite production, antagonism toward the plant-pathogenic fungus Botrytis cinerea, and reduced ability to control Fusarium foot rot disease on wheat, caused by Fusarium graminearum. Transcriptome sequencing of the in vitro interaction between the C. rosea Delta dcl2 strain and B. cinerea or F. graminearum identified the downregulation of genes coding for transcription factors, membrane transporters, hydrolytic enzymes, and secondary metabolites biosynthesis enzymes putatively involved in antagonistic interactions, in comparison with the C. rosea wild-type interaction. A total of 61 putative novel microRNA-like RNAs (milRNAs) were identified in C. rosea, and 11 were downregulated in the Delta dcl2 mutant. In addition to putative endogenous gene targets, these milRNAs were predicted to target B. cinerea and F. graminearum virulence factor genes, which showed an increased expression during interaction with the Delta dcl2 mutant incapable of producing the targeting milRNAs. In summary, this study constitutes the first step in elucidating the role of RNAi in mycoparasitic interactions, with important implications for biological control of plant diseases, and poses the base for future studies focusing on the role of cross-species RNAi regulating mycoparasitic interactions.IMPORTANCE Small RNAs mediated RNA interference (RNAi) known to regulate several biological processes. Dicer-like endoribonucleases (DCLs) play a vital role in the RNAi pathway by generating sRNAs. In this study, we investigated a role of DCL-mediated RNAi in interference interactions between mycoparasitic fungus Clonostachys rosea and the two fungal pathogens Botrytis cinerea and Fusarium graminearum (here called mycohosts). We found that the dcl mutants were not able to produce 11 sRNAs predicted to finetune the regulatory network of genes known to be involved in production of hydrolytic enzymes, antifungal compounds, and membrane transporters needed for antagonistic action of C. rosea. We also found C. rosea sRNAs putatively targeting known virulence factors in the mycohosts, indicating RNAi-mediated cross-species communication. Our study expanded the understanding of underlying mechanisms of cross-species communication during interference interactions and poses a base for future works studying the role of DCL-based cross-species RNAi in fungal interactions

Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens

P. aeruginosa strain FG106 was isolated from the rhizosphere of tomato plants and identified through morphological analysis, 16S rRNA gene sequencing, and whole-genome sequencing. In vitro and in vivo experiments demonstrated that this strain could control several pathogens on tomato, potato, taro, and strawberry. Volatile and non-volatile metabolites produced by the strain are known to adversely affect the tested pathogens. FG106 showed clear antagonism against Alternaria alternata, Botrytis cinerea, Clavibacter michiganensis subsp. michiganensis, Phytophthora colocasiae, P. infestans, Rhizoctonia solani, and Xanthomonas euvesicatoria pv. perforans. FG106 produced proteases and lipases while also inducing high phosphate solubilization, producing siderophores, ammonia, indole acetic acid (IAA), and hydrogen cyanide (HCN) and forming biofilms that promote plant growth and facilitate biocontrol. Genome mining approaches showed that this strain harbors genes related to biocontrol and growth promotion. These results suggest that this bacterial strain provides good protection against pathogens of several agriculturally important plants via direct and indirect modes of action and could thus be a valuable bio-control agent