Age-Dependent Resistance to Rhizoctonia solani in Sugar Beet

Understanding the sugar beet holobiont for sustainable agriculture

The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.

The effect of mature plant resistance in sugar beet (Beta vulgaris spp. vulgaris) on survival, fecundity and behaviour of green peach aphids (Myzus persicae)

Several studies have shown the negative effects of mature plant resistance (MPR) on aphids in sugar beet, which is correlated to the formation of black deposits in their stomach. However, the underlying mechanism of MPR still needs to be elucidated, by understanding the toxicity effects of MPR on aphids and the role of the plant phenological stage and the environment. Here, we report that MPR in sugar beet does not only affect Myzus persicae mortality rate and the formation of a black deposit in the aphid stomach, but also aphid fecundity and behaviour. In addition, experiments in climate-controlled and field settings showed quantitative variation in MPR to M. persicae between six genotypes of sugar beet. Our results indicate that environmental effects, such as temperature, play a major role in MPR and underscore the importance of proper climate-controlled experiments for investigating MPR. In climate-controlled experiments, 83.3% of aphids on old leaves developed a black deposit, in contrast to only 16.8% of aphids on young leaves. This shows that not only plant age, but also leaf age plays a major role in the intensity of MPR. Further research will be needed to identify the underlying mechanism, before MPR can be used as a viable and sustainable solution to aphid pests in sugar beet.

Can disease resistance evolve independently at different ages? Genetic variation in age-dependent resistance to disease in three wild plant species

Juveniles are typically less resistant (more susceptible) to infectious disease than adults, and this difference in susceptibility can help fuel the spread of pathogens in age-structured populations. However, evolutionary explanations for this variation in resistance across age remain to be tested.One hypothesis is that natural selection has optimized resistance to peak at ages where disease exposure is greatest. A central assumption of this hypothesis is that hosts have the capacity to evolve resistance independently at different ages. This would mean that host populations have (a) standing genetic variation in resistance at both juvenile and adult stages, and (b) that this variation is not strongly correlated between age classes so that selection acting at one age does not produce a correlated response at the other age.Here we evaluated the capacity of three wild plant species (Silene latifolia, S. vulgaris and Dianthus pavonius) to evolve resistance to their anther-smut pathogens (Microbotryum fungi), independently at different ages. The pathogen is pollinator transmitted, and thus exposure risk is considered to be highest at the adult flowering stage.Within each species we grew families to different ages, inoculated individuals with anther smut, and evaluated the effects of age, family and their interaction on infection.In two of the plant species, S. latifolia and D. pavonius, resistance to smut at the juvenile stage was not correlated with resistance to smut at the adult stage. In all three species, we show there are significant age × family interaction effects, indicating that age specificity of resistance varies among the plant families. Synthesis. These results indicate that different mechanisms likely underlie resistance at juvenile and adult stages and support the hypothesis that resistance can evolve independently in response to differing selection pressures as hosts age. Taken together our results provide new insight into the structure of genetic variation in age-dependent resistance in three well-studied wild host-pathogen systems.

Molecular Mechanisms Associated with the Resistance of Rhizoctonia solani AG-4 Isolates to the Succinate Dehydrogenase Inhibitor Thifluzamide

Thifluzamide, a succinate dehydrogenase (SDH) inhibitor, possesses high activity against Rhizoctonia. In this study, 144 Rhizoctonia solani AG-4 (4HGI, 4HGII, and 4HGIII) isolates, the predominate pathogen associated with sugar beet seedling damping-off, were demonstrated to be sensitive to thifluzamide with a calculated mean median effective concentration of 0.0682 ± 0.0025 μg/ml. Thifluzamide-resistant isolates were generated using fungicide-amended media, resulting in four AG-4HGI isolates and eight AG-4HGII isolates with stable resistance and almost no loss in fitness. Evaluation of cross-resistance of the 12 thifluzamide-resistant isolates and their corresponding parental-sensitive isolates revealed a moderately positive correlation between thifluzamide resistance and the level of resistance to eight other fungicides from three groups, the exception being fludioxonil. An active efflux of fungicide through ATP-binding cassette and major facilitator superfamily transporters was found to be correlated to the resistance of R. solani AG-4HGII isolates to thifluzamide based on RNA-sequencing and quantitative reverse transcription-PCR analyses. Sequence analysis of sdhA, sdhB, sdhC, and sdhD revealed replacement of isoleucine by phenylalanine at position 61 in SDHC in 9 of the 12 generated thifluzamide-resistant isolates. No other mutations were found in any of the other genes. Collectively, the data indicate that the active efflux of fungicide and a point mutation in sdhC may contribute to the resistance of R. solani AG-4HGI and AG-4HGII isolates to thifluzamide in vitro. This is the first characterization of the potential molecular mechanism associated with the resistance of R. solani AG-4 isolates to thifluzamide and provides practical guidance for the use of this fungicide.

Select and Sequence of a Segregating Sugar Beet Population Provides Genomic Perspective of Host Resistance to Seedling Rhizoctonia solani Infection

Understanding the genetic basis of polygenic traits is a major challenge in agricultural species, especially in non-model systems. Select and sequence (SnS) experiments carried out within existing breeding programs provide a means to simultaneously identify the genomic background of a trait while improving the mean phenotype for a population. Using pooled whole genome sequencing (WGS) of selected and unselected bulks derived from a synthetic outcrossing sugar beet population EL57 (PI 663212), which segregates for seedling rhizoctonia resistance, we identified a putative genomic background involved in conditioning a resistance phenotype. Population genomic parameters were estimated to measure fixation (He), genome divergence (F ST ), and allele frequency changes between bulks (DeltaAF). We report on the genome wide patterns of variation resulting from selection and highlight specific genomic features associated with resistance. Expected heterozygosity (He) showed an increased level of fixation in the resistant bulk, indicating a greater selection pressure was applied. In total, 1,311 biallelic loci were detected as significant FST outliers (p < 0.01) in comparisons between the resistant and susceptible bulks. These loci were detected in 206 regions along the chromosomes and contained 275 genes. We estimated changes in allele frequency between bulks resulting from selection for resistance by leveraging the allele frequencies of an unselected bulk. DeltaAF was a more stringent test of selection and recovered 186 significant loci, representing 32 genes, all of which were also detected using FST. Estimates of population genetic parameters and statistical significance were visualized with respect to the EL10.2 physical map and produced a candidate gene list that was enriched for function in cell wall metabolism and plant disease resistance, including pathogen perception, signal transduction, and pathogen response. Specific variation associated with these genes was also reported and represents genetic markers for validation and prediction of resistance to Rhizoctonia. Select and sequence experiments offer a means to characterize the genetic base of sugar beet, inform selection within breeding programs, and prioritize candidate variation for functional studies.

Field Detection of Rhizoctonia Root Rot in Sugar Beet by Near Infrared Spectrometry

Rhizoctonia root and crown rot (RRCR) is an important disease in sugar beet production areas, whose assessment and control are still challenging. Therefore, breeding for resistance is the most practical way to manage it. Although the use of spectroscopy methods has proven to be a useful tool to detect soil-borne pathogens through leaves reflectance, no study has been carried out so far applying near-infrared spectroscopy (NIRS) directly in the beets. We aimed to use NIRS on sugar beet root pulp to detect and quantify RRCR in the field, in parallel to the harvest process. For the construction of the calibration model, mainly beets from the field with natural RRCR infestation were used. To enrich the model, artificially inoculated beets were added. The model was developed based on Partial Least Squares Regression. The optimized model reached a Pearson correlation coefficient (R) of 0.972 and a Ratio of Prediction to Deviation (RPD) of 4.131. The prediction of the independent validation set showed a high correlation coefficient (R = 0.963) and a root mean square error of prediction (RMSEP) of 0.494. These results indicate that NIRS could be a helpful tool in the assessment of Rhizoctonia disease in the field.

Sensitivity of Rhizoctonia solani Anastomosis Group 2-2 Isolates from Soybean and Sugar Beet to Selected SDHI and QoI Fungicides

Rhizoctonia solani causes root and stem diseases on soybean and sugar beet, and fungicides are commonly used to manage these diseases. Quinone outside inhibitor (QoI) fungicides (pyraclostrobin and azoxystrobin) have been used for in-furrow and postemergence application since 2000. Succinate dehydrogenase inhibitor (SDHI) fungicides (sedaxane, penthiopyrad, and fluxapyroxad) became popular seed treatments after their registration in Minnesota and North Dakota between 2012 and 2016. Periodic monitoring of sensitivity to these fungicides in R. solani anastomosis group (AG) 2-2 is important to detect potential shifts in sensitivity over time. R. solani AG 2-2 isolates (n = 35) collected from soybean and sugar beet in Minnesota and North Dakota were evaluated in vitro for sensitivity. Isolates were considered as baseline or nonbaseline for the above-mentioned fungicides based on previous potential exposure. The effective concentration (EC50) required to suppress radial fungal growth by 50% was determined. The mean EC50 values for sedaxane, penthiopyrad, fluxapyroxad, and pyraclostrobin were 0.1, 0.15, 0.16, and 0.25 (µg ml-1), respectively. The mean EC50 value for azoxystrobin for 22 isolates was 0.76 to 1.56 µg ml-1; and EC50 could not be determined for 13 isolates because of <50% inhibition at the highest concentrations used. The EC50 values for the QoI fungicides did not differ significantly between baseline and nonbaseline isolates. EC50 values for SDHI fungicides were significantly higher for isolates collected from soybean than from sugar beet, and isolates collected from both crops had similar EC50 values for pyraclostrobin. All SDHI fungicides and pyraclostrobin effectively suppressed R. solani isolates from soybean and sugar beet at low concentrations in vitro.

Effects of Inoculum Density and Cultivar Susceptibility on Rhizoctonia Damping-Off and Crown and Root Rot in Sugar Beet

Damping-off and crown and root rot of sugar beet caused by Rhizoctonia solani anastomosis group 2-2 (AG 2-2) are important soilborne diseases in Minnesota and North Dakota. Management involves an integrated approach, including crop rotation, use of resistant cultivars, and timely fungicide application. Our objectives were to evaluate the role of inoculum density and cultivar susceptibility on the onset and development of Rhizoctonia diseases and on yield and quality in sugar beet. Three cultivars varying in susceptibility were sown in field plots inoculated with 0, 20, 40, or 60 kg/ha of R. solani AG 2-2 IIIB infested barley during 2013 and 2015. In both years, there was a significant linear effect of inoculum density with decreasing area under the stand establishment curve (AUSEC), root yield, and sucrose quality as inoculum density increased. Cultivar susceptibility significantly affected AUSEC as well as sucrose quality in both years and root yield in 2013. In both years, there was an inoculum density by cultivar interaction on disease ratings, with the partially resistant cultivar resulting in lower ratings than the moderate and susceptible cultivars, especially as inoculum density increased. These results have implications for cultivar selection and for use and timing of postemergence fungicide application based on field history of inoculum pressure.

Effects of the Age-Related Resistance to Potato virus Y in Potato on the Systemic Spread of the Virus, Incidence of the Potato Tuber Necrotic Ringspot Disease, Tuber Yield, and Translocation Rates Into Progeny Tubers

The recombinant strain of potato virus Y (PVY), PVY^NTN, is the main cause of the potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars, which reduces the quality of potato tubers, in addition to the yield loss. Control of PVY has been the main challenge in most potato-producing areas. Here, the effects of the age-related resistance (ARR) were investigated in transplants of a potato cultivar Yukon Gold to the infection with PVY^NTN strain in greenhouse experiments. Within the first 3 weeks after transplanting into soil (week 1 [W1] to W3), Yukon Gold plants developed ARR that impaired the systemic movement of PVY^NTN into upper noninoculated leaves and concomitant translocation into progeny tubers starting from W4 after transplanting. The yield and quality of tubers from PVY-infected plants with the established ARR (W5 to W8) were comparable with the healthy controls, suggesting that late PVY infection would not significantly affect commercial potato production. Plants inoculated early (W1 to W2), before the establishment of the ARR, exhibited a 100% primary systemic infection with PVY^NTN and produced fewer tubers of smaller sizes, exhibiting PTNRD; this resulted ≤70% yield reduction compared with plants inoculated later in the season (W5 to W8). This ARR greatly restricted the systemic movement of PVY^NTN in the foliage and resulted in very limited translocation rates of the virus into tested progeny tubers: 7.8 and 4.1% in 2017 and 2018, respectively, of all plants inoculated later in the season (W5 to W8). This study suggests that PVY^NTN management programs in Yukon Gold seed potato should focus more on the early stages of the potato development before the onset of the ARR.