Biology subjects

Karisto, P.

Publications and source records attributed to Karisto, P..

11 recordsLinked to original sources

bioRxiv2025

Carrot storage diseases predominantly caused by mixed fungal infections

Fungal pathogens often cause severe post-harvest losses in stored carrot yields. In 2020 and 2021, carrot samples were collected in Finland from 26 fields with different soil types. The proportion of symptomatic carrots was assessed at two time points during the cold storage period. To analyse the occurrence of different fungal pathogens in the symptomatic carrots, DNA samples were prepared and tested for the presence of fungal pathogens by species-specific PCR. The most frequently detected pathogens were Cylindrocarpon spp. with 61% occurrence, followed by Fusarium avenaceum (44%), Mycocentrospora acerina (42%), Botrytis cinerea (12%), and Alternaria spp. (0.8%). B. cinerea and F. avenaceum were more common in carrots grown on organic soil type, while M. acerina was more common in carrots grown on mineral soils. Mixed fungal infections were overrepresented in the symptomatic samples, in particular, Cylindrocarpon spp. often occurred together with F. avenaceum and M. acerina in the same samples. Amplicon sequencing of the fungal internal transcribed spacer region from the DNA of symptomatic tissues revealed that in addition to the pathogens - B. cinerea, M. acerina, Cylindrocarpon spp. and Sclerotinia sclerotiorum - the hyphomycete fungi Tetracladium spp. and the yeast Leucosporidium intermedium were abundant, and that Tetracladium spp. were more abundant in the carrots infected with M. acerina. A pathogenicity test confirmed that F. avenaceum is pathogenic to both the new season and old season carrots.

plant biology↗

bioRxiv2025

High microbial diversity in the rhizosphere and soil improve carrot (Daucus carota L.) postharvest storability

Postharvest diseases can cause significant losses in carrot (Daucus carota) yield during storage. In this study, the effects of soil quality and microbial diversity in the field bulk soil and rhizosphere on the development of postharvest diseases were investigated. Microbial genera in bulk soil and rhizosphere samples were identified by Illumina Miseq amplicon sequencing of bacterial 16S and fungal ITS regions. Disease symptoms in the stored carrots were monitored after six months of cold storage, and the main pathogens were identified. The field sites with mineral soils, which had a higher pH, had a higher bacterial and fungal diversity than organic soils. The organically managed fields had a higher bacterial diversity than the conventionally managed fields. Community structure of both bacteria and fungi was largely driven by field site including its main chemical characteristics, with rhizosphere and bulk soil samples from the same site displaying comparable assemblages. Higher soil microbial diversity was associated with higher postharvest storability in the stored carrots. The weather during the growing season also had an effect on the observed fungal biodiversity, which was higher at sites that had lower temperatures and less rain prior to harvest.

microbiology↗

bioRxiv2022

Positive fitness effects help explain the broad range of Wolbachia prevalences in natural populations

The bacterial endosymbiont Wolbachia is best known for its ability to modify its hosts reproduction by inducing cytoplasmic incompatibility (CI) to facilitate its own spread. Classical models predict either near-fixation of costly Wolbachia once the symbiont has overcome a threshold frequency (invasion barrier), or Wolbachia extinction if the barrier is not overcome. However, natural populations do not all follow this pattern: Wolbachia can also be found at low frequencies (below one half) that appear stable over time. Wolbachia is known to have pleiotropic fitness effects (beyond CI) on its hosts. Existing models typically focus on the possibility that these are negative. Here we consider the possibility that the symbiont provides direct benefits to infected females (e.g. resistance to pathogens) in addition to CI. We discuss an underappreciated feature of Wolbachia dynamics: that CI with additional fitness benefits can produce low-frequency (< 1/2) stable equilibria. Additionally, without a direct positive fitness effect, any stable equilibrium close to one half will be sensitive to perturbations, which make such equilibria unlikely to sustain in nature. The results hold for both diplodiploid and different haplodiploid versions of CI. We suggest that insect populations showing low-frequency Wolbachia infection might host CI-inducing symbiotic strains providing additional (hidden or known) benefits to their hosts, especially when classical explanations (ongoing invasion, source-sink dynamics) have been ruled out.

ecology↗

bioRxiv2021

Measuring splash-dispersal of a major wheat pathogen in the field

Capacity for dispersal is a fundamental fitness component of plant pathogens. Empirical characterization of plant pathogen dispersal is of prime importance for understanding how plant pathogen populations change in time and space. We measured dispersal of Zymoseptoria tritici in natural environment. Primary disease gradients were produced by rain-splash driven dispersal and subsequent transmission via asexual pycnidiospores from infected source. To achieve this, we inoculated field plots of wheat (Triticum aestivum) with two distinct Z. tritici strains and a 50/50 mixture of the two strains. We measured effective dispersal of the Z. tritici population based on pycnidia counts using automated image analysis. The data were analyzed using a spatially-explicit mathematical model that takes into account the spatial extent of the source. We employed robust bootstrapping methods for statistical testing and adopted a two-dimensional hypotheses test based on the kernel density estimation of the bootstrap distribution of parameter values. Genotyping of re-isolated pathogen strains with strain-specific PCR-reaction further confirmed the conclusions drawn from the phenotypic data. The methodology presented here can be applied to other plant pathosystems. We achieved the first estimates of the dispersal kernel of the pathogen in field conditions. The characteristic spatial scale of dispersal is tens of centimeters - consistent with previous studies in controlled conditions. Our estimation of the dispersal kernel can be used to parameterize epidemiological models that describe spatial-temporal disease dynamics within individual wheat fields. The results have the potential to inform spatially targeted control of crop diseases in the context of precision agriculture.

plant biology↗

bioRxiv2020

A population-level invasion by transposable elements in a fungal pathogen

AO_SCPLOWBSTRACTC_SCPLOWGenome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2,456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogens center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.

genomics↗

bioRxiv2019

Spatially-explicit modeling improves empirical characterization of dispersal: theory and a case study

Dispersal is a key ecological process, but remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source one can acquire a dispersal gradient. Although dispersal gradients contain information on dispersal, they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge on dispersal? One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination point. However, the validity of this approximation cannot be established before conducting measurements. We formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. We re-analyzed published dispersal gradients for three major plant pathogens. We also demonstrated using simulations that this approach provides more accurate estimates of dispersal kernels across biologically plausible scenarios. We concluded that the three plant pathogens disperse over substantially shorter distances compared to conventional estimates. Using this method, a significant proportion of published dispersal gradients can be re-analyzed to improve our knowledge about spatial scales of dispersal. Thus, our results can boost progress in characterization of dispersal across taxa.

ecology↗

bioRxiv2019

In-field detection and quantification of Septoria tritici blotch in diverse wheat germplasm using spectral-temporal features

Hyperspectral remote sensing holds the potential to detect and quantify crop diseases in a rapid and non-invasive manner. Such tools could greatly benefit resistance breeding, but their adoption is hampered by i) a lack of specificity to disease-related effects and ii) insufficient robustness to variation in reflectance caused by genotypic diversity and varying environmental conditions, which are fundamental elements of resistance breeding.\n\nWe hypothesized that relying exclusively on temporal changes in canopy reflectance during pathogenesis may allow to specifically detect and quantify crop diseases whilst minimizing the confounding effects of genotype and environment. To test this hypothesis, we collected time-resolved canopy hyperspectral reflectance data for 18 diverse genotypes on infected and disease-free plots and engineered spectral-temporal features representing this hypothesis.\n\nOur results confirm the lack of specificity and robustness of disease assessments based on reflectance spectra at individual time points. We show that changes in spectral reflectance over time are indicative of the presence and severity of septoria tritici blotch (STB) infections. Furthermore, the proposed time-integrated approach facilitated the delineation of disease from physiological senescence, which is pivotal for efficient selection of STB-resistant material under field conditions. A validation of models based on spectral-temporal features on a diverse panel of >300 wheat genotypes offered evidence for the robustness of the proposed method. This study demonstrates the potential of time-resolved canopy reflectance measurements for robust assessments of foliar diseases in the context of resistance breeding.

plant biology↗

bioRxiv2019

Improved control of Septoria tritici blotch in durum wheat using cultivar mixtures

Mixtures of cultivars with contrasting levels of resistance can suppress infectious diseases in wheat, as demonstrated in numerous field experiments. Most studies focused on airborne pathogens in bread wheat, while splash-dispersed pathogens have received less attention, and no studies have been conducted in durum wheat. We conducted a two-year field experiment in Tunisia, to evaluate the performance of cultivar mixtures with varying proportions of resistance (0-100%) in controlling the polycyclic, splash-dispersed disease Septoria tritici blotch (STB) in durum wheat. To measure STB severity, we used a high-throughput method based on digital image analysis of 3074 infected leaves collected from 42 and 40 experimental plots during the first and second years, respectively. This allowed us to quantify pathogen reproduction on wheat leaves and to acquire a large dataset that exceeds previous studies with respect to accuracy and precision. Our analyses show that introducing only 25% of a disease-resistant cultivar into a pure stand of a susceptible cultivar provides a substantial reduction of almost 50% in disease severity compared to the susceptible pure stand. However, comprising the resistant component of two cultivars instead of one did not further improve disease control, contrary to predictions of epidemiological theory. Susceptible cultivars can be agronomically superior to resistant cultivars or be better accepted by growers for other reasons. Hence, if mixtures with only a moderate proportion of the resistant cultivar provide a similar degree of disease control as resistant pure stands, as our analysis indicates, such mixtures are more likely to be accepted by growers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/664078v3_ufig1.gif" ALT="Figure 1"> View larger version (100K): org.highwire.dtl.DTLVardef@1d153c3org.highwire.dtl.DTLVardef@1d23ca7org.highwire.dtl.DTLVardef@18c3045org.highwire.dtl.DTLVardef@b504db_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2018

Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch in European winter wheat

O_LIAccurate, high-throughput phenotyping for quantitative traits is the limiting factor for progress in plant breeding. We developed automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance.\nC_LIO_LI335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform a GWAS.\nC_LIO_LIWe identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four resistance traits. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance.\nC_LIO_LIOur experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes.\nC_LI

plant biology↗

bioRxiv2018

Measurement of infection efficiency of a major wheat pathogen using time-resolved imaging of disease progress

Infection efficiency is a key epidemiological parameter that determines the proportion of pathogen spores able to infect and cause lesions once they have landed on a susceptible plant tissue. In this study, we present an improved method to measure infection efficiency of Zymoseptoria tritici using a replicated greenhouse experiment. Z. tritici is a fungal pathogen that infects wheat leaves and causes Septoria tritici blotch (STB), a major disease of wheat worldwide.\n\nWe devised an original experimental setup, where we (i) attached living wheat leaves to metal plates allowing for time-resolved imaging of disease progress in planta. Since lesions were continuously appearing, expanding and merging during the period of up to three weeks, daily measurements were necessary for accurate counting of lesions. We also (ii) used reference membranes to characterize the density and the spatial distribution of inoculated spores on leaf surfaces. In this way, we captured the relationship between the number of lesions and the number of viable spores deposited on the leaves and estimated the infection efficiency of about 4 % from the slope of this relationship.\n\nOur study provides a proof of principle for an accurate and reliable measurement of infection efficiency of Z. tritici. The method opens opportunities for determining the genetic basis of the component of quantitative resistance that suppresses infection efficiency. This knowledge would improve breeding for quantitative resistance against STB, a control measure considered more durable than deployment of major resistance genes.

epidemiology↗

bioRxiv2017

Ranking quantitative resistance to Septoria tritici blotch in elite wheat cultivars using automated image analysis

Quantitative resistance is likely to be more durable than major gene resistance for controlling Septoria tritici blotch (STB) on wheat. Earlier studies hypothesized that resistance affecting the degree of host damage, as measured by the percentage of leaf area covered by STB lesions, is distinct from resistance that affects pathogen reproduction, as measured by the density of pycnidia produced within lesions. We tested this hypothesis using a collection of 335 elite European winter wheat cultivars that was naturally infected by a diverse population of Zymoseptoria tritici in a replicated field experiment. We used automated image analysis (AIA) of 21420 scanned wheat leaves to obtain quantitative measures of conditional STB intensity that were precise, objective, and reproducible. These measures allowed us to explicitly separate resistance affecting host damage from resistance affecting pathogen reproduction, enabling us to confirm that these resistance traits are largely independent. The cultivar rankings based on host damage were different from the rankings based on pathogen reproduction, indicating that the two forms of resistance should be considered separately in breeding programs aiming to increase STB resistance. We hypothesize that these different forms of resistance are under separate genetic control, enabling them to be recombined to form new cultivars that are highly resistant to STB. We found a significant correlation between rankings based on automated image analysis and rankings based on traditional visual scoring, suggesting that image analysis can complement conventional measurements of STB resistance, based largely on host damage, while enabling a much more precise measure of pathogen reproduction. We showed that measures of pathogen reproduction early in the growing season were the best predictors of host damage late in the growing season, illustrating the importance of breeding for resistance that reduces pathogen reproduction in order to minimize yield losses caused by STB. These data can already be used by breeding programs to choose wheat cultivars that are broadly resistant to naturally diverse Z. tritici populations according to the different classes of resistance.

plant biology↗