Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici

Fungicide resistance has become a challenging problem in management of Septoria tritici blotch (STB), caused by Zymoseptoria tritici, the most destructive disease of winter wheat throughout western and northern Europe. To ensure the continued effectiveness of those fungicides currently used, it is essential to monitor the development and spread of such resistance in field populations of the pathogen. Since resistance to the key families of fungicides used for STB control (demethyalation inhibitors or azoles, succinate dehydrogenase inhibitors or SDHIs and Quinone outside Inhibitors or QoIs) is conferred through target-site mutations, the potential exists to monitor resistance through the molecular detection of alterations in the target site genes. As more efficient fungicides were developed and applied, the pathogen has continuously adapted through accumulating multiple target-site alterations. In order to accurately monitor these changes in field populations, it is therefore becoming increasingly important to completely sequence the targeted genes. Here we report the development of a PacBio assay that facilitates the multiplex amplification and long-read sequencing of the target gene(s) for the azole (CYP51), SDHI (Sdh B, C, and D), and QoI (cytochrome b) fungicides. The assay was developed and optimised using three Irish Z. tritici collections established in spring 2017, which capture the range of fungicide resistance present in modern European populations of Z. tritici. The sequences obtained through the PacBio assay were validated using traditional Sanger sequencing and in vitro sensitivity screenings. To further exploit the long-read and high throughput potential of PacBio sequencing, an additional nine housekeeping genes (act, BTUB, cal, cyp, EF1, GAPDH, hsp80-1, PKC, TFC1) were sequenced and used to provide comprehensive Z. tritici strain genotyping.

Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden

BACKGROUND

Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides.

RESULTS

Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.

CONCLUSIONS

Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.

Considerations in evaluating new treatment alternatives following peripheral nerve injuries: A prospective clinical study of methods used to investigate sensory, motor and functional recovery

The current problem finding reliable and objective methods for evaluating results after peripheral nerve repair is a challenge when introducing new clinical techniques. The aim of this study was to obtain reference material and to evaluate the applicability of different tests used for clinical assessment after peripheral nerve injuries. Fifteen patients with a history of complete median nerve transsection and repair, and 15 healthy volunteers were included. Each subject was investigated using a battery of conventional and new tests for functional, sensory and motor recovery including questionnaires, clinical evaluations, neurophysiological and physiological findings. The results were statistically analysed and comparisons were made within the patient group and between patients and healthy volunteers using a 'per protocol' and an 'intention to treat' approach. Criteria for success were stipulated in order to be able to judge the usefulness of each method. The results showed that 19 of 34 variables, representing six of 16 methods, were not able to fulfil the criteria and were thus questionable for the evaluations of nerve repair in a clinical trial setting. However, 2pd, sensory recovery according to the non-modified British Medical Research Council, sensory neurography, manual muscle test, electromyography, questionnaires (i.e. DASH and the 4 question form) and performance tests (i.e. AMPS and Sollerman's subtests 4 and 8) did fulfil the criteria defined for being useful.

The prevalence of dementia in 95 year olds

The authors determined the prevalence of dementia in 338 (response rate 65%) 95-year-old persons, living in Göteborg, Sweden, and compared the result with a previously examined population sample of 85 year olds. The prevalence of dementia according to the Diagnostic and Statistical Manual of Mental Disorders (3rd rev. ed) was higher in women (55%) than in men (37%) at age 95, and the proportion of mild dementia and vascular dementia was lower in 95 than in 85 year olds.