Biology subjects

Kildea, S.

Publications and source records attributed to Kildea, S..

4 recordsLinked to original sources

bioRxiv2025

Detection of resistance in Phytophthora infestans to the carboxylic acid amide (CAA) fungicides using digital droplet PCR.

BackgroundPotato late blight caused by Phytophthora infestans remains the greatest biotic threat to potato production globally. In northern Europe to prevent the disease and associated yield losses fungicides are heavily relied upon, with multiple applications required during the potato growing season. Unfortunately, such intensive fungicide usage has the potential to compromise control efficacy as it puts in place immense selective pressure for the emergence and spread of fungicide resistant strains of P. infestans. In recent years this scenario has been realised, with the emergence of strains resistant to the carboxylic acid amide (CAA) fungicides. As resistance to the CAA fungicides in P. infestans has been confirmed to result from changes in the pathogens cellulose synthase A3 gene (CesA3), specifically at amino acid position 1105, it opens the possibility to develop molecular tools to rapidly monitor populations of the pathogen for the resistance allele. ResultsUsing the Stilla nacia 3-colour system a droplet digital PCR (ddPCR) was successfully developed to simultaneously detect the P. infestans CesA3 gene irrespective of its CAA sensitivity status, and either the CAA wild-type sequence for position 1105 or that conferring the resistant allele G1105S. Using a drop-off in ratio of positive droplets for either the wild-type or G1105S alleles relative to those positive for the general P. infestans CesA3 it was also possible to demonstrate that using the assay other potential alterations known to confer resistance that may occur at this position (e.g. G1105V) can be detected. The assay was validated using multiple sources of P. infestans DNA, including FTA cards. ConclusionsThe assay developed will allow for the accurate and sensitive detection of CAA resistance conferred by alterations at amino acid position 1105 in the CesA3 gene in P. infestans. The capacity to use the assay with multiple DNA sources and potential to adapt the drop-off approach to different ddPCR platforms will ensure its applicability to the wider P. infestans community in monitoring the continued use of CAA-based fungicides for P. infestans management.

microbiology↗

bioRxiv2024

Barley disease screening: a multiplex digital droplet PCR approach for the detection of Ramularia collo-cygni, Rhynchosporium graminicola and Pyrenophora teres

Barley is the most widely grown cereal crop in Ireland and faces substantial yield loss annually due to airborne, seed-borne, and soil-borne pathogens. The most prevalent and destructive of these include ramularia leaf spot, barley leaf scald and net blotch, caused by Ramularia collo-cygni, Rhynchosporium graminicola and Pyrenophora teres respectively. Infected seeds are considered as the major source of inoculum for these diseases. The absence of varietal resistance for these fungal pathogens suggests the need for better disease management strategies. Accurate pathogen detection is one of the most widely accepted disease management strategies. To facilitate such detections in complex samples, such as seed, we demonstrate two digital droplet PCR (ddPCR) assays, with the initial assay capable of detecting R. graminicola, R.collo-cygni and P. teres. For those identified as positive for P. teres samples, a form-specific assay was designed to distinguish between the two economically significant forms of P. teres; P. teres f. maculata (Ptm; spot form of net blotch) and P. teres f. teres (Ptt; net form of net blotch). The assay offers sensitive and specific pathogen detection from barley seeds up to pico moles/{micro}l level. Limits of detection for R. graminicola, R. collo-cygni and P. teres in the triplex assay were calculated as 1.67 cp/{micro}l, 1.06 cp/{micro}l and 4.21 cp/{micro}l respectively. For form-specific assay, limits of detection were calculated as 1.44 cp/{micro}l for Ptt and 0.82 cp/{micro}l for Ptm assay. Finally, the efficacy of the assay was demonstrated by screening a collection of historical barley seeds.

pathology↗

bioRxiv2024

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

Agricultural diseases are a major threat to sustainable food production. Yet, for many pathogens we know exceptionally little about their epidemiological and population dynamics, and this knowledge gap is slowing the development of efficient control strategies. Here we study the population genomics and molecular epidemiology of wheat powdery mildew, a disease caused by the biotrophic fungus Blumeria graminis forma specialis tritici (Bgt). We sampled Bgt for two consecutive years, 2022 and 2023, from 22 countries in Europe and surrounding regions, and compiled a genomic dataset of 415 Bgt isolates. We found one single epidemic unit in the north of Europe, consisting of a highly homogeneous population. Conversely, the south of Europe hosts smaller local populations which are less interconnected. In addition, we show that the population structure can be largely predicted by the prevalent wind patterns. We identified several loci that were under selection in the recent past, including fungicide targets and avirulence genes. Some of these loci are common between populations, while others are not, suggesting different local selective pressures. We reconstructed the evolutionary history of one of these loci, AvrPm17, coding for an effector recognized by the wheat receptor Pm17. We found evidence for a soft sweep on standing genetic variation. Multiple AvrPm17 haplotypes, which can partially escape recognition by Pm17, spread rapidly throughout the continent upon its introduction in the early 2000s. We also identified a new virulent variant, which emerged more recently and can evade Pm17 resistance altogether. Overall, we highlight the potential of genomic surveillance in resolving the evolutionary and epidemiological dynamics of agricultural pathogens, as well as in guiding control strategies.

evolutionary biology↗

bioRxiv2021

Genome-wide identification of the oat MLO family and identification of a candidate AsMLO associated with powdery mildew susceptibility

Blumeria graminis f. spp. avenae is the causal agent of powdery mildew disease in oats (Avena sativa). It is the most significant limiting factor to oat production, with yield losses ranging from 5%-40%, during high disease pressure conditions. Certain members of the Mildew Locus O (MLO) gene family have been shown to act as powdery mildew susceptibility factors in many different plant species. A loss-of-function mutation of specific MLO genes confers broad-spectrum resistance against powdery mildew pathogens. Potential MLO candidates have not yet been identified in oats. In this study, we identified oat MLOs by querying 341 known MLO protein sequences against the publicly available oat genome. 11 MLO-like sequences were identified in oats. Phylogenetic analysis grouped these candidates into four different clades, one of which, AsMLO1 was grouped together with other cereal MLOs functionally known to contribute to powdery mildew susceptibility. AsMLO1 showed the highest similarity to the known powdery mildew-associated MLO proteins from wheat and barley. Gene expression analysis revealed AsMLO1 expression is up regulated at 12 hours post-infection with Bga and was inferred to be a candidate gene associated with powdery mildew susceptibility in oats. These results are an important step towards more durable strategies to control powdery mildew incidence and severity in oats.

plant biology↗