Louise R. Cooke

Genome analyses of an aggressive and invasive lineage of the Irish potato famine pathogen.

Pest and pathogen losses jeopardise global food security and ever since the 19th century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

Changes in sensitivity to DMI fungicides in Rhynchosporium secalis

Abstract Laboratory tests on 2000 isolates of Rhynchosporium secalis from throughout the UK over a 4-year period revealed a decline in sensitivity to triadimenol and propiconazole but not to prochloraz. Change occurred throughout the UK irrespective of disease pressure, and was not correlated with fungicide use. Resistant isolates were no less pathogenic than sensitive ones. Selection with triadimenol generated a bimodal population distribution, whereas propiconazole produced a gradual shift of unimodal population towards a less sensitive mean. Some cross-resistance occurred between triadimenol, propiconazole and a third triazole, tebuconazole, although the change in sensitivity to tebuconazole was always less than to the other two triazoles. No cross-resistance was observed to the imidazole demethylation inhibitor (DMI), prochloraz. Field-trial data collected over several years showed that the performance of triadimenol, and to a lesser extent, of propiconazole, had declined. Control of Rhynchosporium with these fungicides could be improved by using mixtures with carbendazim. Tebuconazole, either alone or in mixtures with carbendazim or tridemorph, provided the best disease control, and did not appear to select for lower sensitivity. The findings emphasize that certain DMI fungicides may still be used in strategies where performance of other DMIs has been altered because of resistance.

European Union policy on pesticides: implications for agriculture in Ireland

European Community (EC) legislation has limited the availability of pesticide active substances used in effective plant protection products. The Pesticide Authorisation Directive 91/414/EEC introduced the principle of risk assessment for approval of pesticide active substances. This principle was modified by the introduction of Regulation (EC) 1107/2009, which applies hazard, the intrinsic toxicity of the active substance, rather than risk, the potential for hazard to occur, as the approval criterion. Potential impacts of EC pesticide legislation on agriculture in Ireland are summarised. While these will significantly impact on pesticide availability in the medium to long term, regulations associated with water quality (Water Framework Directive 2000/60/EC and Drinking Water Directive 1998/83/EC) have the potential to restrict pesticide use more immediately, as concerns regarding public health and economic costs associated with removing pesticides from water increase. This rationale will further reduce the availability of effective pesticide active substances, directly affecting crop protection and increasing pesticide resistance within pest and disease populations. In addition, water quality requirements may also impact on important active substances used in plant protection in Ireland. The future challenge for agriculture in Ireland is to sustain production and profitability using reduced pesticide inputs within a framework of integrated pest management.

Phenotypic and genotypic characterisation of Northern Ireland isolates of Phytophthora infestans

Genetic and phenotypic diversity of the population of the late blight pathogen Phytophthora infestans in Northern Ireland was assessed from 223 single-lesion isolates collected from 29 sites in 1995 and 1996. The proportion of metalaxyl-resistant isolates was approximately 14%. The A2 mating type was not detected. Allozyme analyses revealed that the Northern Ireland isolates were monomorphic and homozygous at the loci coding for allozymes of glucose-6-phosphate isomerase and peptidase (Gpi 100/100, Pep 100/100). The majority of isolates tested (156 out of 162) were mitochondrial DNA haplotype IIa. Among the remaining isolates, four were haplotype Ia, two were the rare IIb haplotype and none was of the old Ib type. RAPD-PCR analysis of selected isolates revealed relatively little diversity among the Northern Ireland isolates, which clustered separately from isolates from GB and the European mainland.

Effects of fungicides used to control Rhynchosporium secalis where benzimidazole resistance is present

Abstract The effects of fungicides used to control Rhynchosporium secalis in winter barley were investigated in five field trials in Co. Down, Northern Ireland. Benzimidazole resistance was present in the R. secalis population of each site. Fungicide performance was evaluated in terms of disease control, maintenance of green leaf area, grain yield and grain quality. Samples of R. secalis isolates taken before and after treatment in each field were assessed for sensitivity to carbendazim in the laboratory. Carbendazim contributed little to disease control, the maintenance of green leaf area, grain yield or grain quality. Carbendazim was associated with a significant increase in disease severity in some plots. Treatments containing carbendazim, either alone or in mixture, caused an increase in the proportion of carbendazim-resistant isolates within R. secalis populations. Propiconazole-containing treatments performed well in terms of disease control, maintenance of green leaf area and grain quality. They caused no change in carbendazim resistance frequency.

The Influence of Fungicide Sprays on Infection Of Apple cv. Bramley's Seedling By Nectria galligena

In 1990, a long-term trial was initiated by planting young apple trees, cv. Bramleys Seedling, inoculated, at single sites in the leader shoots, with Nectria galligena. The effect of spring–summer and autumn fungicide spray programmes, applied during 1991–1993, on the development of new cankers was assessed up to May 1994. Spring–summer fungicide programmes, applied as for the control of apple scab, reduced numbers of new cankers by between 65% and 76% compared with the untreated control. Sterol demethylation inhibiting fungicides (hexaconazole, myclobutanil, penconazole) had a similar effect on canker to dithianon. Autumn application of copper oxychloride at 5% and 50% leaf-fall further reduced numbers of new cankers. The combination of a spring–summer benzimidazole (carbendazim or thiophanate-methyl) with a scab fungicide (dithianon) and autumn copper oxychloride did not improve canker control compared with applying copper oxychloride after spring–summer myclobutanil+mancozeb. The percentage of fruit which developed rots in long-term storage was decreased by spring–summer benzimidazole application, but not by other fungicide programmes even those which achieved similar levels of canker control.

Benzimidazole resistance in Rhynchosporium secalis and its effect on barley leaf blotch control in the UK

Abstract Surveys of the benzimidazole sensitivity of Rhynchosporium secalis isolates collected from winter barley crops throughout England, Wales and Northern Ireland were carried out in the early 1990s. In Northern Ireland, the frequency of highly benzimidazole-resistant strains increased significantly between 1990 and 1992, but did not change thereafter, having reached an equilibrium at about 40%. In England and Wales, 14 and 17% of isolates were resistant in 1992 and 1993, respectively. Differences in the frequency of carbendazim resistance were found for isolates from different cultivars. Carbendazim resistance was particularly prevalent in the wetter regions, more conducive to proliferation of R. secalis , but did not seem to be strongly correlated with levels of carbendazim use. In field trials carried out in various parts of the UK, carbendazim’s performance in controlling R. secalis was correlated weakly but significantly with the frequency of carbendazim-resistant strains of the pathogen.

Characteristics of Phytophthora infestans isolates from Uruguay

Isolates of Phytophthora infestans were obtained from late blighted plants from several potato-growing regions of Uruguay in 1998 and 1999. Of these, 25 representative isolates (4 from 1998, 21 from 1999) from the main potato-growing areas of the country, were characterised in terms of mating type, metalaxyl resistance, allozyme genotype, mitochondrial haplotype, RG57 fingerprint (1999 isolates only) and pathotype. All isolates proved to be A2 mating type, monomorphic and homozygous at the loci coding for glucose-6-phosphate isomerase and peptidase (Gpi 100/100, Pep 100/100) and to possess mitochondrial haplotype IIa. Metalaxyl-resistant isolates constituted 92% of the total. All the 1999 isolates possessed the same RG57 fingerprint, which was that previously reported as associated with the clonal lineage BR-1 from Brazil and Bolivia, which is also A2, Gpi 100/100, Pep 100/100. Most of the isolates displayed broad-spectrum virulence and five carried virulence to 10 of the 11 R genes tested despite the absence of R genes in commercially grown potato cultivars. It was concluded that the Uruguayan P. infestans isolates resembled isolates from neighbouring South American countries, notably Brazil, and belong to the new populations of the pathogen now predominant in many countries.

Incidence of the A2 mating type ofPhytophthora infestans on potato crops in Northern Ireland

SummaryOf 250 isolates ofPhytophthora infestans obtained from Northern Ireland potato crops between 1981 and 1993, only six proved to be of the A2 mating type, the remainder being A1. The first A2 isolate was obtained from a tuber in 1987. The frequency of A2 isolates from 1987 onwards was 3%, a lower incidence than has been reported for England and Wales and the Republic of Ireland. There was no association between phenylamide resistance and mating type.

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland.

Here we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum genetic lineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012. Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within the clonal lineage that can be useful for tracking its spread.