Using Allele-specific PCR for detecting multiple amino acid substitutions associated with SDHI resistance in Alternaria alternata causing Alternaria late blight in pistachio.

Alternaria late blight caused by Alternaria alternata is a major disease affecting pistachios grown in California and to some degree those grown in Arizona. Alternaria alternata is prone to quick fungicide resistance selection when single-mode of action fungicides are used. For the specific detection of five possible amino acid alterations associated with Alternaria alternata resistance to succinate dehydrogenase inhibitors used in California and Arizona pistachio orchards, we have designed five primer sets to be used as an allele-specific PCR assay (AS-PCR). Within a couple of hours from DNA extraction, the new specific-primers amplify the different PCR product sizes, according to the chosen target, allowing their differentiation on gel agarose. In our study, the AS-PCR assay consistently detected the mutations H277L and H277R at the AaSdhB gene, the mutations H134R and S135R at the AaSdhC gene, and the mutation D123E at the AaSdhD gene from A. alternata isolates collected from pistachio orchards in California and Arizona. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides a rapid and cost-effective way to identify five different genotypes associated with Alternaria alternata resistance to succinate dehydrogenase inhibitors fungicides, used to control Alternaria late blight in pistachio. With the allele-specific method developed here, users will be able to identify genotypes with nucleotide substitutions which lead to a reduced sensitivity or resistance selection using a one-step PCR assay, without the use of restriction enzymes which elevates the reaction costs and the chance for errors. In addition, this study formally includes the identification and sequence accession for SdhB-H277L and SdhC-S135R amino acid substitution in A. alternata sampled from California and Arizona pistachio orchards.

First Report of Fusarium sporotrichioides Causing Foliar Spots on Forage Corn in Chile.

In southern Chile, forage corn (Zea mays L.) is grown for feeding animals in milk diaries and livestock production. In December 2010, corn plants with small circular spots on leaves were collected from three fields located in Río Negro (Los Lagos region). Symptoms began as small, circular white to brown spots of 5 to 10 mm on different parts of the leaf and necrotic tissue with irregular brown to burgundy margins on the border and tip of the leaf. Estimated visual severity was ~5 to 40% for each leaf from field samples. Twelve small blocks of tissue were taken from the edge of necrotic spots from infected leaves, surface disinfected (2 min in 95% ethanol, 2 min in 0.5% NaOCl, followed by three rinses with sterile distilled water), and then placed on PDA and incubated for 7 days at 24 ± 1°C. Seventy five percent of the sampled tissues developed fungal colonies and a 4-mm3 block of agar that contained the advancing hyphal edge of each colony was transferred to PDA and carnation leaf agar and incubated for 10 days at 24 ± 1°C. Colonies were fast growing with pink-white and dense mycelia; with a carmine red color on the undersurface of the plate and orange sporodochia; polyphialides abundant; microconidia abundant, oval or pear-shaped or spindle-shaped, thin walled, hyaline, often with a papilla at the base, and 5.5 to 12.2 × 2.0 to 3.2 µm. Macroconidia were sickle-shaped, 3 to 5 septate, moderately curved to straight, hyaline, thick walled, and 20.5 to 42.9 × 3.5 to 5.0 µm. Morphology of colonies and conidia matched the description of Fusarium sporotrichioides Sherb. (3). Identity of the fungus was confirmed by molecular characterization of the ITS and 18SrRNA regions (universal primers ITS4/5 and NS1/2, respectively) and the ß-tubulin gene (primers Bt1a/Bt1b) of three isolates. BLAST searches of the obtained sequences had between 99 to 100% homology with several isolates of F. sporotrichioides from GenBank (Accession Nos. KC866343 to KC866351). Pathogenicity tests were conducted by dispensing 10 µl of a prepared spore suspension (107 spores/ml) on corn leaves (16 leaves). Negative controls were corn leaves inoculated with sterile distilled water. Inoculated corn leaves were kept at 25 ± 1°C in glass bell jars and monitored for the onset of symptoms for 10 days. The test was conducted twice. Additionally, 20 corn plants of four hybrid lines were inoculated with ~5 ml of a spore suspension (104 macroconidia/ml) 2 months after seeding under field conditions in Valdivia, Los Ríos region, Chile. Seventy five days after sowing, similar lesions to those initially observed on field infected leaves were observed on inoculated leaves but not on water controls. Under field conditions, an extended damage on borders of basal leaves and spots on stems and cobs was observed. The pathogen was reisolated from infected tissues, thereby fulfilling Koch's postulates. F. sporotrichioides is a frequent pathogen in corn silage (1) and cereal crops (3,4), and produces trichothecene mycotoxins that cause toxicosis in animals (2,3). To our knowledge, this is the first report of F. sporotrichioides causing foliar spot on forage corn in Chile and this disease could represent a serious risk of mycotoxin contamination in this crop. References: (1) H. Baath et al. Arch. Tierernahr. 40:397, 1990. (2) A. E. Desjardins et al. Phytopathology 79:170, 1989. (3) J. F. Leslie and B. A. Summerell. Page 256 in: The Fusarium Laboratory Manual. Blackwell Publishing Professional, Hoboken, NJ, 2006. (4) R. H. Vargo et al. Plant Dis. 70:629, 1986.