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

Letters in Applied Microbiology
Paulo S F LichtembergThemis J Michailides

Abstract

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. 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 Alter...Continue Reading

References

Mar 24, 2007·Bioinformatics·Triinu Koressaar, Maido Remm
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Oct 1, 2007·Plant Disease·Herve F Avenot, Themis J Michailides

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Citations

Mar 25, 2020·Microbial Biotechnology·Youming ShenHaifei Li

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