Identification of ALS inhibitor-resistant Amaranthus biotypes using polymerase chain reaction amplification of specific alleles

Polymerase chain reaction (PCR) amplification of specific alleles (PASA) was adapted as a molecular marker-based method for the rapid detection of point mutations in Amaranthus retroflexus and Amaranthus rudis leading to ALS inhibitor resistance. Two pairs of primers were designed for the specific amplification of alleles of the ALS gene of susceptible and resistant biotypes. The allele-specific primer matched the desired allele, but mismatched the different allele at its 3' end. Differentiation was carried out by comparison of the amplified DNA fragments in gel electrophoresis after PASA-PCR. In A. rudis , differentiation was possible with one PCR and genomic DNA as probe. A 'nested' PCR was necessary for the differentiation of sensitive and resistant A. retroflexus . PASA is useful for the identification of resistant weed biotypes and also as a monitoring tool to map resistance occurrence and distribution. Advantages include the fast and clear separation of those plants with and without mutations at an early stage of development, its easy and consistent performance and quick results compared with existing resistance detection tests. These advantages, when combined with management strategies, enable further activities to reduce herbicide resistance.