Detection of resistance to acetohydroxyacid synthase inhibitors in Amaranthus sp. using DNA polymorphisms

Resistance to acetohydroxyacid synthase inhibitors is very widespread worldwide and is generally due to various point mutations in the gene coding for the target enzyme. Rapid resistance confirmation is key for the proper management of resistance. We aimed at determining whether two DNA-based tests, PCR-RFLP and PCR amplification of specific alleles (PASA), could reliably identify common AHAS mutations in Amaranthus sp., and whether individual tests could be multiplexed. DNA was extracted from eight populations of Amaranthus powellii and Amaranthus retroflexus possessing four different resistance alleles. Gains or losses of endonuclease recognition sites due to the presence of resistance alleles allowed reliable detection of all alleles. PASA used an allele-specific primer with a 3′-terminal mismatch to wildtype DNA to selectively amplify a resistance allele. All four resistance alleles were efficiently identified with PASA. Both tests were multiplexed to allow more efficient identification of resistance and up to four distinct mutations could be revealed by a single test. Those tests were relatively easy to use, inexpensive and allowed quick identification of resistance.