SNP markers for black-grass (Alopecurus myosuroides Huds.) genotypes resistant to acetyl CoA-carboxylase inhibiting herbicides

Chloroplastic acetyl CoA-carboxylase (ACCase) is the target of widely used, specific graminicide herbicides: cyclohexanediones (CHDs) and aryloxyphenoxypropionates (APPs). Resistance to these compounds is a worldwide, increasing problem. Population genetic studies aimed at understanding the dynamics of this situation and the diffusion of resistance genes within and between weed populations are challenging because biological assays are not adequate for this purpose, and because different mechanisms of resistance confer a similar resistance phenotype. Molecular markers for specifically detecting resistance genes are therefore urgently needed to conduct such studies. For this purpose, we cloned and sequenced the whole gene encoding chloroplastic ACCase in Alopecurus myosuroides Huds. (Black-grass). We identified two point mutations at nucleotide 5,341 that both cause an isoleucine-leucine substitution at position 1,781. Three bi-directional allele-specific PCR assays were developed, each detecting two distinct ACCase alleles with a single PCR reaction. The sensitivity of 1,190 seedlings of A. myosuroides to one CHD and one APP was determined. Genotyping revealed that, although resistant plants were only selected by APPs, the 1,781Leu ACCase allele is a widespread, dominant gene of resistance to both APPs and CHDs. No other ACCase allele associated with resistance could be identified in this work. Useful applications of allele-specific PCR markers are population genetic studies as well as routine molecular diagnosis of herbicide resistance.