Widespread non-target-site resistance in Setaria viridis to four classes of herbicide

Setaria viridis is a cosmopolitan weed and model genetic system with increasing reports of resistance to multiple classes of herbicides. Our goal was to assess the herbicide resistance and allelic diversity in herbicide target genes in a collection of Setaria genotypes from North America and Eurasia, and identify the occurrence of novel and known target-site mutations that led to resistance. A total of 213 Setaria genotypes were exposed to commonly used herbicides that inhibit specific genes: herbicide action class (HRAC) Group 1 herbicides targeting acetyl CoA carboxylase (ACCase), HRAC 2 targeting acetolactate synthase (ALS), HRAC 9 targeting 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, and HRAC 10 targeting glutamine synthetase. ACCase and ALS genes in 54 accessions were PCR-amplified and sequenced. Whole genome sequencing reads covering the target genes were analyzed for an additional 98 genotypes. Herbicide trials showed that 30% of our accessions set seed following application of at least one herbicide, and 13 accessions were resistant to multiple classes of herbicides. Although there were numerous SNPs, including some known to lead to resistance, in our target genes, SNPs found predominantly in herbicide resistant genotypes were largely intronic or synonymous. A small number of amino acid substitutions in ALS and ACCase indicated potential and incomplete resistance to HRAC 1 and 2 herbicides, but no SNPs putatively associated with herbicide resistance were identified in the other 6 target-site genes. The broader pattern of herbicide resistance in S. viridis is likely driven by non-target mutations that detoxify or compartmentalize applied herbicides.