Unraveling the Genetic and Molecular Changes Associated with Clopyralid Resistance in Common Ragweed (Ambrosia artemisiifolia)

Abstract

Common ragweed (Ambrosia artemisiifolia L.) is a globally distributed, difficult to control weed that can cause severe crop yield losses if not properly managed. Clopyralid is a synthetic auxin herbicide widely used to control A. artemisiifolia and other Asteraceae weeds. In 2016, a highly clopyralid resistant A. artemisiifolia population was reported on a Michigan Christmas tree farm which we call AMBEL-40. We investigated the inheritance and potential clopyralid resistance mechanisms in this population using greenhouse dose response assays, test crosses with a susceptible line - AMBEL-39, and RNA-seq. The ED₅₀ values for AMBEL-40 and AMBEL-39 were 2,110.8 and 74.5 g ha^-1, respectively; therefore, the R/S ratio is 28.3. Dose response results with triclopyr, fluroxypyr, 2,4-D, or dicamba demonstrate no multiple or cross-resistance in AMBEL-40. AMBEL-40 and AMBEL-39 crossed F₁ generations (M3F1, M3F2, and M1F1) showed increased resistance compared to AMBEL-39 with ED₅₀ values of 1,379.2, 1,134.0, and 542.5 g ha^-1. Chi-square tests of three sib-mated F₁ to generate F₂ generations rejected a single-gene 1:3 model and supported a two-gene 3:13 segregation, consistent with multigenic inheritance. We identified 23 Aux/IAA transcripts containing the degron sequence in the published Ambrosia artemisiifolia genome, of these, three contained polymorphisms in our RNAseq data, but none consistently co-segregated with resistance. Differential expression analysis identified 70 genes with 39 upregulated and 31 downregulated in AMBEL-40 including candidates in auxin/ethylene signaling, metabolism, cuticular wax biosynthesis, and stress modulation, supporting a non-target site resistance mechanism. Together, these results indicate that clopyralid resistance in A. artemisiifolia is recessive, and multigenic, with potentially altered signaling, metabolism, and uptake as a mechanism of resistance rather than a single Aux/IAA degron mutation.