A transposable element insertion in IAA16 interrupts normal splicing and generates a novel dicamba resistance allele in Bassia scoparia

Montgomery, J. S.; Soni, N.; Marques Hill, S.; Morran, S.; Patterson, E.; Edwards, S.; Ratnayake, S.; Hung, Y.-H.; Pandesha, P. H.; Slotkin, R. K.; Dayan, F. E.; Gaines, T. A.

doi:10.1101/2024.07.19.604363

bioRxiv · 10.1101/2024.07.19.604363

A transposable element insertion in IAA16 interrupts normal splicing and generates a novel dicamba resistance allele in Bassia scoparia

Montgomery, J. S.·Soni, N.·Marques Hill, S.·Morran, S.·Patterson, E.·Edwards, S.·Ratnayake, S.·Hung, Y.-H.·Pandesha, P. H.·Slotkin, R. K.·Dayan, F. E.·Gaines, T. A.

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Abstract

A dicamba-resistant population of kochia (Bassia scoparia) identified in Colorado, USA in 2012 was used to generate a synthetic mapping population that segregated for dicamba resistance. Linkage mapping associating dicamba injury with genotype derived from restriction-site-associated DNA sequencing identified a single locus in the kochia genome associated with resistance on chromosome 4. A mutant version of Auxin/Indole-3-Acetic Acid 16 (AUX/IAA16; a gene previously implicated in dicamba resistance in kochia) was found near the middle of this locus in resistant plants. Long read sequencing of dicamba-resistant plants identified a recently inserted Ty1/Copia retrotransposon near the beginning of the second exon of AUX/IAA16, leading to disruption of normal splicing. A molecular marker for this insertion allows for rapid detection of resistance. Stable transgenic lines of Arabidopsis thaliana ectopically expressing the mutant and wildtype alleles of AUX/IAA16 were developed. Arabidopsis thaliana plants expressing the mutant AUX/IAA16 allele grew shorter roots on control media. However, transgenic root growth was less inhibited on media containing either dicamba (5 M) or IAA (0.5 M) when compared to non-transgenic plants or those expressing the wildtype allele of AUX/IAA16. In vitro assays indicate reduced binding affinity and more rapid dissociation of the mutant AUX/IAA with TIR1 in the presence of several auxins, and protein modeling suggests the substitution of the glycine residue in the degron domain of AUX/IAA16 is especially important for resistance. A fitness cost associated with the mutant allele of AUX/IAA16 has implications for resistance evolution and management of kochia populations with this resistance mechanism. SignificanceAuxin mimics are amongst the most important herbicides in modern agriculture. Evolution of weeds that are resistant to these herbicides threatens sustainable crop production. Understanding the basis of auxin herbicide resistance informs the development of improved weed control technologies. Additionally, auxin-resistant mutations and their pleotropic effects help us understand auxin perception and signalling. We describe a transposable element insertion within an herbicide target site gene that alters splicing and reduces synthetic and natural auxin perception.

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Montgomery, J. S., Soni, N., Marques Hill, S., Morran, S., Patterson, E., Edwards, S., Ratnayake, S., Hung, Y.-H., Pandesha, P. H., Slotkin, R. K., Dayan, F. E., Gaines, T. A.. 2024-07-23. A transposable element insertion in IAA16 interrupts normal splicing and generates a novel dicamba resistance allele in Bassia scoparia. https://doi.org/10.1101/2024.07.19.604363

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