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Item Open Access Dataset associated with “An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale”(Colorado State University. Libraries, 2021) de Figueiredo, Marcelo R. A.; Küpper, Anita; Malone, Jenna M.; Petrovic, Tijana; de Figueiredo, Ana Beatriz T. B.; Campagnola, Grace; Peersen, Olve B.; Prasad, Kasavajhala V.S.K.; Patterson, Eric L.; Reddy, Anireddy S. N.; Kubeš, Martin F.; Napier, Richard; Dayan, Franck E.; Preston, Christopher; Gaines, Todd A.The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing 9 amino acids in the degron tail (DT) of the auxin co-receptor Aux/IAA2 (SoIAA2). The deletion allele co-segregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This novel mechanism of synthetic auxin herbicide resistance assigns a new in planta function to the DT region of this Aux/IAA co-receptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin resistant crops using gene editing.Item Open Access Dataset associated with “Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America”(Colorado State University. Libraries, 2021) Gaines, T.; Slavov, G.; Hughes, D.; Kuepper, A.; Sparks, C.; Oliva, J.; Vila-Aiub, M.; Garcia, M. A.; Merotto, A.; Neve, P.The global invasion, and subsequent spread and evolution of weeds provides unique opportunities to address fundamental questions in evolutionary and invasion ecology. Amaranthus palmeri is a widespread glyphosate-resistant (GR) weed in the USA. Since 2015, GR populations of A. palmeri have been confirmed in South America, raising questions about introduction pathways and the importance of pre- versus post-invasion evolution of GR traits. We used RAD-Seq genotyping to characterize genetic structure of populations from Brazil, Argentina, Uruguay and the USA. We also quantified gene copy number of the glyphosate target, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS) and the presence of an extra-chromosomal circular DNA (eccDNA) replicon known to confer GR in USA populations. Populations in Brazil, Argentina, and Uruguay were only weakly differentiated (pairwise FST 0.043) in comparison to USA populations (mean pairwise FST = 0.161, range = 0.068-0.258), suggesting a single major invasion event. However, elevated EPSPS copy number and the EPSPS replicon were identified in all populations from Brazil and Uruguay, but only in a single Argentinean population. These observations are consistent with independent in situ evolution of glyphosate resistance in Argentina, followed by some limited recent migration of the eccDNA based mechanism from Brazil to Argentina. Taken together, our results are consistent with an initial introduction of A. palmeri into South America sometime before the 1980s, and local evolution of GR in Argentina, followed by a secondary invasion of GR A. palmeri with the unique eccDNA based mechanism from the USA into Brazil and Uruguay during the 2010’s.Item Open Access Dataset associated with “Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America"(Colorado State University. Libraries, 2020) Ravet, Karl; Sparks, Crystal D.; Dixon, Andrea; Küpper, Anita; Westra, Eric P.; Pettinga, Dean J.; Tranel, Patrick J.; Felix, Joel; Morishita, Don W.; Jha, Prashant; Kniss, Andrew; Stahlman, Phillip W.; Neve, Paul; Patterson, Eric L.; Westra, Philip; Gaines, Todd A.Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that 1) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that 2) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat (SSR) markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains, and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS-duplication genotypes, one having geographic associations with the Northern Plains and the other to the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.Item Open Access Supporting information (SI) for Gill et al. 2016 manuscript(Colorado State University. Libraries, 2015) Gill, Brian A.; Kondratieff, Boris C.; Casner, Kayce L.; Encalada, Andrea C.; Flecker, Alex S.; Gannon, Dustin; Ghalambor, Cameron K.; Guayasamin, Juan M.; Poff, N. LeRoy; Simmons, Mark P.; Thomas, Steven A.; Zamudio, Kelly R.; Funk, W. ChrisItem Open Access Data for the manuscript: Using high-resolution future climate scenarios to forecast Bromus tectorum invasion in Rocky Mountain National Park(Colorado State University. Libraries, 2014) West, Amanda M.This data package was produced by researchers working with the Natural Resource and Ecology Laboratory, the Bioagricultural Sciences and Pest Management Department, and the Forest, Rangeland & Watershed Stewardship Department at Colorado State University, and Rocky Mountain National Park, Colorado in evaluating the distribution and potential spread of the invasive species Bromus tectorum (cheatgrass) for the Park. Our objectives were to: (1) evaluate the current bioclimatic niche including climatic variables that have a significant influence on B. tectorum occurrence in the Park using MaxEnt and high-resolution climatic data generated from ClimateWNA, (2) model the potential bioclimatic niche of B. tectorum in the Park for the year 2050 based on climate change, and (3) create a high-resolution map of B. tectorum habitat in the Park both now and in the future for use by Park managers.