The evolution of dioecy and herbicide resistance: a genomic and transcriptomic exploration of Amaranthus species

Amaranthus tuberculatus (Moq.) Sauer and Amaranthus palmeri S. Wats. are major weeds within North American agriculture and can cause drastic crop yield reductions. The evolution of non-target-site resistance within these species has been leading to management challenges due to its potential to reduce the effectiveness of multiple herbicides. Recently, a novel dicamba resistance trait was identified in A. tuberculatus, prompting its characterization. A comprehensive characterization of the inheritance patterns and resistance levels of the first case of dicamba resistance in A. tuberculatus was conducted. In field trials, dicamba did not provide more than 65% control, while glyphosate and glufosinate provided at least 90% control. Multiple accessions were generated from controlled crosses and evaluated in greenhouse trials. Greenhouse dose-response experiments indicated a resistance level of 5 to 10-fold and an incompletely dominant trait. Segregation analysis indicated that dicamba resistance had moderate heritability and is likely a multigenic trait. To further characterize this novel resistance trait, an RNA-seq study was conducted to identify potential gene candidates for dicamba resistance in A. tuberculatus. Multiple differentially expressed genes and co-expression gene modules were identified and associated with dicamba resistance. Results indicate enhanced oxidative stress response as the primary mechanism for reducing dicamba toxicity. Results also point to potential glycosylation via UDP-glycosyltransferase and conjugation via glutathione-S-transferases of dicamba and its byproducts. Both A. tuberculatus and A. palmeri are dioecious species, with distinct female and male individuals present, providing some evolutionary advantages. In contrast, this biological trait could be exploited as a target for a genetic control tool targeting sex-ratio manipulation as a management strategy. Recent advances in developing genomic resources for both species allow for a comprehensive analysis to understand the sex-determination mechanism in both species. An RNA-seq study was conducted to compare multiple tissue types between females and males within each Amaranthus species. Genes PPR247, WEX, and ACD6 were differentially expressed across the sexes and located at scaffold 20 within or near the MSY region in A. palmeri. For A. tuberculatus, no candidate differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were differentially expressed. Lastly, to further our current knowledge about flowering genes in dioecious species, a comprehensive characterization of MADS-box transcription factors was conducted for multiple Amaranthus species. The analysis of MADS genes in Amaranthus revealed a range of 40 to 64 genes, with 14 to 25 M-type genes and 24 to 39 MIKC genes. Phylogenetic analysis revealed a conserved evolution of the MADS-box family in the analyzed Amaranthus species, with certain key genes showing evolutionary divergence in dioecious species. Structure analysis indicated a conserved intron/exon structure in both M-type and MIKC genes, similar to the structure in other species.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Crop Sciences

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2023

Author dc:creator

• Kopecky Bobadilla, Lucas

Contributors dc:contributor

• Tranel, Patrick J
• Hager, Aaron G
• Lipka, Alexander E
• Marshall-Colon, Amy

• Amaranthus
• Herbicide
• Dicamba
• Dioecy
• Waterhemp
• Palmer Amaranth
• Weeds

Statement dc:rights

• Copyright 2023 Lucas Kopecky Bobadilla

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/121418

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F121418