Elucidating the Cellular Physiology of Glyphosate Resistance in Palmer Amaranth (\u3ci\u3eAmaranthus palmeri\u3c/i\u3e) Using Integrated Omics Approaches

The evolution of resistance to herbicides in weeds poses a major threat to agricultural production systems. To date, herbicide resistance has been reported against 21 modes of action in 266 weed species across 71 countries. More than 50 weed species have developed resistance against glyphosate, the most widely used herbicide worldwide. Although several mechanisms of glyphosate resistance have been discovered, our understanding of alterations in the cellular physiology of glyphosate-resistant weed biotypes, and the induction of the resistance mechanisms remains limited. This knowledge is critical to developing sustainable weed management practices and for a comprehensive understanding of plant stress adaptations. This thesis focuses on elucidating the multi-level regulation of cellular physiology in glyphosate-resistant (GR) and glyphosate-susceptible (GS) biotypes of the weed Palmer amaranth (Amaranthus palmeri) using a combination of omics approaches. Palmer amaranth, also known as pigweed, is a dominant GR weed that causes yield losses ranging from 50-90% in row crop production systems of the southeastern US. The major mechanism of resistance in GR Palmer amaranth is through gene amplification of the target enzyme, 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) where GR plants could contain more than 100-fold gene copies of EPSPS. However, the cellular physiology that is native to this gene amplification is less understood, and so is the inducibility of the resistance mechanism. For example, despite EPSPS amplification in GR biotypes that should ensure the normal functioning of the shikimate pathway in the presence of glyphosate, these biotypes show initial accumulation of shikimic acid, indicating transient glyphosate toxicity. Here I compared the native and stress-induced differences across GS- and GR- biotypes of Palmer amaranth using transcriptomics, proteomics, and metabolomics approaches. Global metabolomics analysis across multiple populations of Palmer amaranth revealed that the innate metabolite differences between GS- and GR-biotypes, in the absence of stress, were minimal, and amplification of the EPSPS gene in GR-biotypes did not translate to a higher abundance of downstream metabolites. Further, glyphosate treatment induced similar metabolic perturbations across GS- and GR-biotypes, from which the GR-biotypes recovered, indicating potential inducibility in the functionalization of the EPSPS enzyme. Interestingly, the accumulation of phenylpropanoids produced downstream of the shikimate pathway that act as potent antioxidants was higher in GR-biotypes than in GS-biotypes. However, this increase was not observed in response to drought stress, where the metabolic perturbations were pervasive but limited in magnitude compared to glyphosate stress. A key finding from this study was that the increase in the abundance of phenylpropanoids in GR-biotypes was induced specifically by glyphosate but not drought, indicating that exposure of GR weeds in field margins to non-lethal doses of glyphosate could prime these weeds against future, more lethal stressors. The second study investigating the multi-level glyphosate-induced response at 24HAT revealed that glyphosate-induced disruptions extend beyond the metabolome with significant perturbations in transcriptome and proteome of both the GS- and GR-biotype. Further, the perturbations were not limited to the shikimate pathway with upregulation of stress signaling cascades (including ABA-activated signaling pathway, transcriptional activators, and kinases) and endochitinases (that mediate plant response to fungal invaders) across the biotypes. Interestingly, GS-biotype also showed an inhibition of basal metabolism, including photosynthesis, electron transport chain, and central carbon metabolism, especially at the transcript and metabolite levels that was not observed in the GR-biotype. Thus, the upregulation of stress response systems in GR-biotype occurred without the growth penalty detected in GS-biotype that could prime GR-biotype against future stress events. Overall, these results support the inducibility of glyphosate resistance mechanism across multiple biotypes of Palmer amaranth and highlight the specificity of the herbicide-induced cellular perturbations in GS- and GR-biotypes, where the identity of stressors dominate the stress response. Further, the impact of glyphosate on cellular physiology extends beyond the targeted shikimate pathway across transcript, protein, and metabolite levels, with a potential to prime GR plants to future biotic/abiotic stressors

Multi-omics assisted breeding for biotic stress resistance in soybean

Biotic stress is a critical factor limiting soybean growth and development. Soybean responses to biotic stresses such as insects, nematodes, fungal, bacterial, and viral pathogens are governed by complex regulatory and defense mechanisms. Next-generation sequencing has availed research techniques and strategies in genomics and post-genomics. This review summarizes the available information on marker resources, quantitative trait loci, and marker-trait associations involved in regulating biotic stress responses in soybean. We discuss the differential expression of related genes and proteins reported in different transcriptomics and proteomics studies and the role of signaling pathways and metabolites reported in metabolomic studies. Recent advances in omics technologies offer opportunities to reshape and improve biotic stress resistance in soybean by altering gene regulation and/or other regulatory networks. We suggest using ‘integrated omics’ to precisely understand how soybean responds to different biotic stresses. We also discuss the potential challenges of integrating multi-omics for the functional analysis of genes and their regulatory networks and the development of biotic stress-resistant cultivars. This review will help direct soybean breeding programs to develop resistance against different biotic stresses