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Abstract
Enhancing food security alongside growing resource shortages, an increasing global population, and climate change requires researchers to devise advanced and sustainable solutions to boost crop productivity. Gaining a deeper insight into the mechanisms underlying complex plant traits is crucial for advancing crop breeding efforts. Advancements in omic technologies, such as transcriptomics and genomics, as well as cutting-edge precise genome editing approaches, have paved new ways for researchers to explore and manipulate complex crop traits, greatly enhancing crop improvement efforts. Despite significant advances, the genetic basis and molecular mechanisms behind many complex traits remain elusive. Furthermore, the task of accurately mapping the associations between complex traits and genetic variations remains a challenge. The research presented in this dissertation first leverages and develops improved computational tools to help identify a wider array of genotype- phenotype relationships in crops and secondly applies the transcriptomics approach to investigate development and stress resistance in two essential crops: peanut and tall fescue. In my first project, I developed a bioinformatics workflow to perform k-mers-based genome-wide association studies (GWAS). This tool enhances the accessibility and streamlines k-mers-based GWAS for wider use and improves the efforts of discovering new gene-phenotype associations. Next, I used a transcriptomic approach to examine the genes and regulatory networks underlying the contrasting reproductive and morphological behaviors between two peanut cultivars, Tifrunner and GT-C2O. I identified several candidate genes and pathways involved in the flowering regulation of these peanut cultivars. Lastly, I employed mRNA sequencing to explore the endophyte-mediated heat stress response in tall fescue plants. The effect of the endophyte was minimal and depended on the host genotype. In addition, I identified potential genes and functional terms involved in endophyte-induced heat tolerance. Overall, the work presented in this dissertation contributes to a deeper understanding of complex crop traits and their potential association with a broad array of genetic variants, ultimately paving the way for more productive and sustainable agriculture.