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Plant genetic engineering relies on the ability to transmit and express cloned DNA sequences in plant cells (transformation) as well as the capacity for the cells carrying this DNA to undergo division and differentiation (regeneration), eventually giving rise to a mature whole plant. The breadth of application for genetic engineering is limited by constraints on one or both of these factors in many plant species and individual varieties. Uncovering plant genes which are involved in important aspects of either component can inform the development of technologies that serve to enable or improve the efficiency of genetic modification methods. The most commonly employed method of delivering exogenous genetic material into plant cells is via disarmed strains of the plant pathogen Agrobacterium tumefaciens. Somatic embryogenesis is a frequently applied mode of plant regeneration following DNA delivery, especially in major cereal crops such as maize, rice, and sorghum. In the work reported here, whole transcriptome sequencing (RNA-seq) was used in two different experiments to capture transcriptional dynamics throughout early somatic embryogenesis in immature zygotic embryo tissue of the major crop plant sorghum (Sorghum bicolor), and throughout early times following host plant inoculation with A. tumefaciens in seedlings of the model plant Arabidopsis thaliana (Chapters 2 and 3, respectively). In both cases, differential expression analysis revealed many genes which were induced either during somatic embryogenesis or in response to inoculation with either virulent or avirulent A. tumefaciens strains. Several of these genes were highlighted as candidates for future study into their potential role in the respective processes. Multiple candidate genes were functionally tested, using transgenic methods, for the possibility of having a role in the regulation of somatic embryogenesis in sorghum (Chapter 4). These experiments failed to confirm an influence over the process for all candidate genes that were evaluated. The experimental work documented herein contributes to a growing body of literature documenting plant genes which could serve as possible targets for techniques that work to enhance the utility of biotechnological methods for improving traits in plants.

Investigation of genes involved in somatic embryogenesis and plant-Agrobacterium interactions through transcriptional profiling