Advancements in molecular biology and computer science have enabled researchers the ability to investigate the transcriptome – the quantification of an organism’s RNA transcripts in response to its environment on a system wide scale. The collective chapters of this thesis utilize high-throughput RNA sequencing, which produces hundreds of millions of high-resolution reads. In combination with computer programs that can mine data with a biological purpose, the field of transcriptomics has changed our understanding of how genomes are expressed. The continual decrease in costs of transcriptomic studies lowers the barriers of partaking in such research.
A RNA-Seq protocol was developed for two varieties of Triticum monococcum, a close ancestor of Triticum urartu, the A-genome progenitor of hexaploid wheat Triticum aestivum. The transcriptome captured in this study aimed to elucidate the genetic response in regulating photomorphogenesis. As no reference genome was available at the time, the T. monococcum transcriptomes were de novo assembled, annotated, and used to identify gene expression differences wild and domesticated diploid wheat. Furthermore, sequence reads were used to identify genetic markers in the form of single nucleotide polymorphisms and simple sequence repeats. This study provides data that contributes to the improvement of Triticum genus genome annotations, insights into transcriptional regulation during photomorphogenesis, and development of genetic markers.
Rice (Oryza sativa) is a monocot grass that is a model cereal crop, but more importantly, responsible for feeding a majority of the world population. To better understand the genetic response of rice under salt stress, a high resolution investigation of the transcriptomic response was conducted over a period of 24 hours. Immediate response time-points were collected at 1, 2, and 5 hours post salt exposure. Prolonged response time-points were collected at 10 and 24 hours. We compared the transcriptomic profiles of IR29 – a salt-sensitive breeding line, and Pokkali – a salt-tolerant native variety. Our investigation reveals the transcriptomic composition of both varieties to be similar, however Pokkali exhibits an hour delay in response to salt stress. Futhermore, at 24 hours post salt exposure, Pokkali returns to a nearly homeostatic condition, whereas IR29 continues to express salt-responsive genes. Sequence reads were aligned to the reference rice genome to identify single nucleotide polymorphisms and transcriptomes were assembled de novo to enable discover of simple sequence repeats.
Altogether, this collective work of transcriptome analyses contributes to our understanding of how organisms respond to environmental cues. By leveraging next-generation sequence technologies, we better understand the relationship between the genome and environment.