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Abstract
In recent years due to drastic reductions in cost, sequencing-based technologies have become more accessible to the scientific community. As a result, these tools have become commonplace within the contemporary literature and have displaced several older genome-based methodologies/techniques. Despite the apparent benefits that these tools possess over the older counterparts, several technical hurdles remain that must be addressed. As such, the current research was conducted to explore and demonstrate the utility and limitations of sequencing-based technologies within two aspects of the agricultural sciences: food safety and meat quality.
In the first study, whole genome sequencing (WGS) of a group of U.S. Department of Agriculture (USDA)-approved non-pathogenic Escherichia coli (E. coli) surrogates and their rifampicin-resistant counterparts was conducted via two popular next generation sequencing (NGS) technologies. The strengths and weaknesses of both long- and short-read sequencing were demonstrated. Neither approach was sufficient for generating a closed bacterial genome, but by combining the short- and long-read assemblies in a hybrid fashion, complete genomes were produced. The hybrid genome and short-read assemblies were most effective for identifying virulence factors and single nucleotide polymorphism (SNPs) that conferred rifampicin resistance. These completed genomes will be valuable for future food safety research activities and our results support recommendations for how WGS can be effectively utilized within industry food safety programs.
The second study sought to further elucidate the physiological mechanisms that contribute to the development of the dark cutting phenotype in beef cattle. Through RNA- sequencing of microRNAs from total RNA extracts of Longissimus lumborum biopsies, expression profiles were generated for each steer carcass. Differential expression analyses compared microRNA expression between normal carcasses and those displaying the dark, firm, and dry (DFD) phenotype via two statistical approaches. These analyses resulted in the identification of 10 candidate microRNAs (miRNAs) that were found to possess potential biological relevance to the DFD phenotype. These findings represent a starting point in uncovering the relationship between of miRNAs and the DFD phenotype and can contribute to the development of screening/intervention-based strategies that can be utilized in better understanding physiological/genomic mechanisms in order to reduce the occurrence of this economically important trait.
