Chicken is an important non-mammalian vertebrate model organism for biomedical research, especially for vaccine production and the study of embryology and development. Chicken is also an important agricultural species and major food source for high-quality protein worldwide. In addition, chicken is an important model organism for comparative and evolution genomics. Exploitation of this genome as a biomedical model is hindered by its incomplete structural and functional annotation. This incomplete annotation makes it difficult for researchers to model their functional genomics datasets. Improving structural and functional annotation of the chicken genome will allow researchers to derive biological meaning from their functional genomics datasets. The objectives of this study were to identify proteins expressed in multiple chicken tissues, to functionally annotate experimentally confirmed proteins expressed in different chicken tissues, to quantify and assess the Gene Ontology (GO) annotation quality, and to facilitate functional annotation of microarray data. The results of this research have proven to be fundamental resource for improving the structural and functional annotation of chicken genome. Specifically, we have improved the structural annotation of the chicken genome by adding support to predicted proteins. In addition, we have improved the functional annotation of the chicken genome by assigning useful biological information to proteomics datasets and the whole genome chicken array. The Gene Ontology Annotation Quality (GAQ) and Array GO Mapper (AGOM) tools developed in this study will sustainably continue to facilitate functional modeling of chicken arrays and high-throughput experimental datasets from microarray and proteomics studies. The ultimate positive impact of these results is to facilitate the field of biomedical research with useful information for comparative biology, better understanding of chicken biological systems, diseases, drug discovery and eventually development of therapies.

Beef and milk production industries represent the largest agricultural industries in the United States with a retail equivalent value of approximately $112 billion (USDA, 2008). Infertility is the major problem for mammalian reproduction. In the United States approximately 66% of cows are bred by Artificial Insemination (AI), but only ~50% of these inseminations result in successful pregnancies. Infertility can occur either from male factor (spermatozoon) or female factor (oocyte) and male contributes approximately 40% of cases. Infertility costs the producer approximately $5 per exposed cow for every 1% reduction in pregnancy rate. In spite of its millions of dollars in economic impact, the precise molecular events/mechanisms that determine the fertilizing potential of an oocyte and spermatozoon are not well defined. The thesis of my doctoral dissertation is that proteomics-based “systems biology” modeling of bovine oocyte and spermatozoon can facilitate rapid understanding of fertility. To test this thesis, I needed to first identify the proteins associated with bovine oocyte and its associated cumulus cells, and spermatozoon. The next step was functional annotation of the experimentally confirmed proteins to identify the major functions associated with the oocyte, cumulus cells and spermatozoon, and finally, generate a proteomics based systems biology model of bovine oocyte and cumulus cell communication and male fertility. The results of my dissertation established the methods that provide afoundation for high-throughput proteomics approaches of bovine oocyte and cumuluscell biology and allowed me to model the intricate cross communication between oocyte and cumulus cells using systems biology approaches. Proteomics based systems biology modeling of oocytes and cumulus cells identified the signaling pathways and proteins associated with this communication that may have implications in oocyte maturation. In addition, systems biology modeling of differential spermatozoa proteomes from bulls of varying fertility rates enabled the identification of putative molecular markers and key pathways associated with male fertility. The ultimate positive impact of these results is to facilitate the field of biomedical research with useful information for comparative biology, better understanding of bovine oocyte and spermatozoon development, infertility, biomarker discovery, and eventually development of therapies to treat infertility in bovine as well as humans.