Date of Graduation

8-2016

Document Type

Thesis

Degree Name

Master of Science in Poultry Science (MS)

Degree Level

Graduate

Department

Poultry Science

Advisor/Mentor

Kong, Byung-Whi

Committee Member

Erf, Gisela F.

Second Committee Member

Rhoads, Douglas D.

Third Committee Member

Anthony, Nicholas B.

Keywords

Biological sciences; Health and environmental sciences; Biomarkers; Divergence; Genomes; Sequencing; Tumors; Viruses

Abstract

Poultry has become especially important to genetic research due to breeding feasibility, short generation turnover, and ease of maintaining large populations. The discovery of virus induced cancer has paved the way for further genetic studies. Rous Sarcoma Virus (RSV) is a tumor-causing virus that infects poultry. While not prevalent today, it can serve as a model for virus-induced cancer in humans and create additional insight to marker assisted selection in poultry. Genetically selected Arkansas Progressor (AP) and Arkansas Regressor (AR) chicken lines have been established and maintained at the Arkansas Experimental Station (AES) in Fayetteville, AR. Previous research has investigated the immunological and genetic characteristics of virus induced tumors. Publication of the Red Jungle Fowl genome has made it possible to perform genome wide studies to identify biomarkers associated with the susceptibility to RSV induced tumors. In this study, whole genomes of AP and AR lines were sequenced and analyzed using Illumina platform next generation sequencing. Over 9,000,000 SNPs were identified against the reference genome and 12,000 were classified as unique SNPs between the AR and AP line. Most SNPs were found in intergenic regions, while few were in protein coding regions. Unique SNPs were categorized by the following mutations: Frameshift (134), No Start (25), No Stop (7), Non-synonymous (6884), and Nonsense (112). Unique SNPs were characterized as occurring in only one line. Nine SNPs were chosen after genomic analyses for testing using PCR and Sanger sequencing in larger populations of AR and AP birds followed by validation in unrelated populations. No statistical correlations were found between the 9 SNPs in the unrelated populations, Giant Jungle Fowl (GJF) and White Leghorn (WL). No genetic difference was detected between birds of differing phenotypes within the GJF and WL lines. SNP frequencies were the same for both birds that regressed tumors and those that progressed tumors. Interestingly, it was observed that the GJF line response to RSV resembled the AR line and the WL line resembled the AP line, and GJF and WL exhibited differing phenotypes, indicating the potential to find biomarkers in larger population sizes.

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