Date of Graduation

12-2013

Document Type

Thesis

Degree Name

Master of Science in Poultry Science (MS)

Degree Level

Graduate

Department

Poultry Science

Advisor

Byung-Whi Kong

Committee Member

Douglas D. Rhoads

Second Committee Member

Nicholas Anthony

Abstract

Poultry is key in genetic research due to breeding feasibility, relatively short generation interval, and distinct phenotypes. It is estimated that 8% of broiler deaths annually can be attributed to ascites, an economically important disease that has been challenging the industry for the past 2 decades. Genetically selected ascites resistant (RES) and susceptible (SUS) chicken lines have been established and maintained by the University of Arkansas, Fayetteville. Intensive research efforts have been made to reveal physiological and biochemical characteristics for the incidence of ascites. Since the whole genome of the major ancestral chicken, the Red Jungle Fowl, has been sequenced, genome-wide genetic study is now possible in chickens to identify genetic variations throughout the entire genome. To identify genetic biomarkers responsible for ascites resistance or susceptibility, whole genome sequences of genetically selected chicken lines (RES and SUS) in addition to the unselected parental Relaxed line (REL) were analyzed using the Illumina platform of next generation sequencing techniques and bioinformatics tools. Over 4 million SNPs were identified in each line and over 95% of SNPs were found in the intergenic regions. In the protein coding regions (CDS), SNPs that generated synonymous, non-synonymous, frameshift, non-sense, no start, and no stop mutations were 69.3%, 29.3%, 1%, 0.3%, 0.07% and 0.03%, respectively. Eight SNPs were chosen by the following parameters: over 75% SNP rate, over 10 depth (read counts of contig), and verified in larger numbers (96) of birds for each line using PCR and Sanger sequencing. A fast and accurate method of genotyping was developed (AS-PCR) in order to investigate genotype/disease association in unrelated (RMQ) and unselected (REL) populations. No statistically significant correlations were found between the 8 SNPs and ascites incidence in the REL or RMQ lines due to sample size. However, CHTF18 continually associated with ascites phenotypic data. The homozygous RJF genotype more often appeared in resistant-type birds while heterozygotes were mostly susceptible.

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