Date of Graduation


Document Type


Degree Name

Doctor of Philosophy in Poultry Science (PhD)

Degree Level



Poultry Science


Byungwhi C. Kong

Committee Member

Walter G. Bottje

Second Committee Member

Young M. Kwon

Third Committee Member

Charles F. Rosenkrans Jr.


Copy Number Variation, MicroRNA, Pedigree Male Broiler, SNP, Stress, Tumor Regression


This dissertation focusses on identifying different molecular markers that have impact on overall poultry production. Chapter one reviews microRNA (miRNA), copy number variation (CNV) and single nucleotide polymorphism (SNP) as markers suggested in different avian species by various studies. It reviews modern genomic approaches that are employed for next generation sequencing data analysis and verification.

Chapter two seeks to identify and validate the muscle specific miRNAs in the breast muscle of modern broilers and its foundational chicken line. Small RNA sequencing was performed to identify differentially expressed mature miRNAs in the breast muscles of these two chicken lines. Results showed that nine different mature miRNAs were differentially expressed (DE) in the breast muscle of modern broilers compared to foundational chicken lines. Target genes of DE miRNAs were involved in MAP/ERK1/2, calcium signaling, axonal guidance signaling and NRF2-mediated oxidative response pathways suggesting their roles in muscle growth and development.

Chapter three is focused on identifying and validating copy number variation in the whole genome of two divergently selected high and low stress quail lines. Whole genome sequencing was performed, and data were analyzed for copy number variation detection in genome of the quail lines. Results showed the unique sets of copy number variable regions and genes in the genomes of high stress and low stress birds. Importantly, these genes were involved in development of nervous/endocrine systems, and humoral/cell-mediated immune responses suggesting that they could be potential biomarkers for understanding effects of stress in the well-being and growth performance of avian species and other animals.

Chapter four focuses on identifying SNPs in whole genome of Arkansas Progressor (AP) and Regressor (AR) chicken lines selected for tumor progression and tumor regression upon v-src oncogene induction. Whole genome sequencing was performed, SNPs were analyzed and validated using allele-specific PCR. Results showed the unique sets of SNPs in AP and AR lines. Based on the functional studies, the candidate SNPs were associated with ubiquitylation, and PI3K and NF-kB signaling pathways, suggesting their role in tumor regression in AR chickens.