Date of Graduation

12-2021

Document Type

Thesis

Degree Name

Master of Science in Poultry Science (MS)

Degree Level

Graduate

Department

Poultry Science

Advisor

Byungwhi C. Kong

Committee Member

Wayne J. Kuenzel

Second Committee Member

Casey M. Owens

Keywords

Nervous System, Neuroendocrine System, Poultry, Quail, SNP, Stress Response

Abstract

As consumer demands for poultry grow, producers work to improve bird productivity in both meat and egg production. This endeavor is multifaceted, as many different factors play a part in influencing the productivity of birds, including environmental conditions, overall health, and genetic potential. One aspect controlled for in all aspects of poultry production optimization is stress management. Mitigation of stress is of primary concern to producers, as improper stress management can have many deleterious effects on chickens. Stress management requires an understanding of poultry stress responses and their physiological mechanisms, which can be more deeply understood through genomic analysis. Chapter 1 of this thesis covers common stressors in poultry production environments, methods of genomic evaluation, and two lines of Japanese quail bred as models of stress responses in poultry. Chapter 2 covers a genome-wide analysis of two lines of Japanese quail – a high stress (HS) and a low stress (LS) line – bred for divergent blood corticosterone levels in response to restraint stress. The goal of this analysis was to identify genetic variations that could influence differential stress responses. Single Nucleotide Polymorphisms (SNPs), specifically non-synonymous SNPs resulting in amino acid changes, were chosen as the genetic mutation for analysis, and their potential effects on physiological function were determined. Genomic resequencing was performed on 24 birds from the HS and LS lines of Japanese quail using Illumina Hiseq 2 x 150 bp end read technology. From 6,364,907 SNPs observed, 2,886 unique, non-synonymous SNPs with a SNP% ≥ 0.90 and a read depth ≥ 10 were identified. Through use of Ingenuity Pathway Analysis (IPA), we identified genes affected by SNPs tied to immune responses, DNA repair, and neurological signaling. Chapter 3 covers a genome-wide analysis of the same two lines of Japanese quail, this time with a focus on nervous and neuroendocrine system functions, as these systems control a large part of stress responses. Focus was also placed on the hypothalamic-pituitary-adrenal (HPA) axis. This axis forms an important connection between the nervous and endocrine system, and it triggers a hormonal cascade in response to stressors that leads to the release of corticosterone hormone. Using IPA, we found that a large portion of genes affected by SNPs were found with the HPA axis, many of which have been implicated in glucocorticoid receptor-dependent gene regulatory networks. Over a third of genes and molecules in the HS line and about a third of the genes and molecules in the LS line are found within the hippocampus and hypothalamus, indicating large genetic changes within the brains and neuroendocrine systems of birds in these lines.

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