Excessive ambient temperature (heat) and Newcastle disease virus are considered the largest abiotic and biotic limitation, respectively, to poultry production in low-income countries. Breeding chickens that are stronger in these challenging environments will reduce mortality and increase the amount of quality protein available for human consumption. From several previous reports, it is clear that response to NDV and heat in chickens is at least partially controlled by the genetic makeup of the bird. After a trait is determined to be influenced by genetics, the next logical step is to search for potential genes or genomic regions that affect the trait. If specific areas of the genome can be associated with a trait, this genomic information can be used to further enhance the trait through selective breeding.

This dissertation characterizes responses of commercial egg-laying lines of chickens to Newcastle disease virus and/or high ambient temperature. For both stressors, heritabilities of various aspects of response were estimated to determine existence of genetic control. Genome wide association studies (GWAS) were conducted to elucidate genes and genomic regions associated with various aspects of response to Newcastle disease virus and/or high ambient temperature. The objectives of these studies were to identify potential biomarkers for prediction of stress response, identify genes or genomic regions associated with response as candidates for use in selective breeding, and to broaden the understanding of the chicken’s response to abiotic and biotic stressors, both phenotypically and genetically.

Chapter 2 identified six suggestive QTL associated with response to NDV and/or growth, including novel and known QTL confirming previously reported associations with related traits. Based on a negative genetic correlation between antibody and Newcastle Disease tolerance (growth under disease) (-0.72 – -0.42) and estimates of moderate to high heritability, we provide evidence that these NDV response traits can be influenced through selective breeding. In chapter 3, seventeen significant effects, among seven genes (TLR7, MX, IFI27L2, SLC5A1, HSP70, IFRD1, IL1R1) and seven phenotypes (growth rate post-NDV, viral load 6 dpi, antibody 10 dpi, BE, HCO3, TCO2, pH), were detected for gene haplotype effects on NDV and heat stress response. These gene effects provide more knowledge of the genomic control of NDV and heat stress response and provide potential SNP (single nucleotide polymorphism) targets for marker-assisted selection.

In chapters 4 and 5, egg production traits, feed intake, body weight, digestibility, egg quality, and the level of thirteen blood components of commercial white egg-laying hens before and during a 4 week heat exposure were quantified. Heritabilities were estimated and SNP associations were tested for these phenotypes using 600k genotype data. All phenotypes exhibited a significant change after heat exposure. Several phenotypes, at various times, had heritability estimates greater than zero. The existence of measureable heritability indicates the existence of genetic control and, therefore, the potential for changing these traits through selective breeding. QTL were identified for some of the phenotypes with measureable heritability. QTL were identified for nine of the blood chemistry traits at one or more time point. These nine traits, however, did not have significant heritability estimates suggesting that while QTL have been identified their effects are generally small.

This dissertation contributes to the knowledge of genomic control of response to NDV and heat stress in laying hens. These findings, coupled with findings from companion studies, inform the genetic improvement of chickens to perform favorably in the face of combined disease and environmental challenges.