Degree Type

Dissertation

Date of Award

2016

Degree Name

Doctor of Philosophy

Department

Animal Science

Major

Genetics and Genomics

First Advisor

Dr. Susan J. Lamont

Second Advisor

Dr. James Reecy

Abstract

Future expansion of livestock production is closely tied to the ability to produce robust animals that are able to adapt to diverse and sometimes demanding environments. This is true for poultry as it represents a product of economic and nutritional gain in many developing countries. Regrettably, many areas best served by expansion of poultry are teeming with environmental effects requiring that poultry be adaptable to their surroundings. Adaptability is an amalgamation of genetic variance/beneficial variations and their impact on phenotypic plasticity within a population. The interplay among the genomic architecture of a population with the natural/artificial selection of their environments can work to generate tolerance or resilience traits that support survival. Deeper understanding of how genomic variation and architecture are related to population survival in one environment can be the key to develop strategies to improve other populations to exist in similar environments. Examination of animals such as chickens that have counterparts that have evolved by adapting to a multitude of environments can prove informative for commercial and subsistence farmers that want to breed chickens that are superior producers in different environments. Analysis of the population’s genomic variation and selective pressure was accomplished using various population genomics and bioinformatics techniques. The analyses examined differences in allele frequencies and haplotype homozygosities to elucidate potential processes and functions under selective pressure allowing for adaptation to the environment. The first study employed highly inbred experimental chicken lines diverged by breed and selective pressure for health and reproduction traits. The first study indicated that analyzing populations for genomic variants could help to elucidate the relationship of breed-dominant phenotypes with their sources of genomic variation. Additionally, the study was able to connect the standing genetic variation that persisted around genes controlling beneficial health and reproduction traits to the divergent, highly inbred Fayoumi and Leghorn chickens under study. The second and third studies utilized outbred populations of chickens from multiple countries in Africa and Northern Europe to create questions about the influence of environment on selection towards tolerance traits. The second study showed evidence of possible selective pressure from stressors such as UV damage on the genomes of the African chickens, while the third study provided evidence that selective pressure from the environment can be one of the drivers of divergence that separates breeds at the genomic level. The second and third studies focus on the change at the genomic level that is influenced by similar or dissimilar environments. Examination of the selection pressure on the African chickens in the second study uncovered processes involving kinases that activate multiple stress pathways, possibly as a tolerance adaptation. This result prompted the contrast in the third study between the diverse climates of Africa and Northern Europe to question the specificity of results from the second study. The contrast was the largest study to date in chickens to compare divergent populations over such an expansive latitude distance to examine the environments effect on adaptation. Together all of the dissertation projects provide new insight on the genomic pliability of chickens that allow for a given population adapt to their environment.

DOI

https://doi.org/10.31274/etd-180810-5328

Copyright Owner

Damarius Shaperio Fleming

Language

en

File Format

application/pdf

File Size

225 pages

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