Jen-Hsiang Ou: Exploring the Genetic Landscape of Chicken Populations: Admixture, Growth QTLs, and Long-Term Selection Dynamics

Abstract

This thesis analyzes the genetic structure of chicken populations across different breeding histories and environments. Genomic methodologies were used to uncover complex traits and domestication history over time. The work consists of three studies contributing to a broader understanding of chicken genetic diversity and the impact of selective breeding practices.

The first study delves into the global chicken population, using genome-wide analysis to uncover the intricate fine structure and historical admixture events that have shaped these populations. The research has unveiled significant connections between populations and pivotal breeding events, highlighting the complex relationships within chicken populations. This study offers intriguing insights into the genetic continuity and admixture patterns across diverse chicken breeds, from junglefowl to commercial lines.

The second study focuses on the genetic complexity within a specific quantitative trait locus (QTL) region known as Growth1, which is influential in chicken growth. This study, conducted using an advanced intercross line from the Virginia body weight line, identifies significant additive, haplotype, and epistasis effects within the Growth1 QTL region. The findings challenge simplistic genetic models by demonstrating the involvement of multiple loci in regulating body weight and contribute to understanding complex trait architecture.

The third study extends the investigation to the long-term effects of selection on chicken lines, providing a deeper understanding of the genetic mechanisms underlying selection responses. By mapping multiple additive QTLs associated with body weight compared with the GWA study results, several novel regions were determined and are still contributing to the selection response even after 40 generations of intense selection.

These different views provide practical insights into chickens' intricate genetic makeup. By analyzing their domestication history, genetic variation effects, and the population's response to selective breeding, we better understand one of the most important economic organisms for humans — the chicken. This understanding can potentially inform and improve selective breeding practices, leading to more efficient and sustainable poultry production.