The Role of Selective Breeding and Microbiome Composition in Chicken Health

In the past 50 years, selectively breeding for accelerated growth has resulted in compromised immune response in commercial chickens. As well, emergence of antimicrobial resistance prompted bans on use of antibiotic growth promoters (AGPs) in chicken feed; alternative supplements that can mimic the impact of AGPs in preventing infections are needed to minimize production losses. In this study, I performed whole genome sequencing analysis of domestic chicken breeds, focusing on three lineages that underwent intensive selective breeding, to detect genetic changes that impact immune response and growth. My results identify two genes, TLR3 and PLIN3, whose genetic variants may enhance growth performance at the expense of immune function. I also characterize the impacts of AGPs on the chicken microbiome through 16S rRNA sequence surveys. Lastly, meta-analysis of the chicken cecal microbiome identifies Lactobacilli species as keystone taxa that are likely crucial for constructing microbial consortia to replace AGPs.M.Sc.2020-07-10 00:00:0