Small chicken, big story: detection of the genetic background of dwarfism in chicken using genomic analyses

Body size of animals is a trait that has received a lot of interest and emphasis during domestication and breeding. The wide variation in size of domesticated animals is reflected in their genomes. An extreme size variation is dwarfism, a condition of unusually reduced growth caused by a variety of genetic components. In chicken, dwarfism is a complex trait studied and utilized for a long time. Because of the reduced body size, incorporating the dwarf trait into the breeding scheme can provide potential advantages and benefits. In this thesis, I focus on two types of dwarfism and analyze the genetic background of these dwarf phenotypes with respect to underlying genetic variants, gene expression, and population genomics. More specifically, I perform fine-mapping to detect the causative genetic variant underlying the autosomal dwarfism (adw) in chickens. Results demonstrate that a novel nonsense mutation in the TMEM263 gene is associated with the adw phenotype resulting in the premature termination of the open reading frame, and a truncation of the transmembrane protein. Moreover, I study the genetic basis of the bantam phenotype in Dutch traditional chicken breeds by using a variety of genomic analyses. Genome mapping and differential gene expression analysis identify novel candidate genes responsible for the bantam phenotype. The results further demonstrate the heterogeneity of this trait and the signaling pathways involved in growth. Furthermore, I focus on the admixed population structure of Dutch chicken breeds and show how human-mediated crossbreeding may influence the genomic landscape of a population in a complex manner. Collectively, I provide a comprehensive understanding of the genetic background of dwarf phenotypes in chicken, which not only can be utilized in poultry breeding but also provides a case study of utilizing multi-omics data to study the phenotype-genotype relation.