Chicken domestication : Effects of tameness on brain gene expression and DNA methylation

Abstract

Domestication greatly increases phenotypic variation in a short time span, with selection for a single phenotype and a plethora of associated phenotypic changes as an outcome of the process. The domestication process influences the underlying genomic architecture of a species, and the success and speed of the process is likely influenced by it. The main aims of my thesis was to study how domestication affects the brain of chickens: specifically changes in morphology, gene expression, and DNA methylation. Differences in gene expression and DNA methylation between White Leghorn and Red Junglefowl chickens were mapped, and inheritance of these patterns were quantified, indicating a faithful transmission of breed-specific epigenetic markers. Selection on the behavioral trait fearfulness, generated high and low fearful lines of Red Junglefowl. Both the parental population and the fifth selected generation were used for the analyses in this thesis. One experiment studied morphological changes in the brain and other vital organs, and found that relative total brain size increased in high fearful birds, as a consequence of an increase in cerebral hemisphere size in high fearful birds and not in low fearful birds. Also, the relative heart, liver, spleen and testis size increased in high fearful birds, indicating correlated morphological changes with selection for fearfulness. Two additional experiments examined differential gene expression in the hypothalamus and the anterior cerebral hemisphere. The hypothalamus differed in expression of genes with reproductive and immunological functions, whilst the cerebral hemisphere differed in expression of genes related to social behaviors and neurological functions especially those upregulated in low fearful birds. These results indicate the occurrence of tissue-and species-specific changes in gene expression as overlap with other domestication events were nearly nonexistent. A fourth experiment sought to associate the change in fear levels and gene expression differences with DNA methylation. Chromosomal regions with differential DNA methylation between high and low fearful birds were identified, and genes in these regions had annotated functions relevant to phenotypic differences between the selection lines. This thesis is the first to study the genetic alterations of domestication using the wild ancestor of an already domesticated species to repeat the domestication process selecting against fear of humans. The findings corroborate results from previous comparisons of wild and domestic animals, and further support the theory that rigorous selection for a behavioral trait can cause a cascade of genetic and epigenetic changes facilitating the domestication of a population. Populärvetenskaplig sammanfattningDomesticering, när en population djur anpassas till ett liv i fångenskap och nära kontakt med människor, är en process som under kort tid ger upphov till stora förändringar hos djuret under selektion, såsom skillnader i beteende, fysiologi, storlek, reproduktion och fä...

Domestication and Feed Restriction Programming Organ Index, Dopamine, and Hippocampal Transcriptome Profile in Chickens

“…The upregulated DEGs of FA were enriched in Parkinson's disease and Huntington's disease compared to the SA group. It is possible that their accelerated breeding speed gives the fast-growing broilers increased potential to develop neural and pharmacological problems ( 4 ). Besides, oxidative phosphorylation in the energy metabolism category in the FA group was higher than in the SA group.…”

“…Modern chickens, the descendants of the Red Junglefowl, have undergone basic changes, including to behavior and reproduction (1)(2)(3), as well as in brain morphology, gene expression, and DNA methylation as compared to their ancestors (4). Of which, the fast-growing breeds under intensive domestication were directly selected for meat in order to meet market demands in the past decades (5).…”