Abstract
Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.
Highlights
Domesticated chicken breeds are diverse with differences in morphology, physiology and behavior [1]
Charles Darwin already noticed the large diversity of phenotypes within the chicken and assumed a single-origin for the domesticated chicken descending from Gallus gallus (Red Junglefowl (RJF)) [2]
Archeological findings suggest that multiple domestication events and multiple geographical regions were involved in the establishment of the domesticated chicken [9] which is supported by molecular genetic evidence [10,11]
Summary
Domesticated chicken breeds are diverse with differences in morphology, physiology and behavior [1]. Traditional breeds are mostly kept for ornamental purposes and display a large diversity in morphological phenotypes between breeds. Charles Darwin already noticed the large diversity of phenotypes within the chicken and assumed a single-origin for the domesticated chicken descending from Gallus gallus (Red Junglefowl (RJF)) [2]. A single-origin was supported by many studies Archeological findings suggest that multiple domestication events and multiple geographical regions were involved in the establishment of the domesticated chicken [9] which is supported by molecular genetic evidence [10,11]. Molecular evidence supports genetic contributions from other Junglefowl species to current domesticated chickens. The yellow skin locus present in several domestic chicken breeds most likely originated from Gallus sonneratii (Grey Junglefowl) [12]
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