Genome scan for selection in South American chickens reveals a region under selection associated with aggressiveness

ABSTRACT Domestic chicken populations have been subjected to selection strategies to improve different production traits. Throughout history, selection coupled with diverse demographic dynamics have shaped the genome of many local populations which might harbor important genetic combinations with potential for production and survival to future unknown climate changes. South American local chickens include several well-adapted local breeds that thrive in extreme environments (e.g., tropical rain forest, high altitude and desert). In addition, there has been a long tradition of game fowl breeding in South America about which very little is known. As game fowl display distinct phenotypes compared to other types of chickens, i.e., aggressiveness, we have screened for single nucleotide polymorphisms ( SNPs ) localized in genes related to behavior that depart from neutrality (i.e., outliers) and therefore might be influenced by selection. Here we used restriction site-associated DNA sequencing ( RADseq ) to identify 122,801 SNPs distributed across the genome to scan for selection signatures in South American chicken populations. We detected 892 SNPs that were under selection. Two SNPs under positive selection localized in a genomic region harboring the Dopamine Receptor 2 ( DRD2 ) gene and the Ankyrin Repeat and Kinase Domain Containing 1 ( ANKK1 ) gene which have been associated with behavior. The population branch statistics analysis ( PBS ) on these two SNPs provided further evidence that these two variants have been under positive selection in game fowl. These findings contribute to the understanding of the genetic architecture behind the aggressiveness behavior in chickens, a trait of paramount importance in the poultry industry.