Genome-wide scanning for selection signatures in two autochthonous Anatolian chicken breeds

1. Double digest restriction site-associated DNA sequencing (ddRADseq) data were utilised to perform genome-wide scanning for selection signatures within Denizli (DNZ) and Gerze (GRZ) by a combination of runs of homozygosity (ROH) and Tajima's D index. The genome of native Anatolian chicken breeds was compared to commercial broiler (BROHIB) and layer (LAYHIB) lines via the Rsb approach to identify genomic regions associated with economically important traits.2. Tajima's D index-based selection signatures were detected in 269 and 772 single nucleotide polymorphisms (SNP) in DNZ and GRZ breeds, respectively, overlapped with 32 and 58 protein-coding genes. These genes were positioned within a ROH island, which indicated their fixation across the population.3. A literature review confirmed that numerous genes under selection in Anatolian chicken breeds were associated with environmental adaptation. These included thermo-tolerance (HIKESHI and DINAJC13), pathogen and disease resistance (OTOGL, GRAP2, ACKR4, CDK1, LRRC3B, DLC1, TRMT9B, GULP1 and ABL2) as well as survival traits including hearing (PTPRQ), vocal learning (GRIN2B), vision (ADAM22 and LONRF1) and reaction to fear (TOR3A). The results of comparative Rsb analysis revealed 10 (DDAH1, BCL10, SYDE2, DNAI3, MCOLN3, MCOLN2, LAMA5, RPS21, CABLES2 and RBBP8NL) and three (NRP1, ITGB1 and EPC1) genes common in native Anatolian chicken breeds and commercial hybrid lines implying that they are likely to affect economically important traits.4.This study confirmed that the genome of native Anatolian chicken breeds has been shaped by natural selection in response to adverse environmental conditions. Among detected genes, GRIN2B seems promising for explaining the genetic underpinnings of the long crowing characteristics of the DNZ breed since it is linked to vocalisation and learning ability in avian species.