P4060 Runs of homozygosity reveal natural selection footprints of some African chicken breeds and village ecotypes

Abstract

The earliest evidence of domestic chicken (Gallus gallus) introduction into Africa was in Egypt in the New Kingdom, 19th Dynasty (1307–1196 BC) through the ancient cinnamon trade. Chickens were introduced in Eastern Africa (EA) later via Egypt or direct introduction via Indian Ocean trading. With the absence of genetic improvement schemes and breeding associations, EA rural chicken populations are likely under natural selection, and most are considered as ecotypes, not breeds. A few populations, e.g., Egyptian Fayoumi have fixed criteria and are registered as a breed. The current study aims to assess probable co-ancestry among six African chicken populations, in comparison with a highly inbred US Fayoumi line, to investigate the inter-population genomic variation due to natural selective pressure and to determine functional variants associated with Runs of Homozygosity (ROH). The populations studied included three indigenous African ecotypes from Uganda (UGN), Rwanda (RWN) and Egyptian naked-neck (ENN); two Egyptian registered breeds; Fayoumi (FEG) and Dandarawi (DEG), one hybrid developed in India and sampled in Uganda, Kuroiler (KRL), and a highly inbred US Fayoumi (FUS). A total of 290 birds were randomly sampled from villagers in Egypt, Rwanda, and Uganda, representing indigenous populations, and 6 birds were sampled from the inbred FUS flock. Birds were genotyped using the Affymetrix 600K Axiom® Genome-Wide Chicken Genotyping Array. ROH were defined using PLINK v1.9, for a minimum ROH length of 500kb, with no more than one missing SNP and one heterozygous SNP genotype per window. A total number of 15,277 ROH were detected across the studied populations. ROH length ranged between 500kb to around 50Mb. ROH were classified into three length categories; short (500kb to < 1Mb, n = 9970; 65.3%); medium (1Mb to < 5Mb, n = 4960; 32.5%) and long (≥ 5Mb, n = 347; 2.3%). The average number of ROH per bird was highest for the inbred FUS (240.7), and the least for the DAN (19.9) indicating outbreeding. Intra-breed regions with a high occurrence of ROH were identified on several chromosomes indicating ROH landscaping, where several genes involved in survivability and tolerance (i.e., reproduction, metabolism, muscle formation, ion-exchange, and heat and oxidative stresses tolerance) were detected. This study illustrates the distribution of ROH and functional variants within ROH in some African breeds and ecotypes. Detecting genomic regions involved in traits under natural selection contributes to our understanding of regions of importance for selection and distribution of functional variants in the chicken genome.