AUTHOR=Elbeltagy Ahmed R. , Bertolini Francesca , Fleming Damarius S. , Van Goor Angelica , Ashwell Chris M. , Schmidt Carl J. , Kugonza Donald R. , Lamont Susan J. , Rothschild Max. F. TITLE=Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes JOURNAL=Frontiers in Genetics VOLUME=Volume 10 - 2019 YEAR=2019 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00376 DOI=10.3389/fgene.2019.00376 ISSN=1664-8021 ABSTRACT=
Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure,