Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes

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, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations’ ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda–Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda–Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions

Natural Selection Footprints among African Chicken Breeds and Village Ecotypes

Supplementary data for publication: Ahmed R. Elbeltagy, Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chris M. Ashwell, Carl J. Schmidt, Donald R. Kugonza, Susan J. Lamont, and Max. F. Rothschild. (2019). Natural Selection Footprints among African Chicken Breeds and Village Ecotypes. Front Genet. 2019; 10: 376

Plink file data for Barki Ruminants (sheep and goats)

The data contains SNP genotype data for Barki sheep and goats that can be used in Plink

Data from: Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species but, natural selection has played the major role amongst indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes are involved in multiple signaling and, signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes which directly or indirectly influence traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (several MYH, TRHDE, ALDH1A3) and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) are identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosome 12 and 10 respectively, providing, most likely, evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping